Network Analysis for Estimating Standardization Trends in Genomics

With the development of biotechnology in genomics, such as droplet digital PCR, sequencing device, gene analysis software, an increase in the clinical application of those new developed technologies in genomics is observed. However, the lack of established international standards regarding the use of genomics in clinics is of concern. To visualize trend of international standards in clinical genomics and explore high demanded sub-specific field, we performed a social network analysis. We searched 16,538 articles using the search keywords, “genomics and standard” and “clinical genomic sequence and standard”. All terms extracted from full text articles were classified into academic and technical categories and conducted general linear model analysis. Assuming from the results, research in the fields of software, proteomics and genetics terminology categories is likely to increase. From our results, such international critical issue of genomics, human genome project in 2003, primary US-FDA approval of sequencing device in 2013, and pandemic state of COVID-19 in 2020, were affected to research of standard in genomics. In further proposal and standardization of new items, summing critical social issues and research trends, we could suggest and considering promising sub-specific field of genomics.

Phenology of flowering and fruiting and effect of KNO3 and H2O2 on germination process of amorphophallus muelleri blume

Amorphophallus muelleriBlume also known as Indonesian Konjac (IK, in short) is a wild plant that spreads out in Indonesia especially in the southern part. The genus Amorphophalluscan also be found in some countries in South-East Asia. The IK tuber contains glucomannan, a compound which has high economic value as raw material in many industries such as food, drink, pharmacy, cosmetics, paper, rubber, textile, film industries and many others. The plant is easy to cultivate. Due to the economic benefit of IK tubers and to the easiness of its cultivation, this study was carried out to increase the productivity of glucomannan. The current productivity is still low compared to foreign demand. For example, in 2020 alone, according to the Ministry of Agriculture, Republic of Indonesia, only 12 % of foreign demand have been fulfilled. Therefore, there is an urgent need to increase the productivity of IK tubers. This is the main problem of this research. Its objectives were two-fold. First, was to study the effect of tuber weight on flowering percentage, flower size, and fruiting which is represented by the number of fruits and the number of seeds. Second, was to find out the right concentration of KNO3and H2O2solutions as well as the soaking time in those solutions to break the dormancy period and to increase the germination rate. For these purposes, a laboratory experiment using completely randomized design with three treatments was conducted and the collected data were analyzed using general linear model, analysis of variance and multiple comparison test. The results indicate that the tuber weight significantly affects the flowering percentage, flower size, number of fruits and number of seeds of IK. The heavier the planted tuber, the higher the flowering percentage and the larger the flower size, number of fruits and number of seeds. The response on dormancy breaking treatment indicates that there is no significant effect of soaking treatment in KNO3 and H2O2 solutions on dormancy period of the IK seeds. The KNO3and H2O2solutions have only effect on increasing the germination rate and on shortening the time period for seeds to germinate. Moreover, unlike H2O2, there is no residual effect of KNO3on seeding growth, and on weight and shape of the IK tuber. To the knowledge of the authors, these findings are unprecedented and could thus,contribute to the literature.

Changes in Adolescent Meal Patterns and Processed Food Consumption Following Sleep Restriction: Results From a Randomized Crossover Trial

Objectives To evaluate if sleep restriction influences 1) meal frequency and late evening food consumption; and 2) intake of ultra-processed foods in male and female adolescents. Methods A total of 92 healthy adolescents 14–17 years old participated in a cross-over experimental sleep protocol, comparing two conditions, each lasting 5 nights: healthy sleep (HS, 9.5 h/night) and shortened sleep (SS, 6.5 h/night). The order of conditions was randomly counterbalanced, and there was a washout period of 2 days between conditions. The study team conducted 24-h dietary recalls on 3 randomly selected days during each sleep condition. For objective 1, we used the timestamps of the meals in each dietary recall to determine number of eating occasion in 24 h, number of eating occasion after 8PM, and kilocalories consumed after 8PM. For objective 2, we used the Nova food classification system to determine kilocalories and % of kilocalories consumed from ultra-processed foods (UPF) over 24 hours and after 8PM. We used general linear model analysis to compare these outcomes between HS and SS conditions. We also explored the moderating impact of individual and experimental factors, including family income and participant age, sex, age- and sex-adjusted body mass index, and the order in which they had the sleep conditions. Results There was no significant difference in number of eating occasions in 24 h across experimental conditions (SS = 4.2, HS = 4.1, P = .25). After 8PM, there was a significantly greater number of eating occasions (0.87 vs. 0.59, P < .001) and higher kilocalorie consumption (354 vs. 223, P < .001) during SS than HS. There was no difference in daily UPF kilocalorie consumption across conditions (SS = 1439, HS = 1397, P = .38), but UPF kilocalories after 8PM were significantly higher during SS than HS (291 vs. 172, P < .001). These findings did not vary based on our exploratory individual and experimental factors. Conclusions Adolescents who are sleep restricted are more likely to eat more frequently, consume greater kilocalories, and eat highly processed foods after 8PM. Considering that these findings were not observed across the entire day, our findings suggest that sleep restriction may most negatively influence dietary patterns in the late evening. Funding Sources NIH.

Genome wide association study for the identification of genes associated with tail fat deposition in Chinese sheep breeds

ABSTRACT Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the molecular genetic basis underlying the phenotypic differences among Chinese indigenous sheep with these three different tail types, we used ovine high-density 600K single nucleotide polymorphism (SNP) arrays to detect genome-wide associations, and performed general linear model analysis to identify candidate genes, using genotyping technology to validate the candidate genes. Tail type is an important economic trait in sheep. However, the candidate genes associated with tail type are not known. The objective of this study was to identify SNP markers, genes, and chromosomal regions related to tail traits. We performed a genome-wide association study (GWAS) using data from 40 large-tailed Han sheep, 40 Altay sheep (cases) and 40 Tibetan sheep (controls). A total of 31 significant (P<0.05) SNPs associated with tail-type traits were detected. For significant SNPs' loci, we determined their physical location and performed a screening of candidate genes within each region. By combining information from previously reported and annotated biological functional genes, we identified SPAG17, Tbx15, VRTN, NPC2, BMP2 and PDGFD as the most promising candidate genes for tail-type traits. Based on the above identified candidate genes for tail-type traits, BMP2 and PDGFD genes were selected to investigate the relationship between SNPs within the tails in the Altay and Tibetan populations. rs119 T>C in exon1 of the BMP2 gene and one SNP in exon4 (rs69 C>A) of the PDGFD gene were detected. rs119 was of the TT genotype in Altay sheep, while it was of the CC genotype in Tibetan sheep. On rs69 of the PDGFD gene, Altay sheep presented with the CC genotype; however, Tibetan sheep presented with the AA genotype.

Ethical and procedural issues for applying researcher-driven multi-national paediatric clinical trials in and outside the European Union: the challenging experience of the DEEP project

Background We describe our experience from a multi-national application of a European Union-funded research-driven paediatric trial (DEEP-2, EudraCT 2012-000353-31; NCT01825512). This paper aims to evaluate the impact of the local and national rules on the trial authorisation process in European and non-European countries. National/local provisions and procedures, number of Ethics Committees and Competent Authorities to be addressed, documentation required, special provisions for the paediatric population, timelines for completing the authorisation process and queries received were collected; compliance with the European provisions were evaluated. Descriptive analysis, Wilcoxon Rank-Sum test and General Linear Model analysis were used to determine factors potentially influencing the timelines. The Cluster Analysis procedure was used to identify homogenous groups of cases. Result The authorisation process was completed in 7.7 to 53.8 months in European countries and in 17.1 to 27.1 months in non-European countries. The main factors influencing these timelines were the requests for changes/clarifications in European countries and the different national legislations in non-European countries. Conclusion This work confirms that the procedures and requirements for the clinical trial application of a paediatric trial are different. In the European Union, the timeframes for submission were generally harmonised but longer. In non-European countries, delays were caused by national dispositions but the entire authorisation process resulted faster with less requests from ECs/CAs. The upcoming application of Regulation (EU) 536/2014 is expected to harmonise practices in Europe and possibly outside. Networks on paediatric research acting at international level will be crucial in this effort.

Quantitative MRI Reveals Grey Matter Abnormalities in Children With Drug-Naïve Attention-Deficit/Hyperactivity Disorder

Purpose To investigate the quantitative profiles of brain GM in pediatric drug-naïve ADHD patients using Synthetic magnetic resonance imaging (SyMRI). Method and Materials: A total of 37 drug-naïve pediatric ADHD and 27 age- and gender-matched healthy controls (HC) were enrolled in this study. Each subject underwent both SyMRI and conventional 3D T1-FSPGR scans. Quantitative parameters, T1 and T2 maps, were extracted from the SyMRI data. Between-group quantitative maps were compared using a general linear model analysis. Pearson correlation analysis was conducted to assess the association between significantly altered MR indices and clinical measurements in ADHD. Results Compared with the HC group, altered T1 and T2 relaxometry times in the ADHD group were mainly distributed in GM regions of the cerebellum, attention and execution control network, default mode network, and limbic areas. Moreover, the T1 value of the right cerebellum 8 was negatively correlated with the attention concentration level in ADHD (R = 0.1401, P = 0.0225). With regards to T2 map, the associations were observed between the attention level of ADHD patients and left fusiform gyrus (R = 0.2509, P = 0.0016), and right cerebellum crus2 (R = 0.1422, P = 0.0214). Conclusion Altered T1, T2 values found in specific regions of GM may reveal widespread micromorphology changes, i.e., brain iron deficiency, low myelin content, and enlarged vascular interstitial space in ADHD patients. Thus, T1, T2 values might be promising imaging markers for future ADHD studies.

Genetic variation of RNF145 gene and blood lipid levels in Xinjiang population, China

Dyslipidemia is one of the main risk factors for coronary heart disease (CHD). The E3 ubiquitin ligase which is encoded by the ring finger protein 145 (RNF145) gene is very important in the mediation of cholesterol synthesis and effectively treats hypercholesterolemia. Thus, the purpose of the present research is to investigate the connection between the polymorphism of the RNF145 gene and cholesterol levels in the populations in Xinjiang, China. A total of 1396 participants (Male: 628, Female: 768) were included in this study for genetic analysis of RNF145 gene, and we used the modified multiple connection detection response (iMLDR) technology to label two SNPs (rs17056583, rs12188266) of RNF145 genotyping. The relationship between the genotypes and the lipid profiles was analyzed with general linear model analysis after adjusting confounding variables. Through the analysis of the two SNPs in RNF145 gene, we discovered that both rs17056583 and rs12188266 were related to total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) concentrations (All P < 0.001). In addition, the association of rs17056583 and rs12188266 with lipid profiles concentrations is still statistically significant after multivariate adjustment of sex, age, smoking, obesity, drinking, diabetes, hypertension and lipid profiles. Meanwhile, we also found that rs17056583 was associated with high triglycerides concentrations before and after adjustment (All P < 0.001). Our study shows that both rs17056583 and rs12188266 SNPs of RNP145 gene are related to TC and LDL-C concentrations in Xinjiang population.

Ethical and Procedural Issues For Applying Researcher-Driven Multi-National Paediatric Clinical Trials in and Outside The European Union: The Challenging Experience of The DEEP Project

Background. We describe our experience from a multi-national application of a European Union-funded research-driven paediatric trial (DEEP-2, EudraCT 2012-000353-31; NCT01825512).This paper aims to evaluate the impact of the local and national rules on the trial authorisation process in European and non-European countries. National/local provisions and procedures, number of Ethics Committees and Competent Authorities to be addressed, documentation required, special provisions for the paediatric population, timelines for completing the authorisation process and queries received were collected; compliance with the European provisions were evaluated.Descriptive analysis, Wilcoxon Rank-Sum test and General Linear Model analysis were used to determine factors potentially influencing the timelines. The Cluster Analysis procedure was used to identify homogenous groups of cases.Result. The authorisation process was completed in 7,7 to 53,8 months in European countries and in 17,1 to 27,1 months in non-European countries. The main factors influencing these timelines resulted the requests for changes/clarifications in European countries and the different national legislations in non-European countries.Conclusion. This work confirms that the procedures and requirements for the clinical trial application of a paediatric trial are different. In the European Union, the timeframes for submission were generally harmonised but longer. In non-EU countries, delays were caused by national dispositions but the entire authorisation process resulted faster with less requests from ECs/CAs. The upcoming application of Regulation (EU) 536/2014 is expected to harmonise practices in Europe and possibly outside. Networks on paediatric research acting at international level will be crucial in this effort.

Effects of location and season on productivity and productive adaptability of two parent stock exotic layer chicken strains in a warm-wet environment

Tropical commercial poultry industry is anchored on exotic strains which suffer varying degrees of productivity and adaptability problems. Adaptability is the ability to produce better or demonstrate least variation in productivity under multiple environments. The study was undertaken to examine the productivity and adaptability of Bevan Nera (IB) and Is a Brown (IB) parent stock strains under two locations and seasons. Data on weekly feed intake (FI g), cock weight (Cockwt, g), hen weight (Henwt, g), hen house production (HHP, %) and egg weight (Ewt, g) were collected from a commercial parent stock breeding farm in Ibadan, Nigeria, on the two strains. Data were subjected to general linear model analysis (GLM) procedures using SAS (1999), while mean separation was by bonferoni t-test (P=0.05). The statistical model was randomized complete block design (RCBD) in factorial. Factors of importance were Genotype (S), Location (L) as Fixed, and Season (S) as random. The effects of location on seasonal productivity and season on locational productivity for strains were 7.38, 4.96; and 4.99, 8.11 (%) for BN, IB respectively. GxL and GxLxS interactions were significant (P<0.043 and <0.013) for adaptability of strains. Locational adaptability indices were 48.59 and 51.41 while Seasonal adaptability indices were 63.32 and 36.68 (%) respectively for BN and IB strains.

The relationship between alexithymia, sensory phenotype and neurophysiological parameters in patients with chronic upper limb neuropathy

In this study, we investigated the relationship between sensory abnormalities evaluated by quantitative sensory testing (QST) and alexithymia, depression and anxiety in patients with neuropathic pain involving the upper limbs. We enrolled 62 patients (34 with carpal tunnel syndrome, 7 with brachial plexopathy, 3 with cervical painful radiculopathy, 5 with ulnar entrapment neuropathy at elbow and 13 with post-burn hypertrophic scars) and 48 healthy controls. All underwent nerve conduction studies (NCS), evaluation of cold, heat pain and vibration detection threshold (VDT) by QST and evaluation of alexithymia by Toronto Alexithymia Scale (TAS-20), depression by Beck Depression Inventory II (BDI-II), anxiety by State-Trait Anxiety Inventory (STAI-Y), level of psychological distress by 12-item General Health Questionnaire (GHQ-12) and perceived social support by the Multidimensional Scale of Perceived Social Support (MSPSS). The general linear model analysis revealed a significant relationship between TAS-20 overall and TAS-20 sub-score for difficulty identifying feelings and VDT z-scores in the left index with no interaction by year of education and sensory NCS results. Our results demonstrated the association between impairment of vibratory sensation of the left hand, reflecting cutaneous mechanoceptor dysfunction, and alexithymia, particularly the difficulty to identify feelings. The importance of delivering to patients with neuropathic pain personalized care that takes into account not only the neurophysiological aspects but also the aspects of mental functioning is discussed.