An improved filtering algorithm for big read datasets and its application to single-cell assembly

Background: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm

An improved filtering algorithm for big read datasets and its application to single-cell assembly

Background: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm

Starting university with high eating self-regulatory skills protects students against unhealthy dietary intake and substantial weight gain over 6 months

Background: There is consistent evidence that suggests first year students are at risk of weight gain, but the reasons for this vulnerability are still unclear. This study aimed to explore whether the ability to regulate eating behaviours is a predictor of weight and dietary changes in first year undergraduate students. Methods: First year undergraduate students from universities situated in London were invited to complete a survey at the beginning of the academic year and at 6-month follow-up. Each survey included the Self-Regulation of Eating Behaviour Questionnaire, food frequency questions, socio-demographic questions and anthropometric questions. Linear and logistic regressions were performed to explore the associations between baseline eating self-regulatory skills and weight and dietary changes. Results: 481 first year undergraduate students took part in the study. Students who entered university with higher eating self-regulatory skills were more likely to maintain or achieve a higher fruit and vegetable (OR = 1.8, p = 0.007) and a lower sweet and salty snack (OR = 1.9, p = 0.001) intake over the course of the first 6 months in university. Higher baseline eating self-regulatory skills were also related to lower weight changes (β = −0.15, p = 0.018) and lower likelihood of gaining 5% initial body weight (OR = 0.52, p = 0.006) at 6-month. Additionally, self-regulatory skills moderated the relationship between baseline BMI and weight changes (β = −0.25, p ≤0.001) and between baseline BMI and 5% weight gain (OR = 0.82, p = 0.008). Conclusions: Starting university with higher eating self-regulatory skills may help students to maintain or achieve a healthy diet and protect them against substantial weight gain, especially among students with overweight

Development of the Top Tips Habit-Based Weight Loss App and Preliminary Indications of Its Usage, Effectiveness, and Acceptability: Mixed-Methods Pilot Study

Background: The Ten Top Tips (10TT) is an intervention based on the habit formation theory that promotes a set of weight management behaviors alongside advice about repetition in a consistent context. Overall, 3 studies have demonstrated that the 10TT can support individuals to lose weight when delivered in a leaflet format. Delivery of 10TT via new technology such as a mobile app could potentially improve its effectiveness and make it more convenient, appealing, and wide reaching. Objective: This study aimed to provide preliminary indications of the usage, effectiveness, and acceptability of an Android app of the 10TT intervention (Top Tips only app) and a second version including self-regulatory strategies for dealing with tempting foods (Top Tips plus app). Methods: The 3-month pilot randomized adults with overweight or obesity to (1) Top Tips only app, (2) Top Tips plus app, or (3) waiting list condition. Automated data from app users were collected. Validated questionnaires assessed self-regulatory skills, weight loss (kg), and behaviors at baseline and 3 months. Users’ feedback on their experience using the app was assessed using open questions. Results: A total of 81 participants took part in the pilot; 28 participants were randomized to the Top Tips only app, 27 to the Top Tips plus app, and 26 to the waiting list condition. On average, participants viewed a mean of 43.4 (SD 66.9) screens during a mean of 24.5 (SD 44.07) log-ins and used the app for 124.2 (SD 240.2) min over the 3-month period. Participants randomized to the Top Tips only app reported the greatest improvement in self-regulatory skills (mean 0.59, SD 1.0), weight loss (mean 4.5 kg, SD 5.2), and adherence to the target behaviors (mean 0.59, SD 0.49) compared with the Top Tips plus (meanself-regulation 0.15, SD 0.42; meanweight −1.9, SD 3.9; and meanbehaviors 0.29, SD 0.29) and waiting list condition (meanself-regulation −0.02, SD 0.29; meanweight −0.01, SD 0.51; and meanbehaviors 0.08, SD 0.38). Participants who reported the largest improvements, on average, viewed pages 2 to 3 times more, had 2 to 3 times more log-ins, logged their weight 2 to 3 times more, and achieved the tips more than those who reported smaller changes in these outcomes. According to users’ feedback, engagement with the app could be increased by making the app more interactive and allowing more tailoring. Conclusions: This study suggests that the Top Tips app could potentially be a useful intervention for promoting eating self-regulatory skills, weight loss, and weight management behaviors among adults with overweight or obesity. Future research should develop the app further based on user feedback and test it in larger sample sizes

Reliability and validity of the Revised General Nutrition Knowledge Questionnaire (GNKQ-R)

BACKGROUND: The General Nutrition Knowledge Questionnaire (GNKQ), was developed in the 1990s and has been widely used. Since then advances in understanding of associations between diet and disease have led to changes in dietary recommendations. This study reports the validity and reliability of an updated version of the GNKQ, bringing it into line with current nutritional advice. / METHODS: Following a review of current recommendations the revised version of the GNKQ (GNKQ-R) was created, consisting of 88 items and four sections. Reliability and validity of the GNKQ-R were determined in four validation studies: 1) reliability was examined using an online sample (n=266), 2) construct validity was assessed with 96 Dietetics students and 89 English students using the “known-groups” method, 3) associations between nutrition knowledge and socio-demographic characteristics were examined using the previously described samples, 4) sensitivity to change was tested by measuring GNKQ-R scores pre- and post- exposure to online nutrition information in written (n=65) and video (n=41) formats. / RESULTS: The reliability was greater than .7 in all sections. Dietetics students scored significantly higher than English students. As predicted, GNKQ-R scores were significantly higher among females vs. males, people with a degree vs. without, and people with very good vs. poor or good health status. They were lower in those older than 50 years vs. younger adults. GNKQ-R Scores were significantly greater after the nutrition interventions in both written and video formats. / CONCLUSION: The GNKQ-R is a valid measure of nutrition knowledge that is consistent, reliable and sensitive to change

Transpiration response of upland rice to water deficit changed by different levels of eucalyptus biochar.

The objective of this work was to evaluate the effect of eucalyptus biochar on the transpiration rate of upland rice 'BRSMG Curinga' as an alternative means to decrease the effect of water stress on plant growth and development. Two‑pot experiments were carried out using a completely randomized block design, in a split-plot arrangement, with six replicates. Main plots were water stress (WS) and no‑water stress (NWS), and the subplots were biochar doses at 0, 6, 12 and 24% in growing medium (sand). Total transpirable soil water (TTSW), the p factor ? defined as the average fraction of TTSW which can be depleted from the root zone before water stress limits growth ?, and the normalized transpiration rate (NTR) were determined. Biochar addition increased TTSW and the p factor, and reduced NTR. Consequently, biochar addition was able to change the moisture threshold (p factor) of the growing medium, up to 12% maximum concentration, delaying the point where transpiration declines and affects yield

Effects of vinasse irrigation on effluent ionic concentration in Brazilian Oxisols.

The irrigation with vinasse can improve soil fertility. However, this use should take into account the characteristics of each soil because the vinasse has unbalanced amounts of mineral and organic elements which might lead to leach the ions, especially nitrate and potassium. The purpose of this study was to evaluate the impacts of vinasse irrigation on effluent ionic concentrations in Brazilian Ferralsols from two areas in Central Brazil: a sugarcane field, and a natural undisturbed savannah area. Soil samples from the two sites were placed into PVC columns with 120 cm height × 25 cm diameter with sugarcane. Undiluted vinasse was applied once on the surface of the soil columns at doses equivalent to 0, 300, 600 and 1200 m3 ha-1. After 0, 60, 90 and 120 days of irrigation, samples of the effluent were collected and the concentrations of dissolved organic matter (DOM), Cl, Ca, Mg, Na, K, total Fe, NH4 +, NO3 -, SO4 2- as well as pH were determined. The ions concentration data were modeled in the chemical equilibrium model Visual Minteq v. 3.0. Results revealed vinasse?s dose, days after irrigation and land use had a relevant effect on most nutrients effluent concentration. Contrasting pH values were observed for both soils and in the savannah soil was observed a decrease in pH at high vinasse doses. This paper thus revealed leaching of the DOM was strongly time dependent. High vinasse doses may lead to increase nutrient leaching and soil dispersion regardless the land use and time after irrigation

Relações da produção de massa seca e as quantidades de nutrientes exportados por Brachiaria brizantha em solos sob o manejo pelo sistema "Barreirão".

Avaliaram-se as relações da produção de massa seca com a exportação de nutrientes num solo do tipo Latossolo Vermelho Escuro, distrófico, fase Cerrado, de textura franco-argilo-arenosa, em áreas de pastagem provenientes da abertura do cerrado original. Formou-se o pasto aplicando 1,5 t/ha de calcário calcítico e fazendo semeio direto com Brachiaria decumbens. Após dez anos de uso, renovou-se a pastagem através do ?Sistema Barreirão?, corrigindo-a com 2,0 t/ha de calcário dolomítico. Numa única operação, semeou-se o arroz e a Brachiara brizantha e procedeu-se à adubação, nas profundidades de 3 a 5 cm e de 8 a 10 cm, respectivamente. Monitoraram-se áreas cujo tempo de implantação do sistema variava de um a seis anos, tendo como referências uma área de mata nativa e outra de dezessete anos de pastejo tradicional. Pelos dados obtidos conclui-se que, para manter a produtividade no sistema, em função dos nutrientes exportados pela pastagem: a) o nitrogênio da matéria orgânica do solo e os níveis de cálcio e magnésio e de fósforo e zinco disponíveis pelo extrator Mehlich-1 no solo são insuficientes a partir do quarto ano; b) o cobre, o ferro e o manganês disponíveis são suficientes por prazos maiores que seis anos; c) quanto à produção de massa seca e à exportação de potássio, não foi possível estabelecer relações coerentes entre ambas

Evolução das propriedades físicas de solos submetidos ao manejo do Sistema Barreirão.

Avaliou-se a evolução histórica das propriedades físicas de um latossolo vermelho-escuro, distrófico, fase cerrado, textura média, em uma área de pastagem proveniente da abertura do cerrado original. Esse pasto foi reformado aplicando-se 1,5 t ha-1 de calcário calcítico e semeio direto com Brachiaria decumbens. Após dez anos de uso, renovou-se esta pastagem através do sistema barreirão. Estas áreas foram corrigidas com 2,0 t ha-1 de calcário dolomítico. Em uma única operação, fez-se a semeadura do arroz e da Brachiara brizantha mais a adubação, nas profundidades de 3 a 5 cm e de 8 a 10 cm, respectivamente. A evolução das propriedades físicas foi monitorada em áreas com um a seis anos de implantação do sistema, tendo como referências uma área de mata nativa e outra com 17 anos de pastejo tradicional. Os dados obtidos permitem concluir que existe uma relação inversa entre a produção de matéria verde com a resistência média à penetração na época seca, na camada de 8 a 16 cm de profundidade, com um nível crítico de 2,22 Mpa

Taxas de decomposição de resíduos de espécies de cobertura em latossolo vermelho distroférrico.

O experimento foi conduzido na Embrapa Arroz e Feijão, no município de Santo Antônio de Goiás-GO, em Latossolo Vermelho Distrófico, sob plantio direto. Empregaram-se as seguintes espécies vegetais: braquiária, braquiária consorciada com milho, guandu, milheto, capim mombaça, sorgo e estilosantes. A fitomassa foi cortada, deixada sobre o solo e coletadas amostras, que foram acondicionadas em saquinhos de náilon. Periodicamente os saquinhos foram pesados, para avaliar as perdas de massa das palhadas e as taxas de decomposição, até os 150 dias após o corte. Em termos de perdas relativas de massa das palhadas aos 150 dias, tomando como referência o tempo inicial, estabeleceuse a ordem decrescente: i) gramíneas ? sorgo (80%) > capim mombaça (64%) > milheto (58%) > braquiária em cultivo solteiro 56%) e consorciado (48%); e ii) leguminosas ? estilosantes (72%) > guandu (65%). Quando as perdas relativas de massa são projetadas para 360 dias, tomando-se como referência o tempo inicial, estabeleceu-se a ordem decrescente: i) gramíneas ? sorgo e braquiária consorciada (86%) > capim mombaça (69%) > milheto 65%) > braquiária solteira (62%); e ii) leguminosas ? estilosantes 83%) > guandu (79%)