bluuebunny/crossref_metadata_2025 huggingface dataset:
Digital gene expression profiling of the transcriptional response to Sclerotinia sclerotiorum and its antagonistic bacterium Bacillus amyloliquefaciens in soybean
Authors: Liu Jianfeng , Hu Xianwen , He Hongli , Zhang Xingzheng , Guo Jinhua , Bai Jing , Cheng Yunqing
Published: November 2022

Soybean Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a common disease in soybean, and effective biological control is urgently needed. We have previously confirmed that Bacillus amyloliquefaciens can effectively antagonize S. sclerotiorum in a plate competition experiment and a soybean seedling inoculation experiment. In this study, the mechanisms underlying plant death caused by S. sclerotiorum and soybean resistance to S. sclerotiorum induced by B. amyloliquefaciens were evaluated. The stems of potted soybean seedlings were inoculated with S. sclerotiorum (Gm-Ss), B. amyloliquefaciens (Gm-Ba), and their combination (Gm-Ba-Ss), using scratch treatments as a control, followed by dual RNA sequencing and bioinformatics analyses. Global gene expression levels in the Gm-Ss treatment were much lower than those in the Gm-Ba, Gm-Ba-Ss, and Gm groups, suggesting that S. sclerotiorum strongly inhibited global gene expression in soybean. In a pairwise comparison of Gm-Ss vs. Gm, 19983 differentially expressed genes (DEGs) were identified. Down-regulated DEGs were involved in various KEGG pathways, including ko01110 (biosynthesis of secondary metabolites), ko01100 (metabolic pathways), ko01120 (microbial metabolism in diverse environments), ko00500 (starch and sucrose metabolism), and ko04075 (plant hormone signal transmission), suggesting that S. sclerotiorum inoculation had a serious negative effect on soybean metabolism. In Gm-Ba vs. Gm, 13091 DEGs were identified, and these DEGs were significantly enriched in ko03010 (ribosome) and ko03008 (ribosome biogenesis in eucaryotes). Our results suggest that B. amyloliquefaciens increases the expression of genes encoding the ribosomal subunit, promotes cell wall biogenesis, and induces systemic resistance. S. sclerotiorum strongly inhibited metabolism in soybean, inhibited the synthesis of the cytoskeleton, and induced the up-regulation of programmed death and senescence-related genes via an ethylene signal transduction pathway. These results improve our understanding of S. sclerotiorum-induced plant death and soybean resistance to S. sclerotiorum induced by B. amyloliquefaciens and may contribute to the improvement of strategies to avoid yield losses.
Host biology and genomic properties of Plumeria mosaic virus, a tobamovirus discovered in a temple tree in India co-infecting with frangipani mosaic virus
Authors: Kumar Alok , Solanki Vikas , Katiyar Akshay , Mandal Bikash
Published: November 2022

Temple tree (Plumeria rubra f. acutifolia), an important fragrant-flower tree extensively used in the urban landscaping is known to be infected with a tobamovirus, frangipani mosaic virus (FrMV). In this study, we describe another tobamovirus, Plumeria mosaic virus (PluMV) infecting temple tree in India. PluMV was isolated from an old temple tree co-infected with FrMV. The presence of another tobamovirus was initially realized based on the distinct symptoms on Gomphrena globosa (globe amaranth), a non-host of FrMV. PluMV was highly transmissible through simple rub-inoculation. In host-range study, brinjal (Solanum melongena), chilli (Capsicum annuum), datura (Datura stramonium), globe amaranth and tobacco (Nicotiana benthamiana, N. glutinosa, N. tabacum cv. Xanthi) could differentiate PluMV from FrMV. The complete genome sequence of PluMV was determined (6,688 nucleotides [nt], GenBank KJ395757), which showed the genome structure typical of tobamovirus encoding four proteins: small replicase (3,549 nt/130 kDa), large replicase (5,061 nt/188 kDa), movement protein (770 nt/29 kDa) and coat protein (527 nt/19 kDa). The 5′ and 3′ UTR of PluMV contained 91 and 284 nt, respectively. The PluMV genome was 45 nts longer than that of FrMV and shared only 71.4–71.6% sequence identity with FrMV and  < 50% sequence identity with the rest of the other members of the genus Tobamovirus. PluMV shared a close but a divergent evolutionary relationship with FrMV. Based on the species demarcation guidelines of ICTV (<90% genome sequence identity), PluMV was considered as a new tobamovirus species. As PluMV was serologically related with FrMV, differential diagnostic assays such as simplex and duplex RT-PCR were developed, which revealed that PluMV naturally existed in both the species of temple tree, P. rubra f. acutifolia and P. rubra f. obtusa in India either alone or in mixed infection with FrMV.
Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families
Authors: Cox Murray P. , Guo Yanan , Winter David J. , Sen Diya , Cauldron Nicholas C. , Shiller Jason , Bradley Ellie L. , Ganley Austen R. , Gerth Monica L. , Lacey Randy F. , McDougal Rebecca L. , Panda Preeti , Williams Nari M. , Grunwald Niklaus J. , Mesarich Carl H. , Bradshaw Rosie E.
Published: November 2022

Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback – a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
Gut microbiota dysbiosis as an inflammaging condition that regulates obesity-related retinopathy and nephropathy
Authors: Li Jie , Lv Jun-lin , Cao Xin-yue , Zhang Hai-ping , Tan Yu-jun , Chu Ting , Zhao Li-li , Liu Zhong , Ren Yu-shan
Published: November 2022

Diabetes-specific microvascular disease is a leading cause of blindness, renal failure and nerve damage. Epidemiological data demonstrated that the high morbidity of T2DM occurs as a result of obesity and gradually develops into serious complications. To date, the mechanisms that underlie this observation are still ill-defined. In view of the effect of obesity on the gut microflora, Leprdb/db mice underwent antibiotic treatment and microbiota transplants to modify the gut microbiome to investigate whether microbes are involved in the development of diabetic nephropathy (DN) and/or diabetic retinopathy (DR). The mouse feces were collected for bacterial 16S ribosomal RNA gene sequencing. Cytokines including TNF-α, TGF-β1, IFN-γ, IL-1β, IL-6, IL-17A, IL-10, and VEGFA were detected by enzyme-linked immunosorbent assay (ELISA), flow cytometry, real-time PCR and immunofluorescent assay. Eyes and kidney were collected for histopathological assay. Intestinal permeability was also detected using Evans Blue. The results showed that obesity influenced metabolic variables (including fast/fed glucose, insulin, and triglyceride), retinopathy and nephropathy, and the gut microbiota. Obesity mainly reduced the ratio of Bacteroidetes/Firmicutes and influenced relative abundance of Proteobacteria, Actinobacteria, and Spirochetes. Obesity also increased intestinal permeability, metabolic endotoxemia, cytokines, and VEGFA. Microbiota transplants confirm that obesity aggravates retinopathy and nephropathy through the gut microbiota. These findings suggest that obesity exacerbates retinopathy and nephropathy by inducing gut microbiota dysbiosis, which further enhanced intestinal permeability and chronic low-grade inflammation.
Antibacterial activity and mechanism of malondialdehyde against Staphylococcus xylosus and Lactiplantibacillus plantarum isolated from a traditional Chinese dry-cured fish
Authors: Zhang Qi , Jia Shiliang , Ding Yicheng , Li Dongmei , Ding Yuting , Zhou Xuxia
Published: November 2022

Malondialdehyde (MDA) is one of the most representative reactive carbonyl species (RCSs) produced by lipid oxidation in food. However, the inhibitory effect of MDA on microorganisms has received little attention. Thus, the aim of this study was to reveal the antibacterial mechanism of MDA on Staphylococcus xylosus and Lactiplantibacillus plantarum isolated from dry-cured fish. The results showed that the minimum inhibitory concentrations (MICs) of MDA on S. xylosus and L. plantarum were 90 μg/ml and 180 μg/ml, respectively. Time-kill curves indicated a concentration-dependent antibacterial activity of MDA. Moreover, cell wall damage, cell membrane depolarization, intracellular adenosine triphosphate (ATP) decline, Ca2+ and Mg2+ leakage, cell morphological destruction and alterations in intracellular biomolecules were observed, which indicated the negative influence of MDA on cell membrane and cellular homeostasis. This study demonstrated the potential antimicrobial properties of MDA and provided theoretical support for the scientific prevention and control of lipid oxidation and microbial contamination in food. This study demonstrated the potential antibacterial properties of MDA and further enriches theoretical studies on the effects of lipid oxidation on microorganisms.
The genome and antigen proteome analysis of Spiroplasma mirum
Authors: Liu Peng , Li Yuxin , Ye Youyuan , Chen Jiaxin , Li Rong , Zhang Qinyi , Li Yuan , Wang Wen , Meng Qingguo , Ou Jingyu , Yang Zhujun , Sun Wei , Gu Wei
Published: November 2022

Spiroplasma mirum, small motile wall-less bacteria, was originally isolated from a rabbit tick and had the ability to infect newborn mice and caused cataracts. In this study, the whole genome and antigen proteins of S. mirum were comparative analyzed and investigated. Glycolysis, pentose phosphate pathway, arginine metabolism, nucleotide biosynthesis, and citrate fermentation were found in S. mirum, while trichloroacetic acid, fatty acids metabolism, phospholipid biosynthesis, terpenoid biosynthesis, lactose-specific PTS, and cofactors synthesis were completely absent. The Sec systems of S. mirum consist of SecA, SecE, SecDF, SecG, SecY, and YidC. Signal peptidase II was identified in S. mirum, but no signal peptidase I. The relative gene order in S. mirum is largely conserved. Genome analysis of available species in Mollicutes revealed that they shared only 84 proteins. S. mirum genome has 381 pseudogenes, accounting for 31.6% of total protein-coding genes. This is the evidence that spiroplasma genome is under an ongoing genome reduction. Immunoproteomics, a new scientific technique combining proteomics and immunological analytical methods, provided the direction of our research on S. mirum. We identified 49 proteins and 11 proteins (9 proteins in common) in S. mirum by anti-S. mirum serum and negative serum, respectively. Forty proteins in S. mirum were identified in relation to the virulence. All these proteins may play key roles in the pathogeny and can be used in the future for diagnoses and prevention.
Pluripotent stem cell strategies for rebuilding the human brain
Authors: Limone Francesco , Klim Joseph R. , Mordes Daniel A.
Published: November 2022

Neurodegenerative disorders have been extremely challenging to treat with traditional drug-based approaches and curative therapies are lacking. Given continued progress in stem cell technologies, cell replacement strategies have emerged as concrete and potentially viable therapeutic options. In this review, we cover advances in methods used to differentiate human pluripotent stem cells into several highly specialized types of neurons, including cholinergic, dopaminergic, and motor neurons, and the potential clinical applications of stem cell-derived neurons for common neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, ataxia, and amyotrophic lateral sclerosis. Additionally, we summarize cellular differentiation techniques for generating glial cell populations, including oligodendrocytes and microglia, and their conceivable translational roles in supporting neural function. Clinical trials of specific cell replacement therapies in the nervous system are already underway, and several attractive avenues in regenerative medicine warrant further investigation.
Role of responsive neurostimulation and immunotherapy in refractory epilepsy due to autoimmune encephalitis: A case report
Authors: Chen Stephanie H. , O'Dea Pamela K. , Sianati Bahareh , Benavides David R.
Published: November 2022

Autoimmune encephalitis (AE) frequently presents with seizures in the acute setting. Seizures are often refractory to anti-seizure medications (ASM) but have been shown to be responsive to immunomodulatory therapies. A subset of patients with AE continues to have refractory epilepsy, recently named “autoimmune-associated epilepsy (AAE),” for years after the acute AE presentation. Optimal treatment for AAE has not been determined. Furthermore, the efficacy of neuromodulation and immunotherapy has not been well established in AAE. Here, we report a patient with probable autoantibody negative AE who initially presented with new onset refractory status epilepticus (NORSE). After his acute presentation, he continued to have frequent seizures that were refractory to four ASMs at therapeutic doses. A responsive neurostimulation (RNS®, NeuroPace) system was implanted for diagnostic and therapeutic purposes, with minimal change in seizure frequency. Due to continued frequent seizures despite ASMs and neurostimulation, he underwent a trial of immunotherapy consisting of high-dose intravenous (IV) corticosteroids and intravenous immunoglobulin (IVIG). Despite the addition of immunotherapy to his treatment regimen, the patient experienced no significant clinical or electrographic change in seizure frequency. This case does not support the use of immunotherapy for treatment of AAE and illustrates the need for consensus guidelines in the management of patients with AAE. Further, the use of electrocorticography (ECoG) data provided an objective surrogate measure of seizure frequency; this may support the role for early neuromodulation in the management of AAE.
Expression of alternative transcription factor 4 mRNAs and protein isoforms in the developing and adult rodent and human tissues
Authors: Sirp Alex , Shubina Anastassia , Tuvikene Jürgen , Tamberg Laura , Kiir Carl Sander , Kranich Laura , Timmusk Tõnis
Published: November 2022

Transcription factor 4 (TCF4) belongs to the class I basic helix–loop–helix family of transcription factors (also known as E-proteins) and is vital for the development of the nervous system. Aberrations in the TCF4 gene are associated with several neurocognitive disorders such as schizophrenia, intellectual disability, post-traumatic stress disorder, depression, and Pitt-Hopkins Syndrome, a rare but severe autism spectrum disorder. Expression of the human TCF4 gene can produce at least 18 N-terminally distinct protein isoforms, which activate transcription with different activities and thus may vary in their function during development. We used long-read RNA-sequencing and western blot analysis combined with the analysis of publicly available short-read RNA-sequencing data to describe both the mRNA and protein expression of the many distinct TCF4 isoforms in rodent and human neural and nonneural tissues. We show that TCF4 mRNA and protein expression is much higher in the rodent brain compared to nonneural tissues. TCF4 protein expression is highest in the rodent cerebral cortex and hippocampus, where expression peaks around birth, and in the rodent cerebellum, where expression peaks about a week after birth. In human, highest TCF4 expression levels were seen in the developing brain, although some nonneural tissues displayed comparable expression levels to adult brain. In addition, we show for the first time that out of the many possible TCF4 isoforms, the main TCF4 isoforms expressed in the rodent and human brain and other tissues are TCF4-B, -C, -D, -A, and-I. Taken together, our isoform specific analysis of TCF4 expression in different tissues could be used for the generation of gene therapy applications for patients with TCF4-associated diseases.
Neuronal mitochondrial morphology is significantly affected by both fixative and oxygen level during perfusion
Authors: Kim Su Yeon , Strucinska Klaudia , Osei Bertha , Han Kihoon , Kwon Seok-Kyu , Lewis Tommy L.
Published: November 2022

Neurons in the brain have a uniquely polarized structure consisting of multiple dendrites and a single axon generated from a cell body. Interestingly, intracellular mitochondria also show strikingly polarized morphologies along the dendrites and axons: in cortical pyramidal neurons (PNs), dendritic mitochondria have a long and tubular shape, while axonal mitochondria are small and circular. Mitochondria play important roles in each compartment of the neuron by generating adenosine triphosphate (ATP) and buffering calcium, thereby affecting synaptic transmission and neuronal development. In addition, mitochondrial shape, and thereby function, is dynamically altered by environmental stressors such as oxidative stress or in various neurodegenerative diseases including Alzheimer’s disease and Parkinson’s disease. Although the importance of altered mitochondrial shape has been claimed by multiple studies, methods for studying this stress-sensitive organelle have not been standardized. Here we address pertinent steps that influence mitochondrial morphology during experimental processes. We demonstrate that fixative solutions containing only paraformaldehyde (PFA), or that introduce hypoxic conditions during the procedure, induce dramatic fragmentation of mitochondria both in vitro and in vivo. This disruption was not observed following the use of glutaraldehyde (GA) addition or oxygen supplementation, respectively. Finally, using pre-formed fibril α-synuclein treated neurons, we show fixative choice can alter experimental outcomes. Specifically, α-synuclein-induced mitochondrial remodeling could not be observed with PFA only fixation as fixation itself caused mitochondrial fragmentation. Our study provides optimized methods for examining mitochondrial morphology in neurons and demonstrates that fixation conditions are critical when investigating the underlying cellular mechanisms involving mitochondria in physiological and neurodegenerative disease models.
To eat or not to eat—an exploratory randomized controlled trial on fasting and plant-based diet in rheumatoid arthritis (NutriFast-Study)
Authors: Hartmann Anika M. , Dell'Oro Melanie , Spoo Michaela , Fischer Jan Moritz , Steckhan Nico , Jeitler Michael , Häupl Thomas , Kandil Farid I. , Michalsen Andreas , Koppold-Liebscher Daniela A. , Kessler Christian S.
Published: November 2022

Background

Fasting is beneficial in many diseases, including rheumatoid arthritis (RA), with lasting effects for up to 1 year. However, existing data dates back several decades before the introduction of modern therapeutic modalities.

Objective

This exploratory RCT compares the effects of a 7-day fast followed by a plant-based diet (PBD) to the effects of the dietary recommendations of the German society for nutrition (Deutsche Gesellschaft für Ernährung, DGE) on RA disease activity, cardiovascular (CV) risk factors, and well-being.

Methods

In this RCT we randomly assigned 53 RA patients to either a 7-day fast followed by an 11-week PBD or a 12-week standard DGE diet. The primary endpoint was the group change from baseline to 12 weeks on the Health Assessment Questionnaire Disability Index (HAQ-DI). Further outcomes included other disease activity scores, body composition, and quality of life.

Results

Of 53 RA patients enrolled, 50 participants (25 per group) completed the trial and were included into the per-protocol analysis. The primary endpoint was not statistically significant. However, HAQ-DI improved rapidly in the fasting group by day 7 and remained stable over 12 weeks (Δ-0.29, p = 0.001), while the DGE group improved later at 6 and 12 weeks (Δ-0.23, p = 0.032). DAS28 ameliorated in both groups by week 12 (Δ-0.97, p < 0.001 and Δ-1.14, p < 0.001; respectively), with 9 patients in the fasting but only 3 in the DGE group achieving ACR50 or higher. CV risk factors including weight improved stronger in the fasting group than in the DGE group (Δ-3.9 kg, p < 0.001 and Δ-0.7 kg, p = 0.146).

Conclusions

Compared with a guideline-based anti-inflammatory diet, fasting followed by a plant-based diet showed no benefit in terms of function and disability after 12 weeks. Both dietary approaches had a positive effect on RA disease activity and cardiovascular risk factors in patients with RA.

Clinical trial registration

https://clinicaltrials.gov/ct2/show/NCT03856190, identifier: NCT03856190.
Potential applications of pulsed electric field in the fermented wine industry
Authors: Feng Yuanxin , Yang Tao , Zhang Yongniu , Zhang Ailin , Gai Lili , Niu Debao
Published: November 2022

Fermented wine refers to alcoholic beverages with complex flavor substances directly produced by raw materials (fruit or rice) through microbial fermentation (yeast and bacteria). Its production steps usually include saccharification, fermentation, filtration, sterilization, aging, etc., which is a complicated and time-consuming process. Pulsed electric field (PEF) is a promising non-thermal food processing technology. Researchers have made tremendous progress in the potential application of PEF in the fermented wine industry over the past few years. The objective of this paper is to systematically review the achievements of PEF technology applied to the winemaking and aging process of fermented wine. Research on the application of PEF in fermented wine suggests that PEF treatment has the following advantages: (1) shortening the maceration time of brewing materials; (2) promoting the extraction of main functional components; (3) enhancing the color of fermented wine; (4) inactivating spoilage microorganisms; and (5) accelerating the formation of aroma substances. These are mainly related to PEF-induced electroporation of biomembranes, changes in molecular structure and the occurrence of chemical reactions. In addition, the key points of PEF treatments for fermented wine are discussed and some negative impacts and research directions are proposed.
Cancer-associated fibroblasts-derived lncRNA signature as a putative biomarker in breast cancer
Authors: Li Zan , Yu Junyi , Lv Chunliu , Luo Zhenhua
Published: November 2022

Long noncoding RNAs (lncRNAs) have been reported to play a key role in regulating tumor microenvironment and immunity. Cancer-associated fibroblasts (CAFs) are abundant in many tumors. However, the functional and clinical significance of lncRNAs specifically expressed in CAFs has not been fully elucidated. In this study, we identified a list of 95 CAF-specific lncRNAs (FibLnc), including HHLA3, TP53TG1, ST7-AS1, LINC00536, ZNF503-AS1, MIR22HG, and MAPT-AS1, based on immune cell transcriptome expression profiling data. Based on the Cancer Genome Atlas and Gene Expression Omnibus datasets, we found that the FibLnc score predicted differences in overall patient survival and performed well in multiple datasets. FibLnc score was associated with the clinical stage of patients with breast cancer but did not significantly correlate with the PAM50 classification. Functional analysis showed that FibLnc was positively correlated with signaling pathways associated with malignant tumor progression. In addition, FibLnc was positively correlated with tumor mutational load and could predict immunotherapy response in patients with breast cancer receiving anti-PD-1 or anti-CTLA4 therapy. Our proposed FibLnc score was able to reflect the status of the immune environment and immunotherapeutic response in breast cancer, which could help explore potential therapeutic decisions and regulatory mechanisms of CAF-specific lncRNAs.
Prediction of the histologic upgrade of ductal carcinoma in situ using a combined radiomics and machine learning approach based on breast dynamic contrast-enhanced magnetic resonance imaging
Authors: Lee Hyo-jae , Park Jae Hyeok , Nguyen Anh-Tien , Do Luu-Ngoc , Park Min Ho , Lee Ji Shin , Park Ilwoo , Lim Hyo Soon
Published: November 2022

Objective

To investigate whether support vector machine (SVM) trained with radiomics features based on breast magnetic resonance imaging (MRI) could predict the upgrade of ductal carcinoma in situ (DCIS) diagnosed by core needle biopsy (CNB) after surgical excision.

Materials and methods

This retrospective study included a total of 349 lesions from 346 female patients (mean age, 54 years) diagnosed with DCIS by CNB between January 2011 and December 2017. Based on histological confirmation after surgery, the patients were divided into pure (n = 198, 56.7%) and upgraded DCIS (n = 151, 43.3%). The entire dataset was randomly split to training (80%) and test sets (20%). Radiomics features were extracted from the intratumor region-of-interest, which was semi-automatically drawn by two radiologists, based on the first subtraction images from dynamic contrast-enhanced T1-weighted MRI. A least absolute shrinkage and selection operator (LASSO) was used for feature selection. A 4-fold cross validation was applied to the training set to determine the combination of features used to train SVM for classification between pure and upgraded DCIS. Sensitivity, specificity, accuracy, and area under the receiver-operating characteristic curve (AUC) were calculated to evaluate the model performance using the hold-out test set.

Results

The model trained with 9 features (Energy, Skewness, Surface Area to Volume ratio, Gray Level Non Uniformity, Kurtosis, Dependence Variance, Maximum 2D diameter Column, Sphericity, and Large Area Emphasis) demonstrated the highest 4-fold mean validation accuracy and AUC of 0.724 (95% CI, 0.619–0.829) and 0.742 (0.623–0.860), respectively. Sensitivity, specificity, accuracy, and AUC using the test set were 0.733 (0.575–0.892) and 0.7 (0.558–0.842), 0.714 (0.608–0.820) and 0.767 (0.651–0.882), respectively.

Conclusion

Our study suggested that the combined radiomics and machine learning approach based on preoperative breast MRI may provide an assisting tool to predict the histologic upgrade of DCIS.
Lung adenocarcinoma concurrent with congenital pulmonary aplasia of the right upper lobe: A case report
Authors: Min Bo , Wang Chu-xu , Liu Juan , Gong Li , Wang Cheng-xiang , Zuo Xiao-hua
Published: November 2022

Lung adenocarcinoma, the most common subtype of lung cancer, has been always imposed serious threat to human health. Congenital pulmonary dysplasia (CPD) lacking typical clinical manifestations is a rare developmental anomaly. Pulmonary aplasia, the rarest subtype of CPD, may present with a variety of symptoms and is frequently associated with other abnormalities. This report describes an 81-year-old woman who presented with an irritant cough. Chest computed tomography (CT) and three-dimensional (3D) reconstruction revealed an irregular mass with a diameter of 5 cm in right lower lobe adjacent to the hilum. CT also indicated a rightward mediastinal shift and the complete absence of ipsilateral upper lobar tissue with bronchus ending in a terminal cecum, resulting in a diagnosis of pulmonary aplasia. The patient accepted lobectomy and lymph node dissection without complication, histopathologic examination combined HE staining with immunohistochemistry identified the tumor as adenocarcinoma. Three months after surgery, the patient was free of respiratory symptoms without chest pain. This report highlights the necessity of comprehensive evaluation for lung malignancy concurrent with CPD and the importance of identifying the diagnosis of pulmonary dysplasia.
Weight loss in adolescents with down syndrome compared to adolescents with other intellectual disabilities enrolled in an 18-month randomized weight management trial
Authors: Ptomey Lauren T. , Bodde Amy E. , Hastert Mary , Suire Kameron B. , Helsel Brian C. , Gorczyca Anna M. , Washburn Richard A. , Rice Annie M. , Donnelly Joseph E.
Published: November 2022

Background

There is limited information on the efficacy of weight management interventions in adolescents with Down Syndrome (DS)

Objective

To compare weight change and intervention compliance between adolescents with DS compared to adolescents with non-DS related intellectual disabilities (ID) who were enrolled in an 18-month weight management trial.

Methods

Participants were adolescents (13–21 years) with mild to moderate ID and overweight or obesity. Participants were randomized in a 1:1:1 allocation to one of 3 intervention arms for an 18-month weight management trial: face-to-face/conventional diet (FTF/CD), remote delivery/conventional diet (RD/CD), or remote delivery/enhanced Stop Light Diet (RD/eSLD). Anthropometrics were assessed at baseline 6, 12, and 18 months by staff blinded to the intervention, and self-monitoring data was collected across the 18-month study. As an unpowered, post-hoc, secondary analysis, two-sample t-tests were used to compare the weight change across 6,12, and 18 mos. and compliance across 18 mos. between adolescents with and without DS randomized to each intervention arm.

Results

Adolescents with ID (n = 110) were randomized to one of three intervention arms: FTF/CD (n = 36, DS = 17, other ID = 19), RD/CD (n = 39, DS = 21, other ID = 18) or RD/eSLD (n = 35, DS = 15, other ID = 20). Body weight at 18 months was obtained from 82%, 76% and 73% of participants with DS and 84%, 83% and 75% of participants with other ID randomized to the FTF/CD, RD/CD, and RD/eSLD arms, respectively Weight change across 18 months was −0.2 ± 8.8 kg (−0.5%), −0.3 ± 5.3 kg (−0.7%), and −2.6 ± 5.0 kg (−4.0%) in adolescents with DS randomized to the FTF/CD, RD/CD and RD/eSLD arms, respectively. There were no significant differences in change in body weight or BMI across 18 months between adolescents with DS or those with other ID in any of the 3 intervention arms (all p > 0.05). Additionally, there were no significant differences in intervention compliance between adolescents with and without DS across 18 mos. (all p > 0.05).

Conclusions

Adolescents with DS respond to a multi-component weight management intervention similar to those with others ID
Michael acceptor molecules in natural products and their mechanism of action
Authors: Liang Song-Ting , Chen Chu , Chen Rui-Xin , Li Rui , Chen Wen-Li , Jiang Gui-Hua , Du Lei-Lei
Published: November 2022

Purpose: Michael receptor molecules derived from plants are biologically active due to electrophilic groups in their structure. They can target nucleophilic residues on disease-related proteins, with significant therapeutic effects and low toxicity for many diseases. They provide a good option for relevant disease treatment. The aim of this study is to summarize the existing MAMs and their applications, and lay a foundation for the application of Michael receptor molecules in life science in the future.

Methods: This review summarizes the published studies on Michael receptor molecules isolated from plants in literature databases such as CNKI, Wanfang Data, PubMed, Web of Science, ScienceDirect, and Wiley. Latin names of plants were verified through https://www.iplant.cn/. All relevant compound structures were verified through PubChem and literature, and illustrated with ChemDraw 20.0.

Result: A total of 50 Michael receptor molecules derived from various plants were discussed. It was found that these compounds have similar pharmacological potential, most of them play a role through the Keap1-Nrf2-ARE pathway and the NF-κB pathway, and have biological activities such as antioxidant and anti-inflammatory. They can be used to treat inflammatory diseases and tumors.

Conclusion: The Michael receptor molecule has electrophilicity due to its unsaturated aldehyde ketone structure, which can combine with nucleophilic residues on the protein to form complexes and activate or inhibit the protein pathway to play a physiological role. Michael receptor molecules can regulate the Keap1-Nrf2-ARE pathway and the NF-κB pathway. Michael receptor molecules can be used to treat diseases such as inflammation, cancer, oxidative stress, etc.
Mechanism of interventional effect and targets of Zhuyu pill in regulating and suppressing colitis and cholestasis
Authors: Yu Han , Zhang Fenghua , Wen Yueqiang , Zheng Zhili , Chen Gaoyang , Pan Yingying , Wu Peijie , Ye Qiaobo , Han Jun , Chen Xiaofeng , Liu Chao , Shen Tao
Published: November 2022

Zhuyu pill (ZYP) is a traditional Chinese medicine prescription composed of two drugs, Coptis chinensis Franch. and Tetradium ruticarpum (A. Jussieu) T. G. Hartley, and is commonly used in the clinical treatment of diseases of the digestive system. However, the mechanism underlying the effect of ZYP on colitis remains unclear. In this study, a colitis rat model was induced with 2,4,6-trinitro-benzenesulfonic acid (TNBS, 100 mg/kg) and treated with ZYP (low dose: 0.6 g/kg, high dose: 1.2 g/kg). Disease activity index, colonic weight index, and weight change ratio were used to evaluate the model and efficacy. LC-MS and 16S rRNA gene sequencing were used to measure differences in fecal metabolism and microorganism population among the control, model, low-dose ZYP, and high-dose ZYP groups. To elucidate the mechanism of interventional effect of ZYP, Spearman correlation analysis was used to analyze the correlation between fecal metabolism and fecal microbial number. High-dose and low-dose ZYP both exhibited significant interventional effects on colitis rat models, and high-dose ZYP produced a better interventional effect compared with low-dose ZYP. Based on a metabolomics test of fecal samples, significantly altered metabolites in the model and high-dose ZYP treatment groups were identified. In total, 492 metabolites were differentially expressed. Additionally, sequencing of the 16S rRNA gene in fecal samples revealed that the high-dose ZYP could improve TNBS-induced fecal microbiota dysbiosis. Ultimately, changes in tryptophan metabolism and Firmicutes and Gammaproteobacteria populations were detected after ZYP treatment in both colitis and cholestasis. Therefore, we conclude that tryptophan metabolism and Firmicutes and Gammaproteobacteria populations are the core targets of the anti-inflammatory effect of ZYP. These findings provide a scientific basis for further investigation of the anti-inflammatory mechanism of ZYP in the future.
Diagnostic and therapeutic strategies for non-alcoholic fatty liver disease
Authors: Fu Yajie , Zhou Yanzhi , Shen Linhu , Li Xuewen , Zhang Haorui , Cui Yeqi , Zhang Ke , Li Weiguo , Chen Wei-dong , Zhao Shizhen , Li Yunfu , Ye Wenling
Published: November 2022

The global incidence rate of non-alcoholic fatty liver disease (NAFLD) is approximately 25%. With the global increase in obesity and its associated metabolic syndromes, NAFLD has become an important cause of chronic liver disease in many countries. Despite recent advances in pathogenesis, diagnosis, and therapeutics, there are still challenges in its treatment. In this review, we briefly describe diagnostic methods, therapeutic targets, and drugs related to NAFLD. In particular, we focus on evaluating carbohydrate and lipid metabolism, lipotoxicity, cell death, inflammation, and fibrosis as potential therapeutic targets for NAFLD. We also summarized the clinical research progress in terms of drug development and combination therapy, thereby providing references for NAFLD drug development.
Network structure indexes to forecast epidemic spreading in real-world complex networks
Authors: Bellingeri Michele , Bevacqua Daniele , Turchetto Massimiliano , Scotognella Francesco , Alfieri Roberto , Nguyen Ngoc-Kim-Khanh , Le Thi Trang , Nguyen Quang , Cassi Davide
Published: November 2022

Complex networks are the preferential framework to model spreading dynamics in several real-world complex systems. Complex networks can describe the contacts between infectious individuals, responsible for disease spreading in real-world systems. Understanding how the network structure affects an epidemic outbreak is therefore of great importance to evaluate the vulnerability of a network and optimize disease control. Here we argue that the best network structure indexes (NSIs) to predict the disease spreading extent in real-world networks are based on the notion of network node distance rather than on network connectivity as commonly believed. We numerically simulated, via a type-SIR model, epidemic outbreaks spreading on 50 real-world networks. We then tested which NSIs, among 40, could a priori better predict the disease fate. We found that the “average normalized node closeness” and the “average node distance” are the best predictors of the initial spreading pace, whereas indexes of “topological complexity” of the network, are the best predictors of both the value of the epidemic peak and the final extent of the spreading. Furthermore, most of the commonly used NSIs are not reliable predictors of the disease spreading extent in real-world networks.
A linear algorithm for the restricted subtraction games
Authors: Yang Zongbao , He Zhimin , Li Lvzhou , Dong Shoubin , Zheng Shenggeng
Published: November 2022

The subtraction game is a well-known problem in the field of game theory, which is often called a one-heap Nim game. There are two players, a heap of tokens, and a strategy matrix, in this game. It is called a restricted subtraction game if some constraints are imposed on the strategy matrix. The subtraction game could be solved by a classical algorithm with a query complexity no less than O(N2) and computed by an O(N32logN) quantum query algorithm with an error probability ϵ≤1N. The restricted subtraction game proposed by Huang et al. can be computed by an exact quantum algorithm with O(N32) queries. They also proved that the classical exact query complexity is Θ(N2). In this study, we use an array and an adjacency list to replace the strategy matrix and propose another more general subtraction game than the one introduced by Huang et al. Based on dynamic programming and the replaced game strategy, two linear classical query algorithms are designed to solve the restricted subtraction game proposed by Huang and this study, respectively.
Research on chemical oxygen demand based on laser Fluorescence-Raman spectroscopy
Authors: Che Xiaohua , Tian Zhaoshuo , Sun Fenghao , Liu Qingcao , Bi Zongjie , Chen Hao , Cui Zihao
Published: November 2022

In this invited paper, a novel water chemical oxygen demand (COD) detection method based on laser spectroscopy is proposed, and the COD value is obtained according to the intensity ratio of laser Fluorescence-Raman signal produced by laser incident into water. Based on the laser Fluorescence-Raman ratio (LFRR) method, we design a portable water quality measurement system. In which, a 405 nm semiconductor laser is used as the light source. The laser is coupled into the delivering port of Y-type fiber and then transmitted into water. The generated Mie scattered light, water Raman light and corresponding fluorescence are received and transmitted into spectrometer through the detecting port of Y-type fiber, and the COD value can be obtained by analyzing the LFRR of water spectra. The mixed solution of sodium humate and glucose is used as the COD standard solution to calibrate the designed system. The experiment results show that the optimal volume ratio of the two solutions is 1:29. When the COD of standard solutions is in the 1–12 mg/L concentration range, a good linear relationship can be found between the COD value and LFRR value with a correlation coefficient of 0.974. In addition, the COD of natural water samples are measured with LFRR method, the results of which are consistent with COD values obtained by rapid digestion spectrophotometry. Meanwhile, experimental results prove that the COD detection method proposed in this paper has the advantages of high sensitivity, high precision, high detection speed and simplicity, which can be widely used in various water areas for real-time COD monitoring.
Solving the inverse problem in electrocardiography imaging for atrial fibrillation using various time-frequency decomposition techniques based on empirical mode decomposition: A comparative study
Authors: Yadan Zhang , Xin Lian , Jian Wu
Published: November 2022

Electrocardiographic imaging (ECGI) can aid in identifying the driving sources that cause and sustain atrial fibrillation (AF). Traditional regularization strategies for addressing the ECGI inverse problem are not currently concerned about the multi-scale analysis of the inverse problem, and these techniques are not clinically reliable. We have previously investigated the solution based on uniform phase mode decomposition (UPEMD-based) to the ECGI inverse problem. Numerous other methods for the time-frequency analysis derived from empirical mode decomposition (EMD-based) have not been applied to the inverse problem in ECGI. By applying many EMD-based solutions to the ECGI inverse problem and evaluating the performance of these solutions, we hope to find a more efficient EMD-based solution to the ECGI inverse problem. In this study, five AF simulation datasets and two real datasets from AF patients derived from a clinical ablation procedure are employed to evaluate the operating efficiency of several EMD-based solutions. The Pearson’s correlation coefficient (CC), the relative difference measurement star (RDMS) of the computed epicardial dominant frequency (DF) map and driver probability (DP) map, and the distance (Dis) between the estimated and referenced most probable driving sources are used to evaluate the application of various EMD-based solutions in ECGI. The results show that for DF maps on all simulation datasets, the CC of UPEMD-based and improved UPEMD (IUPEMD)-based techniques are both greater than 0.95 and the CC of the empirical wavelet transform (EWT)-based solution is greater than 0.889, and the RDMS of UPEMD-based and IUPEMD-based approaches is less than 0.3 overall and the RDMS of EWT-based method is less than 0.48, performing better than other EMD-based solutions; for DP maps, the CC of UPEMD-based and IUPEMD-based techniques are close to 0.5, the CC of EWT-based is 0.449, and the CC of the remaining EMD-based techniques on the SAF and CAF is all below 0.1; the RDMS of UPEMD-based and IUPEMD-based are 0.06∼0.9 less than that of other EMD-based methods for all the simulation datasets overall. On two authentic AF datasets, the Dis between the first 10 real and estimated maximum DF positions of UPEMD-based and EWT-based methods are 212∼1440 less than that of others, demonstrating these two EMD-based solutions are superior and are suggested for clinical application in solving the ECGI inverse problem. On all datasets, EWT-based algorithms deconstruct the signal in the shortest time (no more than 0.12s), followed by UPEMD-based solutions (less than 0.81s), showing that these two schemes are more efficient than others.
Greenhouse gas emissions and carbon footprint of collard greens, spinach and chicory production systems in Southeast of Brazil
Authors: Pereira Breno de Jesus , Cecílio Filho Arthur Bernardes , La Scala Newton , Figueiredo Eduardo Barretto de
Published: November 2022

Food production in sustainable agricultural systems is one of the main challenges of modern agriculture. Vegetable intercropping may be a strategy to mitigate greenhouse gas (GHG) emissions, replacing monoculture systems. The objective is to identify the main emissions sources and to estimate GHG emissions of intercropping and monoculture production of collard greens, New Zealand spinach and chicory. Four scenarios were evaluated: ICS – intercropping collard greens and spinach; MCS – monoculture collard greens and spinach; ICC – intercropping collard greens and chicory; MCC - monoculture collard greens and chicory. The boundaries’ reach from “cradle-to-gate” and the calculation of GHG emissions were performed using IPCC methodology and specific factors (Tier 2). The total GHG emitted was standardized as CO2 equivalent (CO2eq). The GHG emissions in ICS and ICC scenarios were approximately 31% lower than in MCS and MCC scenarios. Carbon footprint in ICS (0.030 kg CO2eq kg-1 vegetables year-1) and ICC (0.033 kg CO2eq kg-1 vegetables year-1) scenarios were also lower than in MCS (0.082 kg CO2eq kg-1 vegetables year-1) and MCC (0.071 kg CO2eq kg-1 vegetables year-1) scenarios. Fertilizers, fuel (diesel) and irrigation were the main contributing sources for total GHG emitted and carbon footprint in all evaluated scenarios. The results suggest that intercropping systems may reduce GHG emissions associated with the production of vegetables evaluated as compared with monoculture.