bluuebunny/crossref_metadata_2025 huggingface dataset:
Recording and Simulating Proton-Related Metabolism in Bacterial Cell Suspensions
Authors: Cypionka Heribert , Reese Jan-Ole
Published: April 2021

Proton release and uptake induced by metabolic activities were measured in non-buffered cell suspensions by means of a pH electrode. Recorded data were used for simulating substrate turnover rates by means of a new freeware app (proton.exe). The program applies Michaelis-Menten or first-order kinetics to the metabolic processes and allows for parametrization of simultaneously ongoing processes. The simulation includes changes of the transmembrane ΔpH, membrane potential and ATP gains, and demonstrates the principles of chemiosmotic energy conservation. In our experiments, the versatile sulfate-reducing bacterium Desulfovibrio desulfuricans CSN (DSM 9104) was used as model organism. We analysed sulfate uptake by proton-sulfate symport, scalar alkalinization by sulfate reduction to sulfide, as well as nitrate and nitrite reduction to ammonia, and electron transport-coupled proton translocation. Two types of experiments were performed: In oxidant pulse experiments, cells were kept under H2, and micromolar amounts of sulfate, nitrate or nitrite were added. For reductant pulse experiments, small amounts of H2-saturated KCl were added to cells incubated under N2 with an excess of one of the above-mentioned electron acceptors. To study electron-transport driven proton translocation, the membrane potential was neutralized by addition of KSCN (100 mM). H+/e– ratios of electron-transport driven proton translocation were calculated by simulation with proton.exe. This method gave lower but more realistic values than logarithmic extrapolation. We could verify the kinetic simulation parameters found with proton.exe using series of increasing additions of the reactants. Our approach allows for studying a broad variety of proton-related metabolic activities at micromolar concentrations and time scales of seconds to minutes.
Exploitation of Novel Bt ICPs for the Management of Helicoverpa armigera (Hübner) in Cotton (Gossypium hirsutum L.): A Transgenic Approach
Authors: Karthik Kesiraju , Negi Jyotsana , Rathinam Maniraj , Saini Navinder , Sreevathsa Rohini
Published: April 2021

Cotton is a commercial crop of global importance. The major threat challenging the productivity in cotton has been the lepidopteron insect pest Helicoverpa armigera or cotton bollworm which voraciously feeds on various plant parts. Biotechnological interventions to manage this herbivore have been a universally inevitable option. The advent of plant genetic engineering and exploitation of Bacillus thuringiensis (Bt) insecticidal crystal proteins (ICPs) marked the beginning of plant protection in cotton through transgenic technology. Despite phenomenal success and widespread acceptance, the fear of resistance development in insects has been a perennial concern. To address this issue, alternate strategies like introgression of a combination of cry protein genes and protein-engineered chimeric toxin genes came into practice. The utility of chimeric toxins produced by domain swapping, rearrangement of domains, and other strategies aid in toxins emerging with broad spectrum efficacy that facilitate the avoidance of resistance in insects toward cry toxins. The present study demonstrates the utility of two Bt ICPs, cry1AcF (produced by domain swapping) and cry2Aa (produced by codon modification) in transgenic cotton for the mitigation of H. armigera. Transgenics were developed in cotton cv. Pusa 8–6 by the exploitation of an apical meristem-targeted in planta transformation protocol. Stringent trait efficacy-based selective screening of T1 and T2 generation transgenic plants enabled the identification of plants resistant to H. armigera upon deliberate challenging. Evaluation of shortlisted events in T3 generation identified a total of nine superior transgenic events with both the genes (six with cry1AcF and three with cry2Aa). The transgenic plants depicted 80–100% larval mortality of H. armigera and 10–30% leaf damage. Molecular characterization of the shortlisted transgenics demonstrated stable integration, inheritance and expression of transgenes. The study is the first of its kind to utilise a non-tissue culture-based transformation strategy for the development of stable transgenics in cotton harbouring two novel genes, cry1AcF and cry2Aa for insect resistance. The identified transgenic events can be potential options toward the exploitation of unique cry genes for the management of the polyphagous insect pest H. armigera.
Antimicrobial Resistance Genes in Bacteria Isolated From Japanese Honey, and Their Potential for Conferring Macrolide and Lincosamide Resistance in the American Foulbrood Pathogen Paenibacillus larvae
Authors: Okamoto Mariko , Kumagai Masahiko , Kanamori Hiroyuki , Takamatsu Daisuke
Published: April 2021

American foulbrood (AFB) is the most serious bacterial disease of honey bee brood. Spores of the causative agent Paenibacillus larvae are ingested by bee larvae via brood foods and germinated cells proliferate in the larval midgut. In Japan, a macrolide antibiotic, tylosin, is used as the approved prophylactic for AFB. Although tylosin-resistant P. larvae has yet to be found in Japan, it may emerge in the future through the acquisition of macrolide resistance genes from other bacteria, and bacteria latent in brood foods, such as honey, may serve as a source of resistance genes. In this study, to investigate macrolide resistance genes in honey, we attempted to isolate tylosin-resistant bacteria from 53 Japanese honey samples and obtained 209 isolates from 48 samples in the presence of 1 μg/ml of tylosin. All isolates were Gram-positive spore-forming bacteria mainly belonging to genera Bacillus and Paenibacillus, and 94.3% exhibited lower susceptibility to tylosin than Japanese P. larvae isolates. Genome analysis of 50 representative isolates revealed the presence of putative macrolide resistance genes in the isolates, and some of them were located on mobile genetic elements (MGEs). Among the genes on MGEs, ermC on the putative mobilizable plasmid pJ18TS1mac of Oceanobacillus strain J18TS1 conferred tylosin and lincomycin resistance to P. larvae after introducing the cloned gene using the expression vector. Moreover, pJ18TS1mac was retained in the P. larvae population for a long period even under non-selective conditions. This suggests that bacteria in honey is a source of genes for conferring tylosin resistance to P. larvae; therefore, monitoring of bacteria in honey may be helpful to predict the emergence of tylosin-resistant P. larvae and prevent the selection of resistant strains.
Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis
Authors: Silva Liliana S. O. , Matias Pedro M. , Romão Célia V. , Saraiva Lígia M.
Published: April 2021

Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron center to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.
Production and Characterization of High Value Prebiotics From Biorefinery-Relevant Feedstocks
Authors: Rajan Kalavathy , D’Souza Doris H. , Kim Keonhee , Choi Joseph Moon , Elder Thomas , Carrier Danielle Julie , Labbé Nicole
Published: April 2021

Hemicellulose, a structural polysaccharide and often underutilized co-product stream of biorefineries, could be used to produce prebiotic ingredients with novel functionalities. Since hot water pre-extraction is a cost-effective strategy for integrated biorefineries to partially fractionate hemicellulose and improve feedstock quality and performance for downstream operations, the approach was applied to process switchgrass (SG), hybrid poplar (HP), and southern pine (SP) biomass at 160°C for 60 min. As a result, different hemicellulose-rich fractions were generated and the chemical characterization studies showed that they were composed of 76–91% of glucan, xylan, galactan, arabinan, and mannan oligosaccharides. The hot water extracts also contained minor concentrations of monomeric sugars (≤18%), phenolic components (≤1%), and other degradation products (≤3%), but were tested for probiotic activity without any purification. When subjected to batch fermentations by individual cultures of Lactobacillus casei, Bifidobacterium bifidum, and Bacteroides fragilis, the hemicellulosic hydrolysates elicited varied responses. SG hydrolysates induced the highest cell count in L. casei at 8.6 log10 cells/ml, whereas the highest cell counts for B. fragilis and B. bifidum were obtained with southern pine (5.8 log10 cells/ml) and HP hydrolysates (6.4 log10 cells/ml), respectively. The observed differences were attributed to the preferential consumption of mannooligosaccharides in SP hydrolysates by B. fragilis. Lactobacillus casei preferentially consumed xylooligosaccharides in the switchgrass and southern pine hydrolysates, whereas B. bifidum consumed galactose in the hybrid poplar hydrolysates. Thus, this study (1) reveals the potential to produce prebiotic ingredients from biorefinery-relevant lignocellulosic biomass, and (2) demonstrates how the chemical composition of hemicellulose-derived sources could regulate the viability and selective proliferation of probiotic microorganisms.
Veliparib Is an Effective Radiosensitizing Agent in a Preclinical Model of Medulloblastoma
Authors: Buck Jessica , Dyer Patrick J. C. , Hii Hilary , Carline Brooke , Kuchibhotla Mani , Byrne Jacob , Howlett Meegan , Whitehouse Jacqueline , Ebert Martin A. , McDonald Kerrie L. , Gottardo Nicholas G. , Endersby Raelene
Published: April 2021

Medulloblastoma is the most common malignant childhood brain tumor, and 5-year overall survival rates are as low as 40% depending on molecular subtype, with new therapies critically important. As radiotherapy and chemotherapy act through the induction of DNA damage, the sensitization of cancer cells through the inhibition of DNA damage repair pathways is a potential therapeutic strategy. The poly-(ADP-ribose) polymerase (PARP) inhibitor veliparib was assessed for its ability to augment the cellular response to radiation-induced DNA damage in human medulloblastoma cells. DNA repair following irradiation was assessed using the alkaline comet assay, with veliparib inhibiting the rate of DNA repair. Veliparib treatment also increased the number of γH2AX foci in cells treated with radiation, and analysis of downstream pathways indicated persistent activation of the DNA damage response pathway. Clonogenicity assays demonstrated that veliparib effectively inhibited the colony-forming capacity of medulloblastoma cells, both as a single agent and in combination with irradiation. These data were then validated in vivo using an orthotopic implant model of medulloblastoma. Mice harboring intracranial D425 medulloblastoma xenografts were treated with vehicle, veliparib, 18 Gy multifractionated craniospinal irradiation (CSI), or veliparib combined with 18 Gy CSI. Animals treated with combination therapy exhibited reduced tumor growth rates concomitant with increased intra-tumoral apoptosis observed by immunohistochemistry. Kaplan–Meier analyses revealed a statistically significant increase in survival with combination therapy compared to CSI alone. In summary, PARP inhibition enhanced radiation-induced cytotoxicity of medulloblastoma cells; thus, veliparib or other brain-penetrant PARP inhibitors are potential radiosensitizing agents for the treatment of medulloblastoma.
Sleep Timing and Risk of Dementia Among the Chinese Elderly in an Urban Community: The Shanghai Aging Study
Authors: Li Xiantao , Ding Ding , Zhao Qianhua , Wu Wanqing , Xiao Zhenxu , Luo Jianfeng , Yaffe Kristine , Leng Yue
Published: April 2021

Background: Growing evidence has suggested a link between poor sleep quality and increased risk of dementia. However, little is known about the association between sleep timing, an important behavior marker of circadian rhythms, and dementia risk in older adults, and whether this is independent of sleep duration or quality.

Methods: We included data from 1,051 community-dwelling older men and women (aged≥ 60y) without dementia from the Shanghai Aging Study. At baseline, participants reported sleep timing, duration, and quality using the Chinese version of the Pittsburgh Sleep Quality Index (CPSQI). Dementia diagnosis over the following 7.3 years was determined by neurologists using DSM-IV criteria. We used Cox proportional hazards models to examine the association between bedtime (before 9 p.m., after 11 p.m. vs. 9–11 p.m.), rise time (before 6 a.m., after 8 a.m. vs. 6–8 a.m.), and risk of dementia.

Results: A total of 238 (22.8%), 675 (64.5%), and 133 (12.7%) participants reported going to bed before 9 p.m., between 9 and 11 p.m., and after 11 p.m., respectively, while 272 (26%), 626 (59.9%), and 148 (14.2%) reported getting up before 6 a.m., between 6 and 8 a.m., and after 8 a.m., respectively. Participants who reported going to bed earlier had a lower education level, were less likely to be smokers, more likely to have hypertension or diabetes, and had longer sleep duration but poorer sleep quality compared to those who reported a later bedtime. We found 47 incidents of dementia among 584 participants followed up over an average of 7.3 years. After adjustment for demographics, education, income, body mass index, depressive symptoms, smoking, alcohol use, physical activity, comorbidities, APOE4 genotype, and baseline MMSE, those with a bedtime of before 9 p.m. were two times more likely to develop dementia [hazard ratio (HR)=2.16 (95%CI: 1.06–4.40)], compared to those going to bed between 9 and 11 p.m. Later bedtime (i.e., after 11 p.m.) showed the opposite but had a non-significant association with dementia risk (HR=0.15, 95%CI: 0.02–1.29). We did not find an association for rise time and risk of dementia.

Conclusion: Earlier sleep timing in older adults without dementia was associated with an increased risk of dementia. Future studies should examine the underlying mechanisms of this association and explore the usefulness of sleep timing as a preclinical marker for dementia.
Transductive Transfer Learning for Domain Adaptation in Brain Magnetic Resonance Image Segmentation
Authors: Kushibar Kaisar , Salem Mostafa , Valverde Sergi , Rovira Àlex , Salvi Joaquim , Oliver Arnau , Lladó Xavier
Published: April 2021

Segmentation of brain images from Magnetic Resonance Images (MRI) is an indispensable step in clinical practice. Morphological changes of sub-cortical brain structures and quantification of brain lesions are considered biomarkers of neurological and neurodegenerative disorders and used for diagnosis, treatment planning, and monitoring disease progression. In recent years, deep learning methods showed an outstanding performance in medical image segmentation. However, these methods suffer from generalisability problem due to inter-centre and inter-scanner variabilities of the MRI images. The main objective of the study is to develop an automated deep learning segmentation approach that is accurate and robust to the variabilities in scanner and acquisition protocols. In this paper, we propose a transductive transfer learning approach for domain adaptation to reduce the domain-shift effect in brain MRI segmentation. The transductive scenario assumes that there are sets of images from two different domains: (1) source—images with manually annotated labels; and (2) target—images without expert annotations. Then, the network is jointly optimised integrating both source and target images into the transductive training process to segment the regions of interest and to minimise the domain-shift effect. We proposed to use a histogram loss in the feature level to carry out the latter optimisation problem. In order to demonstrate the benefit of the proposed approach, the method has been tested in two different brain MRI image segmentation problems using multi-centre and multi-scanner databases for: (1) sub-cortical brain structure segmentation; and (2) white matter hyperintensities segmentation. The experiments showed that the segmentation performance of a pre-trained model could be significantly improved by up to 10%. For the first segmentation problem it was possible to achieve a maximum improvement from 0.680 to 0.799 in average Dice Similarity Coefficient (DSC) metric and for the second problem the average DSC improved from 0.504 to 0.602. Moreover, the improvements after domain adaptation were on par or showed better performance compared to the commonly used traditional unsupervised segmentation methods (FIRST and LST), also achieving faster execution time. Taking this into account, this work presents one more step toward the practical implementation of deep learning algorithms into the clinical routine.
Case Report: Efficacy of Ninjin'yoeito Treatment for Idiopathic Pulmonary Fibrosis
Authors: Kushima Hisako , Ishii Hiroshi , Fujita Masaki
Published: April 2021

Ninjin'yoeito, a Kampo prescription, was administered to two patients with idiopathic pulmonary fibrosis (IPF) over a period of 12 weeks to improve loss of appetite and lassitude. In Case 1, improvements were observed in appetite, lassitude, and breathlessness, as well as increases or increasing tendencies in body weight, blood albumin level, and hemoglobin (Hb) level. Case 2 showed no changes in appetite but improvements in lassitude and no deterioration of breathlessness. His body weight and his blood albumin and Hb levels increased or showed increasing trends. In both cases, a trend for improvement of respiratory function was observed. In summary, ninjin'yoeito trended to improve the subjective symptoms and nutritional status of a patient with pulmonary fibrosis.
Quercetin Ameliorates Gut Microbiota Dysbiosis That Drives Hypothalamic Damage and Hepatic Lipogenesis in Monosodium Glutamate-Induced Abdominal Obesity
Authors: Zhao Lijun , Zhu Xiaoqiang , Xia Mengxuan , Li Jing , Guo An-Yuan , Zhu Yanhong , Yang Xiangliang
Published: April 2021

Monosodium glutamate (MSG)-induced abdominal obesity, conventionally caused by hypothalamic damage, is a critical risk factor for health problem. Microbiota-gut-brain axis plays important roles in a variety of metabolic diseases. However, whether gut microbiota is involved in the pathogenesis for MSG-induced abdominal obesity and the effect of quercetin on it remains unclear. Herein, we find that MSG-induced gut microbiota dysbiosis contributes to neuronal damage in the hypothalamus, as indicated by antibiotics-induced microbiota depletion and co-house treatment. Inspired by this finding, we investigate the mechanism in-depth for MSG-induced abdominal obesity. Liver transcriptome profiling shows retinol metabolism disorder in MSG-induced abdominal obese mice. In which, retinol saturase (RetSat) in the liver is notably up-regulated, and the downstream lipogenesis is correspondingly elevated. Importantly, microbiota depletion or co-house treatment eliminates the difference of RetSat expression in the liver, indicating gut microbiota changes are responsible for liver retinol metabolism disorder. Moreover, this study finds dietary quercetin could modulate MSG-induced gut microbiota dysbiosis, alleviate hypothalamic damage and down-regulate liver RetSat expression, thus ameliorating abdominal obesity. Our study enriches the pathogenesis of MSG-induced abdominal obesity and provides a prebiotic agent to ameliorate abdominal obesity.
The Efficacy of Combined Cisplatin and Nanoparticle Albumin-Bound Paclitaxel in a Stage IV Pancreatic Squamous Cell Carcinoma Patient With a Somatic BRCA2 Mutation: A Case Report
Authors: Huang Xiaozhun , Wang Chunling , Ma Teng , Huang Zhangkan , Zhou Houhong , Xu Lin , Zhang Renjie , Zhao Jianjun , Zhang Yefan , Huang Zhen , Shao Lin , Wang Yang , Yang Fan , Che Xu
Published: April 2021

Pancreatic squamous cell carcinoma (SCC) is a rare primary pancreatic malignancy with a poor prognosis. The median overall survival (OS) for metastatic setting is only 4 months and the optimal management remains poorly defined. In the present study, we report a 52-year-old female patient with stage IV primary SCC of the pancreas harboring a deleteous BRCA2 somatic mutation. After 10 cycles of chemotherapy of cisplatin combined with nanoparticle albumin-bound paclitaxel, metastatic lesions in the liver and lymph nodes achieved radiographic complete responses and pancreatic lesion shrank from 5.7 to 1.5 cm in diameter. The patient subsequently underwent a posterior radical antegrade modular pancreatosplenectomy with R0 resection and residual liver lesions were also resected. After 3 months, a tumor relapsed in the liver. She was then treated with olaparib combined with pembrolizumab and achieved stable disease on the liver lesion. The patient eventually died from cerebral hemorrhage with a long OS of 21 months. Our case demonstrated a favorable clinical activity and survival advantage of the combined cisplatin and nanoparticle albumin-bound paclitaxel, which might serve as a therapeutic option for the patient with BRCA-mutant pancreatic SCC.
A Radiomics Nomogram for Preoperative Prediction of Early Recurrence of Small Hepatocellular Carcinoma After Surgical Resection or Radiofrequency Ablation
Authors: Wen Liting , Weng Shuping , Yan Chuan , Ye Rongping , Zhu Yuemin , Zhou Lili , Gao Lanmei , Li Yueming
Published: April 2021

Background

Patients with small hepatocellular carcinoma (HCC) (≤3 cm) still have a poor prognosis. The purpose of this study was to develop a radiomics nomogram to preoperatively predict early recurrence (ER) (≤2 years) of small HCC.

Methods

The study population included 111 patients with small HCC who underwent surgical resection (SR) or radiofrequency ablation (RFA) between September 2015 and September 2018 and were followed for at least 2 years. Radiomic features were extracted from the entire tumor by using the MaZda software. The least absolute shrinkage and selection operator (LASS0) method was applied for feature selection, and radiomics signature construction. A rad-score was then calculated. Multivariable logistic regression analysis was used to establish a prediction model including independent clinical risk factors, radiologic features and rad-score, which was ultimately presented as a radiomics nomogram. The predictive ability of the nomogram was evaluated using the area under the receiver operating characteristic (ROC) curve and internal validation was performed via bootstrap resampling and 5-fold cross-validation method.

Results

A total of 53 (53/111, 47.7%) patients had confirmed ER according to the final clinical outcomes. In univariate logistic regression analysis, cirrhosis and hepatitis B infection (P=0.015 and 0.083, respectively), hepatobiliary phase hypointensity (P=0.089), Child-Pugh score (P=0.083), the preoperative platelet count (P=0.003), and rad-score (P<0.001) were correlated with ER. However, after multivariate logistic regression analysis, only the preoperative platelet count and rad-score were included as predictors in the final model. The area under ROC curve (AUC) of the radiomics nomogram to predict ER of small HCC was 0.981 (95% CI: 0.957, 1.00), while the AUC verified by bootstrap is 0.980 (95% CI: 0.962, 1.00), indicating the goodness-of-fit of the final model.

Conclusions

The radiomics nomogram containing the clinical risk factors and rad-score can be used as a quantitative tool to preoperatively predict individual probability of ER of small HCC.
Letermovir Administration to Prevent Cytomegalovirus Reactivation Is the Potential Risk of Chronic Graft-Versus-Host Disease in Patients Who Received Haploidentical Stem-Cell Transplantation With Post-Transplant Cyclophosphamide
Authors: Terao Toshiki , Matsuoka Ken-ichi , Narita Kentaro , Tsushima Takafumi , Yuyama Satoshi , Kuzume Ayumi , Tabata Rikako , Miura Daisuke , Takeuchi Masami , Matsue Kosei
Published: April 2021

The prevention of chronic graft-versus-host disease (cGVHD) is important for recipients of hematopoietic stem-cell transplantation (HSCT). As one of the etiologies, the relationship between early T-cell recovery and subsequent cGVHD development has been the focus of attention. Recently, letermovir (LTV) was approved for preventing cytomegalovirus (CMV) reactivation in the early transplantation phase. Although CMV affects the immune reconstitution after HSCT, the impacts of LTV to prevent CMV reactivation on early T-cell recovery and cGVHD have not been fully investigated. We aimed to identify early T-cell recovery under LTV at day 30 in 15 and 33 recipients from matched related donors (MRDs) and haploidentical donors with post-transplant cyclophosphamide (PTCy-haplo), respectively. Early increases in the levels of total lymphocytes and HLA-DR+ activated T-cells at day 30 were observed under CMV prophylaxis by LTV only in PTCy-haplo recipients and not in MRD recipients. Moreover, PTCy-haplo recipients with LTV showed a significantly higher incidence of cGVHD, but not acute GVHD. Our observations suggest that an early increase in the levels of HLA-DR+ activated T-cells may be implicated in the development of cGVHD in patients treated with PTCy who received LTV. Further studies are warranted to validate our results and elucidate the detailed mechanisms of our new insights.
Strategies for the Construction of Mouse Models With Humanized Immune System and Evaluation of Tumor Immune Checkpoint Inhibitor Therapy
Authors: Guo Wenwen , Zhang Caiqin , Qiao Tianyun , Zhao Jumei , Shi Changhong
Published: April 2021

Immunotherapy has been used as a first-line treatment for a variety of advanced tumors, allowing remarkable progress to be made in cancer treatment. Nonetheless, only a small number of patients can benefit from immune checkpoint inhibitor monotherapy. To improve the effect of immunotherapy, the underlying mechanism of combination therapy was investigated in the context of an intact human tumor immune microenvironment using mice with a human immune system (HIS) bearing human tumors. Herein, we summarize and discuss strategies for the development and use of HIS mice models in tumor immunotherapies. Most importantly, this review proposes a method of t11umor identification and classification in HIS mice based on the tumor-infiltrating lymphocytes and PD-L1 expression, and according to this classification, we propose different combination treatment strategies that can be utilized to enhance the effect of immunotherapy. Thus, we provide effective experimental schemes for tumor immunotherapy in HIS mice models.
Using Machine Learning to Predict the Diagnosis, Management and Severity of Pediatric Appendicitis
Authors: Marcinkevics Ricards , Reis Wolfertstetter Patricia , Wellmann Sven , Knorr Christian , Vogt Julia E.
Published: April 2021

Background:Given the absence of consolidated and standardized international guidelines for managing pediatric appendicitis and the few strictly data-driven studies in this specific, we investigated the use of machine learning (ML) classifiers for predicting the diagnosis, management and severity of appendicitis in children.

Materials and Methods:Predictive models were developed and validated on a dataset acquired from 430 children and adolescents aged 0-18 years, based on a range of information encompassing history, clinical examination, laboratory parameters, and abdominal ultrasonography. Logistic regression, random forests, and gradient boosting machines were used for predicting the three target variables.

Results:A random forest classifier achieved areas under the precision-recall curve of 0.94, 0.92, and 0.70, respectively, for the diagnosis, management, and severity of appendicitis. We identified smaller subsets of 6, 17, and 18 predictors for each of targets that sufficed to achieve the same performance as the model based on the full set of 38 variables. We used these findings to develop the user-friendly online Appendicitis Prediction Tool for children with suspected appendicitis.

Discussion:This pilot study considered the most extensive set of predictor and target variables to date and is the first to simultaneously predict all three targets in children: diagnosis, management, and severity. Moreover, this study presents the first ML model for appendicitis that was deployed as an open access easy-to-use online tool.

Conclusion:ML algorithms help to overcome the diagnostic and management challenges posed by appendicitis in children and pave the way toward a more personalized approach to medical decision-making. Further validation studies are needed to develop a finished clinical decision support system.
Qing-Yi Decoction in the Treatment of Acute Pancreatitis: An Integrated Approach Based on Chemical Profile, Network Pharmacology, Molecular Docking and Experimental Evaluation
Authors: Wei Tian-Fu , Zhao Liang , Huang Peng , Hu Feng-Lin , Jiao Ju-Ying , Xiang Kai-Lai , Wang Zhi-Zhou , Qu Jia-Lin , Shang Dong
Published: April 2021

Background: Qing-Yi Decoction (QYD) is a classic precompounded prescription with satisfactory clinical efficacy on acute pancreatitis (AP). However, the chemical profile and overall molecular mechanism of QYD in treating AP have not been clarified.

Methods: In the present study, a rapid, simple, sensitive and reliable ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS)-based chemical profile was first established. An integration strategy of network pharmacology analysis and molecular docking based identified ingredients was further performed to screen out the potential targets and pathways involved in the treatment of QYD on AP. Finally, SD rats with acute pancreatitis were constructed to verify the predicted results through a western blot experiment.

Results: A total of 110 compounds, including flavonoids, phenolic acids, alkaloids, monoterpenes, iridoids, triterpenes, phenylethanoid glycosides, anthraquinones and other miscellaneous compounds were identified, respectively. Eleven important components, 47 key targets and 15 related pathways based on network pharmacology analysis were obtained. Molecular docking simulation indicated that ERK1/2, c-Fos and p65 might play an essential role in QYD against AP. Finally, the western blot experiments showed that QYD could up-regulate the expression level of ERK1/2 and c-Fos, while down-regulate the expression level of p65.

Conclusion: This study predicted and validated that QYD may treat AP by inhibiting inflammation and promoting apoptosis, which provides directions for further experimental studies.
Population Pharmacokinetic Model of Iohexol in Dogs to Estimate Glomerular Filtration Rate and Optimize Sampling Time
Authors: Baklouti Sarah , Concordet Didier , Borromeo Vitaliano , Pocar Paola , Scarpa Paola , Cagnardi Petra
Published: April 2021

Monitoring iohexol plasma clearance is considered a useful, reliable, and sensitive tool to establish glomerular filtration rate (GFR) and early stages of kidney disease in both humans and veterinary medicine. The assessment of GFR based on iohexol plasma clearance needs repeated blood sampling over hours, which is not easily attainable in a clinical setting. The study aimed to build a population pharmacokinetic (Pop PK) model to estimate iohexol plasma clearance in a population of dogs and based on this model, to indicate the best sampling times that enable a precise clearance estimation using a low number of samples. A Pop PK model was developed based on 5 iohexol plasma samples taken from 5 to 180 minutes (min) after an intravenous iohexol nominal dose of 64.7 mg/kg from 49 client-owned dogs of different breeds, sexes, ages, body weights, and clinical conditions (healthy or presenting chronic kidney disease CKD). The design of the best sampling times could contain either 1 or 2 or 3 sampling times. These were discretized with a step of 30 min between 30 and 180 min. A two-compartment Pop PK model best fitted the data; creatinine and kidney status were the covariates included in the model to explain a part of clearance variability. When 1 sample was available, 90 or 120 min were the best sampling times to assess clearance for healthy dogs with a low creatinine value. Whereas for dogs with CKD and medium creatinine value, the best sampling time was 150 or 180 min, for CKD dogs with a high creatinine value, it was 180 min. If 2 or 3 samples were available, several sampling times were possible. The method to define the best sampling times could be used with other Pop PK models as long as it is representative of the patient population and once the model is built, the use of individualized sampling times for each patient allows to precisely estimate the GFR.
Analysis of Genetic and Non-genetic Predictors of Levodopa Induced Dyskinesia in Parkinson’s Disease
Authors: Tirozzi Alfonsina , Modugno Nicola , Palomba Nicole Piera , Ferese Rosangela , Lombardi Alessia , Olivola Enrica , Gialluisi Alessandro , Esposito Teresa
Published: April 2021

Background: Levodopa (L-Dopa), representing the therapeutic gold standard for the treatment of Parkinson disease (PD), is associated with side effects like L-Dopa induced dyskinesia (LID). Although several non-genetic and genetic factors have been investigated for association with LID risk, contrasting results were reported and its genetic basis remain largely unexplored.

Methods: In an Italian PD cohort (N = 460), we first performed stepwise multivariable Cox Proportional Hazard regressions modeling LID risk as a function of gender, PD familiarity, clinical subtype, weight, age-at-onset (AAO) and years-of-disease (YOD), L-Dopa dosage, severity scores, and scales assessing motor (UPDRS-III), cognitive (MoCA), and non-motor symptoms (NMS). Then we enriched the resulting model testing two variants—rs356219 and D4S3481—increasing the expression of the SNCA gene, previously suggested as a potential mechanism of LID onset. To account for more complex (non-linear) relations of these variables with LID risk, we built a survival random forest (SRF) algorithm including all the covariates mentioned above.

Results: Among tested variables (N = 460 case-complete, 211 LID events; total follow-up 31,361 person-months, median 61 months), disease duration showed significant association (p < 0.005), with 6 (3–8)% decrease of LID risk per additional YOD. Other nominally significant associations were observed for gender—with women showing a 39 (5–82)% higher risk of LID—and AAO, with 2 (0.3–3)% decrease of risk for each year increase of PD onset. The SRF algorithm confirmed YOD as the most prominent feature influencing LID risk, with a variable importance of about 8% in the model. In genetic models, no statistically significant effects on incident LID risk was observed.

Conclusions: This evidence supports a protective effect of late PD onset and gender (men) against LID risk and suggests a new independent protective factor, YOD. Moreover, it underlines the importance of personalized therapeutic protocols for PD patients in the future.
Sodium–Glucose CoTransporter-2 Inhibitor Empagliflozin Ameliorates Sunitinib-Induced Cardiac Dysfunction via Regulation of AMPK–mTOR Signaling Pathway–Mediated Autophagy
Authors: Ren Changzhen , Sun Kaiqiang , Zhang Yanda , Hu Yangxi , Hu Bowen , Zhao Jian , He Zhiqing , Ding Ru , Wang Weizhong , Liang Chun
Published: April 2021

Background: Sodium–glucose cotransporter-2 (SGLT2) inhibitors have been shown to decrease the adverse cardiac events and risks of cardiovascular mortality among patients with or without diabetes, which has made these drugs promising treatment options for patients with chronic heart failure. Cardiac dysfunction is a common and severe side effect induced by cancer chemotherapies, which seriously affects the prognosis and life quality of tumor patients. However, it is not clear whether SGLT2 inhibitors have cardiovascular benefits in patients with cancer chemotherapy–related cardiac dysfunction. We aimed to determine whether empagliflozin (EMPA), an SGLT2 inhibitor, has a protective role against sunitinib (SNT)-induced cardiac dysfunction in a mouse model.

Methods: Male C57BL/6J mice were randomized into control (control, n = 8), empagliflozin (EMPA, n = 8), sunitinib (SNT, n = 12), or sunitinib and empagliflozin coadministration (SNT + EMPA, n = 12) groups. EMPA, SNT, or SNT-combined EMPA was given via oral gavage for consecutive 28 days. Cardiovascular functions and pathological changes were examined, and the underlying mechanisms of EMPA’s effects were investigated in H9c2 cardiomyocytes.

Results: Mice in the SNT group exhibited dramatically elevated blood pressure (systolic blood pressure [SBP] 134.30 ± 6.455 mmHg vs. 114.85 ± 6.30 mmHg) and impaired left ventricular function (left ventricular ejection fraction [LVEF] 50.24 ± 3.06% vs. 84.92 ± 2.02%), as compared with those of the control group. However, EMPA could ameliorate SNT-induced cardiotoxicity, both in terms of SBP (117.51 ± 5.28 mmHg vs. 134.30 ± 6.455 mmHg) and LVEF (76.18 ± 5.16% vs. 50.24 ± 3.06 %). In H9c2 cardiomyocytes, SNT-induced cardiomyocyte death and cell viability loss as well as dysfunction of adenosine 5’-monophosphate–activated protein kinase–mammalian target of rapamycin (AMPK-mTOR) signaling–mediated autophagy were restored by EMPA. However, these favorable effects mediated by EMPA were blocked by the inhibition of AMPK or autophagy.

Conclusion: EMPA could ameliorate SNT-induced cardiac dysfunction via regulating cardiomyocyte autophagy, which was mediated by the AMPK-mTOR signaling pathway. These findings supported that SGLT2 inhibitor therapy could be a potential cardioprotective approach for cardiovascular complications among patients receiving SNT. However, these favorable effects still need to be validated in clinical trials.
Systems Biology Modeling of the Complement System Under Immune Susceptible Pathogens
Authors: Zewde Nehemiah T. , Hsu Rohaine V. , Morikis Dimitrios , Palermo Giulia
Published: April 2021

The complement system is assembled from a network of proteins that function to bring about the first line of defense of the body against invading pathogens. However, complement deficiencies or invasive pathogens can hijack complement to subsequently increase susceptibility of the body to infections. Moreover, invasive pathogens are increasingly becoming resistant to the currently available therapies. Hence, it is important to gain insights into the highly dynamic interaction between complement and invading microbes in the frontlines of immunity. Here, we developed a mathematical model of the complement system composed of 670 ordinary differential equations with 328 kinetic parameters, which describes all three complement pathways (alternative, classical, and lectin) and includes description of mannose-binding lectin, collectins, ficolins, factor H-related proteins, immunoglobulin M, and pentraxins. Additionally, we incorporate two pathogens: (type 1) complement susceptible pathogen and (type 2)Neisseria meningitidislocated in either nasopharynx or bloodstream. In both cases, we generate time profiles of the pathogen surface occupied by complement components and the membrane attack complex (MAC). Our model shows both pathogen types in bloodstream are saturated by complement proteins, whereas MACs occupy <<1.0% of the pathogen surface. Conversely, the MAC production in nasopharynx occupies about 1.5–10% of the totalN. meningitidissurface, thus making nasal MAC levels at least about eight orders of magnitude higher. Altogether, we predict complement-imbalance, favoring overactivation, is associated with nasopharynx homeostasis. Conversely, orientating toward complement-balance may cause disruption to the nasopharynx homeostasis. Thus, for sporadic meningococcal disease, our model predicts rising nasal levels of complement regulators as early infection biomarkers.
Variations of Training Workload in Micro- and Meso-Cycles Based on Position in Elite Young Soccer Players: A Competition Season Study
Authors: Nobari Hadi , Vahabidelshad Reyhaneh , Pérez-Gómez Jorge , Ardigò Luca Paolo
Published: April 2021

The objectives of this study were to quantify the matches and training workload in micro-cycles of an elite young soccer team considering field position and to explain meso-cycles based on change of weekly acute (wAWL), chronic load (wCWL), acute-to-chronic workload ratio, training monotony (wTM), and training strain (wTS) between early-, mid-, and end-season periods considering playing position and whole team. Twenty-six under-16 elite young soccer players participated in this study, including six wide defenders and wide midfielders (WM), five central defenders (CD) and central midfielders, and four strikers (ST). Daily monitoring was performed by players for 20 weeks with the rating of perceived exertion using the Borg CR-10 scale. In comparison with early-season, results showed that there was a significant increase, in all playing positions, in wAWL and wCWL (except ST) and in wTM (except CD and ST) compared with end-season. On the other hand, there were significant reductions in wTS in CD, WM, and ST at the end-season. According to the results, coaches should consider the field position in different situations. Differences between training workload and matches can be a good guide for coaches, who have a special understanding of what causes the most load in training programs. Excessive training workload can potentially cause injury to adolescent athletes and controlling wTM can prevent this.
Phytochromes in Agrobacterium fabrum
Authors: Lamparter Tilman , Xue Peng , Elkurdi Afaf , Kaeser Gero , Sauthof Luisa , Scheerer Patrick , Krauß Norbert
Published: April 2021

The focus of this review is on the phytochromes Agp1 and Agp2 of Agrobacterium fabrum. These are involved in regulation of conjugation, gene transfer into plants, and other effects. Since crystal structures of both phytochromes are known, the phytochrome system of A. fabrum provides a tool for following the entire signal transduction cascade starting from light induced conformational changes to protein interaction and the triggering of DNA transfer processes.
Role of Hydraulic Signal and ABA in Decrease of Leaf Stomatal and Mesophyll Conductance in Soil Drought-Stressed Tomato
Authors: Li Shuang , Liu Junming , Liu Hao , Qiu Rangjian , Gao Yang , Duan Aiwang
Published: April 2021

Drought reduces leaf stomatal conductance (gs) and mesophyll conductance (gm). Both hydraulic signals and chemical signals (mainly abscisic acid, ABA) are involved in regulating gs. However, it remains unclear what role the endogenous ABA plays in gm under decreasing soil moisture. In this study, the responses of gs and gm to ABA were investigated under progressive soil drying conditions and their impacts on net photosynthesis (An) and intrinsic water use efficiency (WUEi) were also analyzed. Experimental tomato plants were cultivated in pots in an environment-controlled greenhouse. Reductions of gs and gm induced a 68–78% decline of An under drought conditions. While soil water potential (Ψsoil) was over −1.01 MPa, gs reduced as leaf water potential (Ψleaf) decreased, but ABA and gm kept unchanged, which indicating gs was more sensitive to drought than gm. During Ψsoil reduction from −1.01 to −1.44 MPa, Ψleaf still kept decreasing, and both gs and gm decreased concurrently following to the sustained increases of ABA content in shoot sap. The gm was positively correlated to gs during a drying process. Compared to gs or gm, WUEi was strongly correlated with gm/gs. WUEi improved within Ψsoil range between −0.83 and −1.15 MPa. In summary, gs showed a higher sensitivity to drought than gm. Under moderate and severe drought at Ψsoil ≤ −1.01 MPa, furthermore from hydraulic signals, ABA was also involved in this co-ordination reductions of gs and gm and thereby regulated An and WUEi.
The α-Gliadins in Bread Wheat: Effect of Nitrogen Treatment on the Expression of the Major Celiac Disease Immunogenic Complex in Two RNAi Low-Gliadin Lines
Authors: Sánchez-León Susana , Giménez María José , Barro Francisco
Published: April 2021

Celiac Disease (CD) is an autoimmune disorder that affects approximately 1% of the worldwide population. The α-gliadins of wheat contain the 33-mer peptide, the most active peptide in CD both in adults and pediatric patients. In this study, we have characterized the variants and expression profile of an α-gliadins amplicon, harboring the 33-mer peptide, in two low-gliadin RNAi wheat lines, under two different Nitrogen (N) treatments. We estimated that the amplicon expands 45 different α-gliadin variants with high variability due to length, randomly distributed SNPs, and the presence of encoded CD epitopes. Expression of this amplicon is reduced in both RNAi lines in comparison to the wild type. High N treatment significantly increases transcripts of the amplicon in the wild type, but not in the transgenic lines. Classification of α-gliadin variants, considering the number of epitopes, revealed that amplicon variants containing the full complement of 33-mer peptide were affected by N treatment, increasing their expression when N was increased. Line D793 provided higher and more stable silencing through different N fertilization regimes, expressing fewer CD epitopes than D783. Results of this study are important for better understanding of RNAi α-gliadin silencing in response to N treatments, and for undertaking new strategies by RNAi or CRISPR/Cas toward obtaining new varieties suitable for people suffering gluten intolerances.