bluuebunny/crossref_metadata_2025 huggingface dataset:
Stimulation of Phenolic Compounds Accumulation and Antioxidant Activity in In Vitro Culture of Salvia Tebesana Bunge in Response to Nano-TiO2 and Methyl Jasmonate Elicitors
Authors: Shoja Amin allah , Cheniany Monireh - , Ganjeali Ali
Published: July 2021

In the present study, we first attempted to achieve an efficient procedure for optimizing callogenesis from apical meristem and leaf explants of S. tebesana on MS media containing different concentrations of BAP alone and in combination with 2,4-D. Then, the inducing effect of nano-TiO2 (10, 60, and 120 mg L− 1) and methyl jasmonate (50, 100, and 200 µM), as abiotic elicitors were studied on the enhancement of phenolic compounds, rosmarinic acid, and some individual flavonoids as well as antioxidant capacity of callus extracts. According to the results, the highest callogenesis rate (100 and 93.33, respectively) and DW (0.55 ± 0.03 and 0.36 ± 0.02 g, respectively) per responsive explant were achieved from apical meristem on MS media containing "BAP 1 + 2,4-D 1" mg L− 1 and from leaf explant on the medium supplemented with "BAP 0.5 + 2,4-D 1" mg L− 1. The elicitation with 10 and 60 mg L− 1 nano-TiO2 (respectively for apical meristem and leaf), and 50µM MeJa could significantly promote the production of predominant phenolic derivatives in S. tebesana calli, where the highest content of total phenolics, O-diphenols, phenolic acid, flavonoid, flavone and flavonol, proanthocyanidin was recorded. Additionally, in increasing the amount of rosmarinic acid of callus, nano-TiO2 treatment was more effective than the elicitation with MeJa. Also, the highest content of Apigenin (0.33 ± 0.02 µg g− 1 DW) was detected after MeJa-elicitation (50µM), while the maximum level of Quercetin (2.61 ± 0.09 µg g− 1 DW) and Rutin (13.79 ± 08 µg g− 1 DW) were obtained after exposure to 60 mg L− 1 nano-TiO2, both from leaf-derived calli. While a significant positive correlation was recorded between antioxidant assays (DPPH and FRAP) and phenolic derivatives of treated calli; a very strong correlation occurred between the content of rosmarinic acid of apical meristem-derived calli and DPPH and FRAP values (r2 = -0.921 and r2 = -0.913, P < 0.01 respectively). Our results showed that the combination of in vitro culture and elicitation would be a good technique to successfully produce and enhance the content of pharmacologically valuable metabolites in S. tebesana.
Dual Electrochemical Sensing of Spiked Virus and SARS-CoV-2 Using Natural Bed-Receptor (MV-gal1)
Authors: ghazizadeh lham , Neshastehriz Ali , Firoozabadi Ali Dehghani , Saievar-Iranizad Esmail , Einali Samira
Published: July 2021

It has been necessary to use methods that can detect the specificity of a virus during virus screening. In this study, we use a dual platform to identify any spiked virus and specific SARS-CoV-2 antigen, sequentially. We introduce a natural bed-receptor surface as Microparticle Vesicle-Galactins1 (MV-gal1) with the ability of glycan binding to screen every spiked virus. MV are the native vesicles which may have the gal-1receptor. Gal-1 is the one of lectin receptor which can bind to glycan. After dropping the MV-gal1 on the SCPE/GNP, the sensor is turned on due to the increased electrochemical exchange with [Fe(CN)6] -3/-4 probe. Dropping the viral particles of SARS-CoV-2 cause to turn off the sensor with covering the sugar bond (early screening). Then, with the addition of Au /Antibody-SARS-CoV-2 on the MV-gal1@ SARS-CoV-2 Antigen, the sensor is turned on again due to the electrochemical amplifier of AuNP (specific detection). As a result, our sensor has the capacity of screening of every spike virus, and the specific detection of covid-19 (LOD: 4.57 × 102 copies/mL) by using the natural bed-receptor and a specific antibody in the solid biosensor, for the first time.
An Experimental Validation Study of Ferrofluid Evaporation
Authors: YU Wenjuan , Li Decai , Niu Sifang
Published: July 2021

Kerosene based ferrofluid was put into a test tube to evaporate under different conditions. The weight losses of samples were measured and the evaporation rates were calculated. The predictions of evaporation rates were made based on Bolotov’s model. It was found that the magnetic particles prevent the base fluid from evaporation and lower volume fraction leaded to higher evaporation rate. Bolotov’s model had a certain deviation but still well responsive to different variables. It was also found that the magnetic field made a difference to the evaporation rate.
An Unconstrained Face Recognition Method Based on Siamese Networks
Authors: CunLi Song , Ji Shouyong
Published: July 2021

It is aimed at the low accuracy and low efficiency of face recognition under unlimited conditions.In this paper, a Siamese neural Network model SN-LF (Siamese Network based on LBP and Frequency Feature perception) is designed based on the Local Binary Pattern (LBP) and the Frequency sensing model.Based on Siamese neural networks, the network adopts circular LBP algorithm and frequency feature perception to realize face recognition under unrestricted conditions.The LBP algorithm can eliminate the influence of light on the image and provide directional input to the network model at the same time.Frequency feature sensing divides the image features into low frequency features and high frequency features. The low frequency features are compressed in the Siamese neural network to increase the recognition efficiency of the network. At the same time, information is exchanged with the high frequency features, so that the target noise data can be eliminated while the feature data is retained.In this way, the recognition rate of the network is maintained, and the computing speed of the network is improved.Simulation experiments are carried out on standard face dataset CASIA-Webface and Yale-B, and compared with other network models. The experimental results show that the proposed SN-LF network structure can improve the recognition accuracy of the algorithm, and achieve a good recognition accuracy.
A Pythagorean Cubic Fuzzy Methodology Based on TOPSIS and TODIM Methods and its Application to Software Selection Problem
Authors: Seker Sukran , Kahraman Cengiz
Published: July 2021

Software selection process for many organizations is a challenging task to conduct their business activities and sustain competitiveness. This paper develops a new hybrid multi-criteria decision making (MCDM) method to select the most effiecient vendor-supplied software package which is used in all business activities for planning or designing, organizing, and supervising functions by operations management of a fuel oil company operated in Turkey. The proposed method is a hybridization of two well-known MCDM approaches, namely TODIM (an acronym in Portuguese for Interactive and Multi criteria Decision Making) and TOPSIS (technique for order preference by similarity to an ideal solution) using Pythagorean cubic fuzzy sets (PCFS) to manage uncertainty, subjectivity and bias of decision makers (DMs). To prove the efficiency and applicability of the proposed method, a real life application to select best software package for fuel oil company, is conducted. Finally, a sensitivity and comparison analyses are carried out to verify validity and stability of the results obtained by the proposed approach.
Multi-scale neural signatures of major depressive, anxiety, and stress-related disorders
Authors: Zhukovsky Peter , Wainberg Michael , Milic Milos , Tripathy Shreejoy , Mulsant Benoit , Felsky Daniel , Voineskos Aristotle
Published: July 2021

The extent of shared and distinct neural mechanisms underlying major depressive disorder (MDD), anxiety and stress-related disorders is still unclear. We compared the neural signatures of these disorders in 5,405 UK Biobank patients and 21,727 healthy controls. We found the greatest case-control differences in resting-state functional connectivity and cortical thickness in MDD, followed by anxiety and stress-related disorders. Neural signatures for MDD and anxiety disorders were highly concordant, namely in altered frontostriatal connectivity, whereas stress-related disorders showed a distinct pattern. Controlling for cross-disorder genetic risk somewhat increased the similarity between functional neural signatures of stress-related disorders and both MDD and anxiety disorders. Among cases and healthy controls, reduced within-network and increased between-network frontoparietal and default mode connectivity was associated with poorer cognitive performance (processing speed, attention, associative learning and fluid intelligence). These results provide evidence for distinct neural circuit function impairments in MDD and anxiety disorders compared to stress disorders; yet cognitive impairment appears unrelated to diagnosis and varies with circuit function.
Oral Health Among Children with Haematological Malignancies in Syria
Authors: Alhaffar MHD Bahaa Aldin , Mustafa Khattab , Alsabbagh Samira , Alhaffar Ola , Kakaje Ameer
Published: July 2021

Background:Since 2011, Syria has been facing a conflict that impacted all aspects of life. Haematological malignancies are mainly treated with chemotherapy which can further harm oral health. This study evaluates oral health of children with haematological malignancies and on chemotherapy in Syria.Methods: This is a cross-sectional study of (40) patients from the major paediatric hospital in Damascus. Decayed, Missing, Filled Teeth (DMFT) and Oral Assessment Guide (OAG) indices were used to evaluate oral health. Data about cancer was collected from medical records. Results: Patients aged between 3-14 years. Three types of paediatric cancer were included; acute lymphoblastic leukaemia (ALL) 52.2%, Hodgkin’s Lymphoma (HL) 27.5%, and Burkitt Lymphoma (BL) 20%. Average DMFT was (6.7 ± 3.2) and average OAG index was (10.8 ± 1.7). DMFT was significantly correlated with OAG (r=0.021). In patients undergoing chemotherapy, better DMFT and OAG indices were reported in males who had cancer for shorter periods, had higher frequency of toothbrushing, or/and were helped while toothbrushing. However, age and cancer type did not significantly affect DMFT and OAG.Conclusion: Children undergoing chemotherapy in Syria had worse oral health and pain compared to other children from the same age in similar studies. More attention should be given to these patients in order to improve their overall health and their quality of life especially during the ongoing conflict.
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Authors: Rhie Arang , Cartney Ann Mc , Shafin Kishwar , Alonge Michael , Bzikadze Andrey , Formenti Giulio , Fungtammasan Arkarachai , Howe Kerstin , Jain Chirag , Koren Sergey , Logsdon Glennis , Miga Karen , Mikheenko Alla , Paten Benedict , Shumate Alaina , Soto Daniela , Sović Ivan , Wood Jonathan , Zook Justin , Phillippy Adam
Published: July 2021

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies
Phenotypic Clusters On Computed Tomography Reflects Asthma Heterogeneity And Severity
Authors: Kim Sujeong , Choi Sanghun , Kim Taewoo , Jin Kwang Nam , Cho Sang-Heon , Lee Chang Hyun , Kang Hye-Ryun
Published: July 2021

The authors have requested that this preprint be removed from Research Square.
Assessment of Factors Associated with PSA Level in Prostate Cancer Cases and Controls from Three Geographical Regions.
Authors: Karunasinghe Nishi , Minas Tsion Zewdu , Bao Bo-Ying , Lee Arier , Wang Alice , Zhu Shuotun , Masters Jonathan , Goudie Megan , Huang Shu-Pin , Jenkins Frank J. , Ferguson Lynnette R
Published: July 2021

Introduction- It is being debated whether prostate-specific antigen (PSA)-based screening effectively reduces prostate cancer mortality. Some of the uncertainty could be related to deficiencies in the age-based PSA cut-off thresholds used in screening. Methods- Current study considered 2779 men with prostate cancer and 1606 men without a cancer diagnosis, recruited for various studies in New Zealand, US and Taiwan. Association of PSA with demographic, lifestyle, clinical characteristics (for cases), and the aldo-keto reductase 1C3 (AKR1C3) rs12529 genetic polymorphisms were analysed using multiple linear regression and univariate modelling.Results- Pooled multivariable analysis of cases showed that PSA was significantly associated with demographic, lifestyle and clinical data with an interaction between ethnicity and age further modifying the association. Pooled multivariable analysis of controls data also showed that demographic and lifestyle are significantly associated with PSA level. Independent case and control analyses indicated that factors associated with PSA were specific for each cohort. Univariate analyses showed a significant age and PSA correlation among all cases and controls except for the US-European cases while genetic stratification in cases showed variability of correlation. Conclusion- Data suggests that unique PSA cut-off thresholds factorized with demographics, lifestyle and genetics may be more appropriate for prostate cancer screening.
Developing a Japanese Version of The Short Form of The Expanded Version of The Posttraumatic Growth Inventory (PTGI-X-SF-J): A Cross-Sectional Study
Authors: Oshiro Rei , Soejima Takafumi , Kita Sachiko , Benson Kayla , Kibi Satoshi , Hiraki Koichi , Kamibeppu Kiyoko , Taku Kanako
Published: July 2021

Background

The 10-item short form of the Posttraumatic Growth Inventory (PTGI-SF) has been utilized worldwide. However, there is no Japanese version. Furthermore, the PTGI-SF does not capture a broader category of existential spiritual growth that has been incorporated in the more recent Expanded version of the PTG Inventory (PTGI-X). Thus, we developed a Japanese version of the Short Form (PTGI-X-SF-J), which reflects more diverse perspectives on existential and spiritual growth.
Methods

A cross-sectional study using questionnaires was conducted in Japan. The first sample consisted of 408 university students, and the second sample comprised 284 university students. Exploratory factor analysis was performed using data from the first sample. Confirmatory factor analysis was conducted, and reliability and validity were confirmed using the second sample.
Results

The PTGI-X-SF-J is composed of 10 items including two items from each of the five subscales of the PTGI-X, similar to the original version of the PTGI-SF, and this model fits the data well. Items concerning existential/spiritual change in the PTGI-X-SF-J were “I feel more connected with all of existence” and “I have a greater sense of harmony with the world,” which were not included in the original PTGI-SF. The score of the PTGI-X-SF-J was significantly correlated with the scores of the Core Beliefs Inventory and the Event Related Rumination Inventory-Deliberate; however, no correlation was observed with the scores of the PTSD Checklist for DSM-5.
Conclusions

We developed the PTGI-X-SF-J using 10 items to measure PTG among people whose first language is Japanese and confirmed its factor structure, reliability, and validity. The PTGI-X-SF-J is useful for assessing PTG more efficiently and accurately as it considers more diverse spiritual/existential experiences of personal growth and reduces physical and psychological burdens due to its brevity.
Measures of The Direct Impact of Hematophagous Flies On Feeder Cattle: An Unexpectedly High Potential Economic Impact
Authors: Boonsaen Phoompong - , Nevot Adèle , Onju Sathaporn , Fossaert Clément , Chalermwong Piangjai , Thaisungnoen Kornkanok , Lucas Antoine , Thévenon Sophie , Masmeatathip Roungthip , Jittapalapong Sathaporn , Desquesnes Marc
Published: July 2021

Beside blood pathogens transmission, insects of the order Diptera affect livestock by visual and contact harassment; blood-feeders are responsible of painful bites and blood despoliation, generating behavioural modifications, anaemia and production losses. Knowledge of their economic impact is a basis for cost-effective control. Here, we measured the global impact of Diptera by comparing two batches of six feeder cattle, one in open air, the other protected by a mosquito net. Analytical data were: insect density in open air, and, for feeder cattle: tail-flick counts, hematocrit values (Ht), feed intake, feed conversion ratio (FCR) and live body weight gains (LBWG). Over a period of five months, results showed significant losses of LBWG of cattle exposed to insects, estimated at 8.0±1.5 Kg/month [2.7;13.3], with a total loss reaching 40.0±5.5 Kg/head. Main diurnal insects were Stomoxys spp. and M. crassirostris. There was a strong correlation between fly density and diurnal tail-flicks. Night trapping and tail-flicks showed a potentially important role of mosquitoes to be further explored. Ht of exposed animals was 3-4% lower than controls. FCRs indicated that exposed animals needed 33% more dry matter intake/Kg of LBWG. Economic assessment showed that dipterans were responsible of 10-11% loss of LBWG during the main growing period of feeder-cattle (10-15 months). A feedlot of 100 calves would register a total loss of 16,000$ within 5 months, which appears to be an unexpectedly huge loss caused by dipterans. Investing part of this money in fly control would probably be beneficial.
Effects of High-Fat Diet and Treadmill Running on The Hypothalamic Kiss-1-GPR54 Signaling Pathway in Growing Male Rats
Authors: XU RUI , FENG Junpeng , LIANG Chunyu , SONG Ge , YAN Yi
Published: July 2021

Background: Kiss-1 neurons, one of the metabolic sensors in the hypothalamic, is necessary for puberty initiating and acts through G protein-coupled receptor, known as GPR54. This study investigated the mechanism of the hypothalamic Kiss-1-GPR54 signaling pathway in high-fat diet and exercise on the growing male rats. Methods: 135 three-week-old weaned male rats were underwent high-fat diet and exercise (60–70% VO2max, 1 h/day, 5 days/ week). These mice were randomly divided into control group, control and exercise group, high-fat diet group, high-fat diet and exercise group. Hypothalamic, testis, and serum samples of each group were collected at PND (postanal day)21st day (21D, early childhood), PND 43rd day (43D, puberty) and PND 56th day (56D, maturity). Immunofluorescence, Quantitative real-time PCR, hematoxylin and eosin staining, chemiluminescent immunoassays were used in studies. Analysis of variance (ANOVA) was used to analyze the effects of age (PND 21,43,56), exercise (exercise, sedentariness), and diet (high-fat, normal) on the biological indexes in ratsResults: The mRNA and protein expression of Kiss-1, GPR54 in the hypothalamic were gradually increased along with growing and peaked at PND 43, and the serum testosterone increased and peaked at PND 56. High-fat diet increased the expression of Kiss-GPR54 system in hypothalamic, while the serum testosterone decreased during different stages of growth. Exercise decreased the expression of Kiss-1 at PND 56 and increased the expression of Kiss-1at PND 43, meanwhile decreased testosterone and the deposition of lipid droplets in the testis at all age of development. Conclusions: The expression of Kiss-1-GPR54 in male rats showed fluctuated change during growth and development. High-fat diet can upregulate the expression of Kiss-1-GPR54 system in hypothalamic. Exercise can correct the adverse effect of high-fat diet on Kiss-1-GPR54 signaling pathway in hypothalamic and the function of hypothalamic-pituitary-testicular (HPT) axis, upregulate Kiss-1 at puberty and downregulate of Kiss-1 at maturity of high-fat diet male rats.
Time To Relapse of Severe Acute Malnutrition And Its Determinants Among Children Treated In The Health Posts of Hadiya Zone, Southern Ethiopia.
Authors: Lambebo Abera , Temiru Desselegn , Belachew Tefera
Published: July 2021

Back ground: In developing countries including Ethiopia, children under five years old are likely to suffer from repeated bouts of SAM. There is lack of study that documented time to relapse of SAM and its determinants. Objective: This study aimed to identify time of relapse and its determinants among children discharged after treatment for SAM in health facilities of Hadiya Zone, South, Ethiopia Methods: An institution based retrospective cohort study was carried out from data spanning from 2014/2015 to 2019/2020. After checking all the assumptions, multivariable CPH model was fitted to isolate independent determinants of time to relapse. All tests were two sided and statistical significance at P values <0.05. Result: The mean(±SD) time for relapse of SAM among under five children was 22(±9.9) weeks from discharge to relapse time. On multivariable CPH model, the hazard of relapse for SAM was significantly higher for children who had edema (AHR =2.02 ,95%, CI: 1.17-3.50), age of 6-11 months (AHR = 5.2, 95%, CI:1.95-13.87), had discharge low MUAC (AHR = 12,95%, CI: 7.90-19.52)Concussion: The finding showed that children discharged from SAM are likely to have relapse in 3 weeks.
Diagnosis and Classification of Diabetes Mellitus Type 1 and Type 2 Through Super Learner
Authors: A Nisha , G Kavitha
Published: July 2021

Diabetes Mellitus (DM) plays a significant role in increasing the associated health problems worldwide by acting as a Comorbid condition. Moreover, it is a progressive illness without severe external symptoms leading to a fatal impact on the human body if left unnoticed or untreated. This research work aims to associate an individual’s lifestyle and ethnic background in assessing the risk of Diabetes acting as a comorbid condition. A detailed assessment of lockdown impact with rapid modification in individual’s lifestyle due to the pandemic gives specific insight into individuals becoming susceptible to Diabetes Mellitus. An ensemble of ML algorithms is utilized in predicting the risk of individuals turning Diabetic. The ensemble of the ML model is trained on the Pima Indian dataset and Vanderbilt biostatistics diabetes dataset providing the impact of Type 1 diabetes mellitus. The proposed super learner model provides the highest classification accuracy of T1DM & T2DM with 97% compared to an ensemble of algorithms in identifying and classifying the individuals as being susceptible to DM due to the lifestyle and ethnic background.
Expressions of Actor Power in Implementation: A Qualitative Case Study of a Health Service Intervention in South Africa
Authors: Schneider Helen , Mukinda Fidele , Tabana Hanani , George Asha
Published: July 2021

Background Implementation frameworks and theories acknowledge the role of power as a factor in the adoption (or not) of interventions in health services. Despite this recognition, there is a paucity of evidence on how interventions at the front line of health systems confront or shape existing power relations. This paper reports on a study of actor power in the implementation of an intervention to improve maternal, neonatal and child health care quality and outcomes in a rural district of South Africa. Methods A retrospective qualitative case study based on interviews with 34 actors in three ‘implementation units’ – a district hospital and surrounding primary health care services – of the district, selected as purposefully representing full, moderate and low implementation of the intervention some three years after it was first introduced. Data are analysed using Veneklasen and Miller’s typology of the forms of power – namely ‘power over’, ‘power to’, ‘power within’ and ‘power with’. Results Multiple expressions of actor power were evident during implementation and played a plausible role in shaping variable implementation, while the intervention itself acted to change power relations. The ability to mobilise collective action (power with) was a key dimension of successful implementation, but potentially poses a threat to hierarchical power (power over) at higher levels of the system, affecting sustainability. Conclusions A systematic approach to the analysis of power in implementation research may provide insights into the fate of interventions. Intervention designs need to consider how they shape power relations, especially where interventions seek to widen participation and responsiveness in local health systems.
The Spatial Analysis for Malaria Surveillance in Yogyakarta Special Region, Indonesia : A Cross Sectional Study
Authors: Nuraisyah Fatma , Kusnanto Hari , Palutturi Sukri , Nurlaily Nova , Adistiyapuri Panggita , Irjayanti Apriyana , Mapandin Wahida , Anggraini Vidya Aries , Ruliyandari Rochana , Sugiarto
Published: July 2021

BackgroundMalaria case elimination have been seriously issue. Although the prevalence of malaria cases in Indonesia has decreased from 1.3% (2013) to 0.6% (2017), the policy of has been eliminating malaria cases remains unresolved problem. Kulon Progo is one of contributes to malaria cases in Special Region Yogyakarta. Although number of cases has been decreasing year, malaria transmission continues to be a significant.PurposeStrengthen the surveillance system and cluster areas of malaria cases through Q-GIS with buffering analysis and spatial analysis in Kulon Progo District in 2015–2018. Method: Cross sectional was done. Instruments include secondary data on malaria cases occurring from 2015 to 2018 and confirmation data sheets. The questionnaire was used to collected data from 240 respondents.ResultsMalaria case trend was in the watershed area at a distance of < 250meters in Kokap Sub-district. Malaria cases were mostly found in rice fields with a distance of < 250meters in Samigaluh Sub-district. All malaria cases were in the garden areas of < 250meters in Nanggulang and the forest area of > 250meters in the Kalibawang Sub-district.ConclusionProbability malaria transmission are river, rice fields and gardens. It is necessary to hold training on the use of the Q-GIS application for surveillance officers.
Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiome in wild and farmed large yellow croaker
Authors: Zhu Jun , Li Hao , Jing Ze-Zhou , Zheng Wei , Luo Yuan-Rong , Chen Shi-Xi , Guo Feng
Published: July 2021

BackgroundRevealing the potential divergence of gut microbiome between farmed and wild fishes, and its underlying mechanism are informative to improve its mariculture, as well as establish the molecular marker of host source tracking, which is an alternative to the yet-to-be-established host genetic marker. A candidate for testing the feasibility is the large yellow croaker, Larimichthys crocea , which is carnivorous and ranking the top maricultural fish in China with depleted wild resource and frequently farmed individuals escaping and fry releasing for wild stock enhancement. ResultsThe rectums of wild (n=212) and farmed (n=79) individuals from multiple batches were collected for the profiling of gut bacterial communities. The farmed individuals had a higher alpha diversity and lower bacterial loading than the wild individuals. The gut microbiota of the two sources exhibited divergence and high inter-batch variation, featured by the dominance of Psychrobacter spp. in the wild group. Predicted function of gut microbiome and representative isolates suggested that diet could be a key factor for the divergence, which was linked to the high ratio and diverse source of carbohydrate in formulated feed and low pH of rectum contents in farmed fishes. The non-stochastic distribution patterns of the core gut microbiota of the wild and farmed individuals indicated the feasibility of microbiota-based host source tracking through machine learning algorithm. Random forest classifier building on the divergence and non-stochastic assembly of gut microbiome was robust in host source tracking for individuals from all batches including a newly introduced batch. ConclusionsOur study revealed the divergence of the gut microbiota between wild and farmed croakers and suggested that diet change is an underlying key factor for the divergence. As the first time, we verified that with less biased datasets and non-stochastic pattern, gut microbiota can be robustly applied to the tracking of host source even in carnivorous fish.
A Validated Analysis Pipeline for Mass Spectrometry-Based Vitreous Proteomics: Insights Into Proliferative Diabetic Retinopathy
Authors: Weber Sarah R , Zhao Yuanjun , Ma Jingqun , Gates Christopher , Leprevost Felipe da Veiga , Basrur Venkatesha , Nesvizhskii Alexey I. , Gardner Thomas W. , Sundstrom Jeffrey M.
Published: July 2021

Background: Vitreous is an accessible, information-rich biofluid that has recently been studied as a source of retinal disease-related proteins and pathways. However, the number of samples required to confidently identify perturbed pathways remains unknown. In order to confidently identify these pathways, power analysis must be performed to determine the number of samples required.Methods: Control (n=27) and proliferative diabetic retinopathy (n=23) vitreous samples were treated as biologically distinct individuals or pooled together and aliquoted into technical replicates. Quantitative mass spectrometry with tandem mass tag labeling was used to identify proteins in individual or pooled control samples to determine technical and biological variability. To determine effect size and perform power analysis, control and proliferative diabetic retinopathy samples were analyzed across four 10plexes. Pooled samples were used to normalize the data across plexes and generate a single data matrix for downstream analysis. Results: The total number of unique proteins identified was 1,152 in experiment 1, 989 of which were measured in all samples. In experiment 2, 1,191 proteins were identified, 727 of which were measured across all samples in all plexes. Data are available via ProteomeXchange with identifier PXD025986. Spearman correlations of protein abundance estimations revealed minimal technical (0.99-1.00) and biological (0.94-0.98) variability. Each plex contained two unique pooled samples: one for normalizing across each 10plex, and one to internally validate the normalization algorithm. Spearman correlation of the validation pool following normalization was 0.86-0.90. Principal component analysis revealed stratification of samples by disease and not by plex. Subsequent differential expression and pathway analyses demonstrated significant activation of metabolic pathways and inhibition of neuroprotective pathways in proliferative diabetic retinopathy samples relative to controls.Conclusions: This study demonstrates a feasible, rigorous, and scalable method that can be applied to future proteomic studies of vitreous sampled directly from patients in order to advance understanding of pathways altered in retinal disease.
Terpene-rich Fractions of Ficus Mucoso (Welw) Modulate Lipopolysaccharide-induced Inflammatory Mediators and Aberrant Permeability of the Inner Mitochondrial Membrane in Murine Animal Model
Authors: Oyebode Olubukola , Olanlokun John Oludele , Salami Olamilekan , Obi Ifeanyi , Bodede Olusola , Prinsloo Gerhard , Olorunsogo Olufunso
Published: July 2021

Ficus mucoso is traditionally used to treat various infections. This study compared the efficacy of terpene-rich fractions of F. mucoso root bark on LPS-induced inflammation, liver mitochondrial permeability transition (mPT) pore, an index of mitochondrial health, and associated pathological alterations. Terpene-Rich fractions of Dichloromethane (TRDF) and Ethylacetate fractions of F. mucoso (TREF) were obtained according to the method described by Ferguson (1956). A single intraperitoneal injection of 1 mg/kg lipopolysaccharide (LPS) were given to mice to induce systemic inflammation for 72hrs. Evaluation of the effects of the TRDF and TREF on levels of pro-inflammatory mediators (TNF-α, IL-1β, IL-6) and antioxidant indices against LPS-induced hepatic damage were carried out. Mitochondrial swelling was monitored spectrophotometrically as well as mitochondrial ATPase activity and lipid peroxidation. This study reveals that TRDF and TREF possess anti-inflammatory potentials which is related to reduction in levels of pro-inflammatory cytokines, restoration of antioxidant status, reduction in levels of liver marker enzymes as well as associated pathological injury. Furthermore, LPS caused induction of opening of the liver mPT pore which was significantly inhibited by TRDF at 100 and 200 mg/kg bw by 71% and 88% respectively, but only at 100 mg/kg TREF. Furthermore, mitochondrial ATPase activity was inhibited largely by TRDF. The UPLC-ESI-MS analysis revealed the presence of terpenoid derivatives and a few aromatic metabolites in TRDF. The terpene dominance of TRDF metabolites was further justified on the 1H NMR fingerprint.Overall, TRDF is more effective as a cocktail of anti-inflammatory compounds than TREF against LPS-induced acute systemic inflammation.
Comparative Analysis of The Correction Effect of Different Environmental Loading Products On Global GNSS Coordinate Time Series
Authors: He Yuefan , Nie Guigen , Wu Shuguang , Li Haiyang
Published: July 2021

The global navigation satellite system (GNSS) coordinate time series is affected by the environmental loading (including atmospheric loading (ATML), hydrological loading (HYDL), non-tidal oceanic loading (NTOL), etc.) and many organizations now provide grid products of these loadings. The temporal and spatial resolutions of these products, the loading models and data sources used are not the same, so the effect of correcting the nonlinear deformation of the GNSS coordinate time series is obviously different. This study mainly selects the three agencies, namely, School and Observatory of Earth Sciences (EOST) in France, German Research Center for Geosciences (GFZ) in Germany, and International Mass Loading Service (IMLS) in the United States, including 6 types of ATML models, 7 types of HYDL models and 5 NTOL models. The classification of these 18 environmental loading models was discussed, and the root mean square (RMS) reduction rate of the GNSS coordinate time series after environmental loading corrections (ELCs) was used to evaluate the performance differences of various models. Our results show that both the different models provided by the same organization and the same model provided by different organizations have different correction effects. Regardless of the models, it has a significant impact on the vertical coordinate time series. In order to correct the nonlinear deformation of the GNSS stations to the greatest extent, based on the above analysis, this study selects the optimal model combination of three environmental loadings as ECMWF_IB+MERRA2+ECCO1, and then explores its influence on the periodic signals in the GNSS coordinate time series. Research suggests that environmental loadings have a significant impact on the amplitude and phase of GNSS time series. Especially in the vertical direction, the largest RMS value can reach 8.42 mm. Before and after ELCs, the maximal difference of the annual amplitude and the half-annual amplitude at global 631 stations can reach 8.96 mm and 1.51 mm, respectively. Among them, 84.60% of the stations were corrected by the optimal environmental loading combination model, thus the nonlinear deformation was weakened.
Human α-synuclein overexpression in mouse serotonin neurons triggers a depressive-like phenotype. Rescue by oligonucleotide therapy
Authors: Bortolozzi Analia , Miquel-Rio Lluis , Alarcón-Aris Diana , Torres-López María , Coppola-Segovia Valentín , Pavia-Collado Rubén , Paz Verónica , Ruiz-Broanchal Esther , Campa Leticia , Casal Carmen , Montefeltro Andrés , Artigas Francesc , Vila Miquel , Revilla Raquel
Published: July 2021

Anxiety and depression affect 35–50% of patients with Parkinson's disease (PD), often precede the onset of motor symptoms, and have a negative impact on their quality of life. Dysfunction of the serotonergic (5-HT) system, which regulates mood and emotional pathways, occurs during the premotor phase of PD and contributes to a variety of non-motor symptoms. Furthermore, α-synuclein (α-Syn) aggregates were identified in raphe nuclei in the early stages of the disease. However, there are very few animal models of PD-related neuropsychiatric disorders. Here, we develop a new mouse model of α-synucleinopathy in the 5-HT system that mimics prominent histopathological and neuropsychiatric features of human PD. We showed that adeno-associated virus (AAV5)-induced overexpression of wild-type human α-Syn (h-α-Syn) in raphe 5-HT neurons triggers progressive accumulation, phosphorylation, and aggregation of h-α-Syn protein in the 5-HT system. Specifically, AAV5-injected mice displayed axonal impairment in the output brain regions of raphe neurons, and deficits in brain-derived neurotrophic factor (BDNF) expression and 5-HT neurotransmission, resulting in a depressive-like phenotype. Intracerebroventricular treatment with an indatraline-conjugated antisense oligonucleotide (IND-ASO) for four weeks induced an effective and safe reduction of h-α-Syn synthesis in 5-HT neurons and its accumulation in the forebrain, alleviating early deficits of 5-HT function and improving the behavioural phenotype. Altogether, our findings show that α-synucleinopathy in 5-HT neurons negatively affects brain circuits that control mood and emotions, resembling the expression of neuropsychiatric symptoms occurring at the onset of PD. Early preservation of 5-HT function by reducing α-Syn synthesis/accumulation may alleviate PD-related depressive symptoms.
Researches on the Fast Determination of Cell Type of Cartesian Grid
Authors: Li Xueliang , Bi Lin , Meng Shuang , Liu Hongkang , Wang Tiantian , Yuan Xianxu
Published: July 2021

The relationship between the spatial cell and the object is unknown for the Cartesian grid using the immersed boundary method. For the researches about complex geometry or multi-body relative motion, grid generation is a very time-consuming work, and the consumption is mainly concentrated in the position determination of the Cartesian cells, which we called the cell type determination. In this study, based on the axis-aligned bounding box method and the ray casting method, we employed the dot product method and the painting algorithm to investigate the acceleration method for Cartesian grid generation. The octree structure is used to store the Cartesian cells, and the k-dimensional tree is used to store the object surface. These data management strategy can minimize the CPU’s resource while have a small memory usage. The grid generation results show that the strategy we proposed has a high efficiency and well robustness, and the time consume can reduce more than 50% compare with the original method. When dealing with a enough complex problem, the time consume can even reaches several orders of magnitude difference compared with the original method.
Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation.
Authors: Venzon Mericien , Bernard-Raichon Lucie , Klein Jon , Axelrad Jordan , Hussey Grant , Sullivan Alexis , Casanovas-Massana Arnau , Noval Maria , Valero-Jimenez Ana , Gago Juan , Wilder Evan , Team Yale IMPACT Research , Iwasaki Akiko , Thorpe Lorna , Littman Dan , Dittmann Meike , Stapleford Kenneth , Shopsin Bo , Torres Victor , Ko Albert , Cadwell Ken , Schluter Jonas
Published: July 2021

The microbial populations in the gut microbiome have recently been associated with COVID-19 disease severity. However, a causal impact of the gut microbiome on COVID-19 patient health has not been established. Here we provide evidence that gut microbiome dysbiosis is associated with translocation of bacteria into the blood during COVID-19, causing life-threatening secondary infections. Antibiotics and other treatments during COVID-19 can potentially confound microbiome associations. We therefore first demonstrate that the gut microbiome is directly affected by SARS-CoV-2 infection in a dose-dependent manner in a mouse model, causally linking viral infection and gut microbiome dysbiosis. Comparison with stool samples collected from 97 COVID-19 patients at two different clinical sites also revealed substantial gut microbiome dysbiosis, paralleling our observations in the animal model. Specifically, we observed blooms of opportunistic pathogenic bacterial genera known to include antimicrobial-resistant species in hospitalized COVID-19 patients. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data obtained from these patients suggest that bacteria translocate from the gut into the systemic circulation of COVID-19 patients. These results are consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID 19.
Optimized Sparse Polynomial Chaos Expansion With Entropy Regularization
Authors: Zeng SiJie , Duan XiaoJun , Chen JiangTao , Yan Liang
Published: July 2021

Sparse Polynomial Chaos Expansion(PCE) is widely used in various engineering fields to quantitatively analyse the influence of uncertainty, while alleviate the problem of dimensionality curse. However, current sparse PCE techniques focus on choosing features with the largest coefficients, which may ignore uncertainties propagated with high order features. Hence, this paper proposes the idea of selecting polynomial chaos basis based on information entropy, which aims to retain the advantages of existing sparse techniques while considering entropy change as output uncertainty. A novel entropy-based optimization method is proposed to update the state-of-the-art sparse PCE models. This work further develops an entropy-based synthetic sparse model, which has higher computational efficiency. Two benchmark functions and a CFD experiment are used to compare the accuracy and efficiency between the proposed method and classical methods. The results show that entropy-based methods can better capture the features of uncertainty propagation, and the problem of over-fitting in existing sparse PCE methods can be avoided.
Transcriptome Analysis of Skin Color Variation During and after Overwintering of Malaysian Red Tilapia
Authors: Jiang bingjie , Wang lanmei , Luo mingkun , Fu jianjun , Zhu wenbin , dong zaijie
Published: July 2021

The commercial value of red tilapia is hampered by variations in skin color during overwintering. In this study, three types skin of red tilapia, including the skin remained pink color during and after overwintering (WP), the skin changed from pink color to black color during overwintering and remained black color after overwintering (PB), and the skin changed from pink color to black color during overwintering but recovered to pink color when the temperature rose after overwintering (BP), were used to analyze their molecular mechanisms of color variation. The transcriptome results revealed that the PB, WP, and BP libraries had 42, 43, and 43 million clean reads, respectively. The top 10 abundance mRNAs and specific mRNAs (specificity measure SPM > 0.9) were screened. After comparing intergroup gene expression levels, there were 2528, 1924 and 1939 differentially expressed genes (DEGs) between BP and PB, BP and WP, and PB and WP, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of color-related mRNAs showed that a number of DEGs, including tyrp1, tyr, pmel, mitf, mc1r, asip, tat, hpdb and foxd3, might play a potential role in pigmentation. Additionally, the co-expression patterns of genes were detected within the pigment-related pathways by PPI network from PB_WP group. Furthermore, DEGs from the apoptosis and autophagy pathways, such as baxα, beclin1, and atg7, might be involved in the fading of red tilapia melanocytes. The findings will aid in understanding the molecular mechanism underlying skin color variation in red tilapia during and after overwintering, as well as lay a foundation for future research aimed at improving red tilapia skin color characteristics.
A Novel Mathematical Model of Tumor Growth Kinetics with Allee Effect under Fuzzy Environment
Authors: Khaliq Rubeena , Iqbal Pervaiz , Bhat Shahid Ahmad
Published: July 2021

Most of the cancer growth models have described the exponential growth patterns at the very initial stage with low cell population density. Eventually, decreasing the tumor growth rate at higher cell population densities because of deficiency in resources such as space and nutrients. However, recent studies at clinical and preclinical investigations of cancer initiation or reappaearance showed a population dynamics evincing that the growth rate increases as cell number increases. Hence, showing behaviour analogous to cooperative mechanism in the ecosystem and ecological effect called Allee effect. Based on these observations with two arguments i.e. change in initial population and growth rate. In this paper, the novel mathematical model of tumor growth kinetics with Allee effect under fuzzy environment is proposed. In this model the Generalized Hukuhara derivative approach is utilized to solve the fuzzy differential equations. Moreover, it is showen that the change in initial value and growth rate affects the cell density with the Allee effect under the fuzzy environment. Finally the superiority of model has been showen with the help of numerical simulation.
Comparison of macrobenthic communities between the invasive Spartina alterniflora and native Suaeda glauca habitats in the Yellow River Delta
Authors: Han Qiuying , Han Qingxi , Wang Yujue , Liu Dongyan
Published: July 2021

Salt marsh habitats in estuaries play important roles in species compositions and macrobenthos abundances. Here, the macrobenthic communities and environmental conditions in two habitats, which are dominated by the invasive species Spartina alterniflora (SA) and native species Suaeda glauca (SG), in the Yellow River Delta were studied to assess habitat function. The seasonal data showed that the species diversity and abundance of macrobenthos in the SA habitat were much higher than those in the SG habitat. The functional groups in the former showed significant seasonal changes and shifted from polychaeta (68%) in spring to mollusca (97%) in autumn, but in the latter, it was dominated by crustacea (63-86%), mollusca (1-25%) and polychaeta (9-13%), and only mollusca exhibited obvious seasonal changes. The sediments in the SA habitat contained richer organic matter contents and exhibited higher Chl- a concentrations than those in the SG habitat, although the grain sizes were coarser in the SA habitat. At the seasonal scale, macrobenthos in the SA habitat displayed significant negative correlations with salinity and organic matter. The results indicated that the macrobenthos functional groups in the SA habitat were simpler and more sensitive to environmental changes than those in the SG habitat. The vegetation structures may give rise to the differences in macrobenthos distributions in both habitats, which need to be further observed and explored.