scholarly journals Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies

2021 ◽  
Author(s):  
Hélène Borges ◽  
Anne-Marie Hesse ◽  
Alexandra Kraut ◽  
Yohann Couté ◽  
Virginie Brun ◽  
...  
Keyword(s):  
Large Scale ◽  
Clinical Sample ◽  
Block Design ◽  
Cross Contamination ◽  
Batch Effects ◽  
Sample Analysis ◽  
Multiple Group ◽  
Randomized Block Design ◽  
Biochemical Preparation ◽  
User Friendly

Abstract Summary Many factors can influence results in clinical research, in particular bias in the distribution of samples prior to biochemical preparation. Well Plate Maker is a user-friendly application to design single- or multiple-well plate assays. It allows multiple group experiments to be randomized and therefore helps to reduce possible batch effects. Although primarily fathered to optimize the design of clinical sample analysis by high throughput mass spectrometry (e.g. proteomics or metabolomics), it includes multiple options to limit edge-of-plate effects, to incorporate control samples or to limit cross-contamination. It thus fits the constraints of many experimental fields. Availability and implementation Well Plate Maker is implemented in R and available at Bioconductor repository (https://bioconductor.org/packages/wpm) under the open source Artistic 2.0 license. In addition to classical scripting, it can be used through a graphical user interface, developed with Shiny technology.

scholarly journals Evaluation of water-stress tolerance of Acala SJ 2 and Auburn 2 cotton cultivars in a phenotyping platform

2017 ◽  
Vol 12 (4) ◽  
pp. 629 ◽  
Author(s):  
Cleber Morais Guimarães ◽  
Luís Fernando Stone ◽  
Giovani Greigh de Brito ◽  
Jair Heuert
Keyword(s):  
Water Stress ◽  
Stress Tolerance ◽  
Large Scale ◽  
Agronomic Traits ◽  
Block Design ◽  
Soil Layer ◽  
Water Restriction ◽  
Water Regimes ◽  
Water Stress Tolerance ◽  
Randomized Block Design

Due to the current scarcity of water, which may be aggravated by climate changes, it is important to develop cultivars tolerant to water stress. For this, information regarding the variability of the tolerance of cultivars to this stress is required. This information can be obtained by using phenotyping platforms, which allow a large-scale and automated assessment of crop traits related to productivity under water stress. This study took place in a greenhouse and used a phenotyping platform to evaluate some agronomic and physiological traits of two cotton cultivars with differing tolerances to this stress. The experiment was performed in a randomized block design, in a split-plot scheme with four replicates. The main plots were composed of five water regimes and the subplots of two cultivars, Acala SJ 2 and Auburn 2. The water regimes consisted of a well-irrigated treatment (daily replacement of 100% of evapotranspired water) and four water restriction regimes (20%, 40%, 60% and 80% of evapotranspired water at the well-irrigated treatment). The phenotyping platform and protocol (different percentages of daily replacement of evapotranspired water) employed were suitable to the evaluated cotton cultivars for water-stress tolerance, and allowed the determination of the cultivar most tolerant (Acala SJ 2) and of the cultivar most sensitive (Auburn 2) to water stress. ‘Acala SJ 2’ displayed better physiological and agronomic traits in all water regimes, including higher root density in the upper soil layer, as well as higher water use than ‘Auburn 2’, which explained its higher seed yield under the conditions employed.

scholarly journals Fertigation and growth regulator on coffee seedling production in tubes

2018 ◽  
Vol 48 (4) ◽  
pp. 350-357 ◽  
Author(s):  
Victor Peçanha de Miranda Coelho ◽  
Kelly Martins Rosa ◽  
Paulo Eduardo Branco Paiva ◽  
Édimo Fernando Alves Moreira ◽  
Mychelle Carvalho
Keyword(s):  
Growth Regulator ◽  
Large Scale ◽  
Block Design ◽  
Scale Production ◽  
Seedling Production ◽  
Conventional System ◽  
New Production ◽  
Randomized Block Design ◽  
Large Scale Production ◽  
Production Technologies

ABSTRACT The use of quality seedlings is important in establishing a productive coffee crop. However, the most widely used method to produce coffee seedlings is time consuming (6-12 months) and lacks new production technologies. This study aimed to assess the use of fertigation and a growth regulator in the production of coffee seedlings, in order to develop a system faster than the conventional method. For that, Topázio coffee cultivar seeds were pre-germinated and planted in tubes filled with substrate (composted pine bark), in a protected nursery. A randomized block design was used, in a 4 x 2 (fertigation levels x the use or not of growth regulator) factorial scheme, with four replications. Daily fertigation positively influenced all the growth variables evaluated. The foliar spraying of the growth regulator had little effect on seedling growth. When compared to the conventional system described in the literature, the coffee seedling production system described here reduced, by around 60 days, the production time and enables a large-scale production.

scholarly journals RESPON STEK PUCUK TANAMAN MIANA (COLEUS ATROPURPUREUS (L.) BENTH) TERHADAP PEMBERIAN ZAT PENGATUR TUMBUH

2019 ◽  
Vol 19 (2) ◽  
pp. 277
Author(s):  
Eltis Panca Ningsih ◽  
Imas Rohmawati
Keyword(s):  
Plant Growth ◽  
Growth Regulator ◽  
Plant Growth Regulator ◽  
Large Scale ◽  
Block Design ◽  
Ornamental Plant ◽  
Coconut Water ◽  
Plant Materials ◽  
Randomized Block Design ◽  
Number Of Shoots

Abstrak : Tanaman miana saat ini dimanfaatkan sebagai tanaman hias. Perbanyakan Tanaman miana dapat dilakukan dengan cara generatif maupun vegetatif. Stek pucuk merupakan cara perbanyakan vegetatif tanaman miana yang relatif mudah dilakukan. Pembibitan dengan cara ini merupakan salah satu cara cepat dalam memenuhi kebutuhan bahan tanaman skala besar. Penelitian ini bertujuan untuk mengetahui pengaruh pemberian Zat Pengatur Tumbuh terhadap stek pucuk tanaman miana (Coleus atropurpureus (L.) Benth. Penelitian dilaksanakan di di laboratorium agroekologi, Fakultas Pertanian, Universitas Sultan Ageng Tirtyasa. Penelitian akan dilaksanakan pada bulan pada bulan Maret sampai Mei 2017. Penelitian ini menggunakan Rancangan Acak Kelompok (RAK) yang yang terdiri dari empat perlakuan dan diulang tiga kali. Perlakuan yang diuji dalam percobaan ini adalah: kontrol (Tanpa ZPT), IAA 750 ppm, Growtone 500 ppm, dan air kelapa 10%. Hasil penelitian menunjukkan bahwa pemberian zat pengatur tumbuh berpengaruh terhadap jumlah tunas dan jumlah akar. Jumlah tunas terbanyak terdapat pada perlakuan Growtone sebesar 7.50 tunas. Jumlah akar terbanyak terdapat pada perlakuan IAA sebesar 91.00 buah. Rekomendasi budidaya tanaman miana dengan cara stek dapat menggunakan IAA 750 ppm maupun Growtone 500 ppm.Kata Kunci : miana, stek, zat pengatur tumbuhAbstract : Miana plant is currently used as an ornamental plant. The multiplication of miana crops can be done in a generative and vegetative way. Cuttings is a vegetative way of reproduction of miana plant which is relatively easy to do. Breeding in this way is one of the quick ways in meeting the needs of large-scale plant materials. This research aims to determine the effect of giving Plant Growth Regulator to the shoots cuttings of Miana (Coleus atropurpureus (L.) Benth). Research conducted in the Agroecological laboratory, Faculty of Agriculture, University of Sultan Ageng Tirtyasa. The research will be held in the month of March to May 2017. The study conducted by randomized block design (RBD) which consists of four treatments and is repeated three times. The treatment tested in this experiment was: control (without plant growth regulator), IAA 750 ppm, Growtone 500 ppm, and 10% coconut water. The results showed that the treatment of plant growth regulator affected in the number of shoots and the number of roots. The most number of shoots is in the Growtone treatment of 7.50 shoots. The highest number of roots is in the IAA treatment of 91.00 pieces. Recommendations for cultivation of miana crops with cuttings can use IAA 750 ppm maupun Growtone 500 ppm.Keyword : Miana, cuttings, growing regulatory substances 

scholarly journals Phytoregulators and stem subdivision in the production of young forage palms (Opuntia ficus-indica and Nopalea cochellinifera)

2020 ◽  
pp. 1742-1747
Author(s):  
Wellington Silva Gomes ◽  
Samy Pimenta ◽  
Poliana Soares da Cruz Mascarenhas ◽  
Luciana Cardoso Nogueira Londe ◽  
Arles Matheus Pickler de Barros do Vale ◽  
...  
Keyword(s):  
Large Scale ◽  
Lower Cost ◽  
Block Design ◽  
Naphthaleneacetic Acid ◽  
Scale Production ◽  
Stem Size ◽  
Randomized Block Design ◽  
Large Scale Production ◽  
Additional Control ◽  
Length Width

The propagation of plants through stem subdivision and the incorporation of phytoregulators can be a viable and efficient technique in the large-scale production of young forage palm at a lower cost. This study was conducted in order to evaluate the influence of stem subdivision and phytoregulators on the production of young forage palms under greenhouse conditions. Three experiments (I, II and III) were performed. Experiments I and II consisted of young palm of the Miúda genotype, formed from fragmented stems submitted to solutions containing gradually increasing concentrations of benzylaminopurine (0,0; 0,5; 1,0 e 1,5 mg. L-1) and kinetin (0,0; 0,25; 0,5 e 0,75 mg. L-1) combined with naphthaleneacetic acid (1,5 mg. L-1). An additional control without the use of phytoregulators was also included. These treatments were distributed in a randomized block design (RBD), in a factorial scheme with the additional plot: 4 x 4 + 1. In experiment III, different sized fractions of four forage palm genotypes were tested: Gigante, Orelha de elefante, IPA Sertânia, and Miúda. For this test, the experimental design was RBD, with twelve treatments, distributed in five blocks with five plants per plot. There was no influence of phytoregulators on the characteristics evaluated in experiments I and II. Significant differences were found. However, for the variables length, width, and thickness of sprouts among treatments in experiment III. Therefore, the application of phytoregulators in young forage palms at the dosages used is not recommended. For the Gigante, Orelha de Elefante and Miúda genotypes, the fractional stem size recommended is 5x3 cm whereas for IPA Sertânia, the size recommended is 4x2 cm.

scholarly journals Selectivity of chemical weed control systems in conventional cotton

2014 ◽  
Vol 32 (4) ◽  
pp. 827-841 ◽  
Author(s):  
J.G.Z. Arantes ◽  
J. Constantin ◽  
R.S. Oliveira Jr. ◽  
G.B.P. Braz ◽  
C.A.S. Barbosa ◽  
...  
Keyword(s):  
Control Systems ◽  
Weed Control ◽  
Crop Yield ◽  
Large Scale ◽  
Block Design ◽  
Control Measures ◽  
Herbicide Application ◽  
Randomized Block Design ◽  
Crop Cycle ◽  
Over The Top

Cotton is highly susceptible to the interference imposed by weed community, being therefore essential to adopt control measures ensuring the crop yield. Herbicides are the primary method of weed control in large-scale areas of production, and usually more than one herbicide application is necessary due to the extensive crop cycle. This study aimed to evaluate the selectivity of different chemical weed control systems for conventional cotton. The experiment took place in the field in a randomized block design, with twenty nine treatments and four replications in a split plot layout (adjacent double check). Results showed that triple mixtures in pre-emergence increased the chance of observing reductions in the cotton yield. To avoid reductions in crop yield, users should proceed to a maximum mixture of two herbicides in pre-emergence, followed by S-metolachlor over the top, followed by one post-emergence mixture application of pyrithiobac-sodium + trifloxysulfuron-sodium.

scholarly journals Performance of New Rice Variety (Inpari 24) at Subak Amerta Nadi Kerta Village Payangan Sub-district of Gianyar Bali

2017 ◽  
Vol 2 (6) ◽  
pp. 617
Author(s):  
I Ketut Kariada ◽  
I. B. Aribawa
Keyword(s):  
Large Scale ◽  
Cropping Systems ◽  
Block Design ◽  
Rice Variety ◽  
Model Development ◽  
Cropping System ◽  
New Variety ◽  
Pilot Model ◽  
Lower Productivity ◽  
Randomized Block Design

Model development of rice farming in the production centre area at Payangan Sub-district of Gianyar is designed to introduce a model called rice field laboratory. The principle of the model used is "build, operate and transfer (BOT), refering to a the disseminated model of innovation which is a  large scale pilot model at the grass root level. The study introduced new varieties “Inpari”24 as an attempt to replace the old varieties that has lower productivity. Cultivation technology by implementing  Legowo System 2: 1. The aim of this study was to determine the performance of new variety Inpari 24 in the cropping system in Subak Amerta Nadi, Kerta Village, Sub-district of Payangan Gianyar in the growing season 2014. This study used a randomized block design with two treatments of different cropping systems, namely: Legowo 2: 1 (40 x 20 x 10 cm) and tiles (20 x 20 cm), repeated 10 times. Variables observed in this study were: plant height, number of tillers, panicle length, number of grains per panicle and empty grains and yield per hectare. Data were analysed through analysis of variance, then followed by LSD test at 5% level. It was concluded that: (a) cropping systems significantly affected all variables of rice production, (b) the highest productivity was Legowo System which was 7.50 tons / ha, increased by 26.68% compared to tiles cropping system (the method used by farmers).Keywords: Inpari 24; planting system; rice

scholarly journals Effect of container and potting media on raising quality seedlings of Acacia auriculiformis in the nursery

2019 ◽  
Vol 3 (01) ◽  
Author(s):  
MD. ARIFUL ISLAM ◽  
RAYHANUR RAHMAN ◽  
MOHAMMED KAMAL HOSSAIN
Keyword(s):  
Root Length ◽  
Quality Index ◽  
Large Scale ◽  
Growth Parameters ◽  
Block Design ◽  
Dry Weight ◽  
Acacia Auriculiformis ◽  
Cow Dung ◽  
Randomized Block Design ◽  
Potting Media

Abstract. Islam MDA, Rahman MDA, Hossain MK. 2019. Effect of container and potting media on raising quality seedlings of Acacia auriculiformis in the nursery. Asian J Agric 3: 26-32. The study elucidates the effect of container and potting media on raising quality seedlings of Acacia auriculiformis in the nursery of the Institute of Forestry and Environmental Sciences, University of Chittagong to find out a suitable container and potting media for raising large scale quality seedlings. The seedlings were evaluated by five container and seven potting media treatments for eight months. A Completely Randomized Block Design (CRBD) was adopted for the study with three replications for each treatment. The Analysis of variance (ANOVA) and Duncan’s Multiple Range Test (DMRT) was tested for the analysis to explore the possible treatment variations. However, the study reveals nodulation with growth parameters; shoot and root dry biomass production and quality index were highest in 20 cm × 15 cm size polybags whereas the highest root length and shoot-root ratio was observed in 15 cm × 10 cm and 15 cm × 13 cm size polybag respectively. Considering the potting media, highest nodulation, growth parameters, shoot dry and fresh weight, shoot- root ratio and biomass were found in combination of soil + cow dung + phosphorus (0.16 g/polybag). Highest root length, root fresh and dry weight, and quality index were found in the combination of soil + cow dung (3:1). Therefore, it is recommended that containers of 20 cm × 15 cm size polybag and with a potting media of soil + cow dung + phosphorus (3 parts soil, 1 parts cow dung + 0.16 g/polybag) combination produce quality A. auriculiformis seedlings in the nursery.

Optimal Test Assembly in Practice

2013 ◽  
Vol 221 (3) ◽  
pp. 190-200 ◽  
Author(s):  
Jörg-Tobias Kuhn ◽  
Thomas Kiefer
Keyword(s):  
Particle Physics ◽  
Large Scale ◽  
Block Design ◽  
Linear Optimization ◽  
Mixed Integer ◽  
Optimal Test ◽  
Automated Test Assembly ◽  
Test Assembly ◽  
Block Level ◽  
Mixed Integer Linear Optimization

Several techniques have been developed in recent years to generate optimal large-scale assessments (LSAs) of student achievement. These techniques often represent a blend of procedures from such diverse fields as experimental design, combinatorial optimization, particle physics, or neural networks. However, despite the theoretical advances in the field, there still exists a surprising scarcity of well-documented test designs in which all factors that have guided design decisions are explicitly and clearly communicated. This paper therefore has two goals. First, a brief summary of relevant key terms, as well as experimental designs and automated test assembly routines in LSA, is given. Second, conceptual and methodological steps in designing the assessment of the Austrian educational standards in mathematics are described in detail. The test design was generated using a two-step procedure, starting at the item block level and continuing at the item level. Initially, a partially balanced incomplete item block design was generated using simulated annealing, whereas in a second step, items were assigned to the item blocks using mixed-integer linear optimization in combination with a shadow-test approach.

Innovation of Natural Preservation of Mackerel (Rastrelliger kanagurta) Using Coconut Coconut Ashes with Drying Time Variations on Hedonics

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Rika Agustina ◽  
Rita Sunartaty ◽  
Teuku Makmur
Keyword(s):  
Research Design ◽  
Block Design ◽  
Drying Time ◽  
Basic Ingredient ◽  
Randomized Block Design ◽  
Salt Substitute ◽  
Long Time ◽  
Time Variations ◽  
Rastrelliger Kanagurta

Coconut frond ash is one of the wastes from coconut trees which has not been maximally utilized. Coconut frond ash contains MgCl2 and KCl so that it can be used as a salt substitute in the process of preserving fish. In this study coconut frond ash was used as a basic ingredient for making dried mackerel with a long time of drying to storage. The purpose of this study was to determine the effect of drying time on mackerel storage. The research design used was a Randomized Block Design (RCBD) with 2 factors studied. The first factor is the drying time consists of 3 levels, namely P1 = 3 days, P2 = 4 days, P3 = 5 days. The second factor is storage which consists of 3 levels, namely S1 = 30 days, S2 = 60 days, S3 = 90 days. Each treatment was repeated 2 times to obtain 18 experimental units to observed hedonic tests. From the results of the study it can be stated that the treatment has a very significant effect (P≥0.01) on the hedonic test which includes (color, aroma, taste and texture).

Kualitas Semen Cair Kambing Boer Berbahan Pengencer Air Kelapa Muda Varietas Viridis Setelah Simpan Dingin

2019 ◽  
Vol 6 (1) ◽  
pp. 78
Author(s):  
Muhammad Ade Salim ◽  
Muhammad Nur Ihsan ◽  
Nur Isnaini ◽  
Trinil Susilawati
Keyword(s):  
Semen Quality ◽  
Block Design ◽  
Animal Husbandry ◽  
Egg Yolk ◽  
Coconut Water ◽  
Boer Goat ◽  
Randomized Block Design ◽  
Frozen Semen ◽  
Artificial Vagina

ABSTRAKAir kelapa muda varietas viridisdapat dijadikan pengencer aletrnatif semen cair bagi program IB di daerah minim sarana semen beku. Tujuan penelitian ini untuk menguji pengaruh penggunaan air kelapa muda viridissebagai bahan pengencer terhadap kualitas semen cair kambing Boer setelah didinginkan. Dilaksanakanselama 3 bulan di Laboratorium Fakultas Peternakan UBUnit SumberSekar,Malang. Metodenya yaitu eksperimen. Semen dari  3 pejantan Boer umur 3-5 tahun, dikoleksi seminggu sekali dengan VB. Air kelapa mudaviridis umur 5-7 bulan serta tris aminomethane sebagai kontrol. Didesain menggunakan Rancangan Acak Kelompok (RAK) dengan 2 perlakuan yaitu P0 (tris aminomethane + 10% KT) dan  P1 (air kelapa muda viridis + 10% KT) masing-masing diulang 10 kali. Data dianalisis dengan analisis Ragam (Anova) dengan software Genstat 18. Variabelnya yaitu motilitas individu, viabilitas dan abnormalitas. Hasil penelitian yaitu motilitas individu pada P1bertahan sampai 4 hari (40,5± 24,3%), viabilitas terbaik sampai hari ke-5 (42±24,6%), abnormalitas terendah di hari ke-7(1,31± 0,6). Kesimpulannya, Pengencer air kelapa muda viridis dapat mempertahankan kualitas semen cair kambing Boer selama 4 hari untuk motilitas dan 5 hari untuk viabilitas.Kata Kunci:pengencer, air kelapa, varietas viridisABSTRACTYoung viridis coconut water could be used as an alternative to liquid semen diluent for artificial insemination program in the area with limited facility for frozen semen production. This study evaluated the use of young coconut water as a diluent on liquid semen quality of Boer goat after cold storage. This study was carried out for 3 months at Sumber Sekar Laboratory, Faculty of Animal Husbandry, University of Brawijaya, Malang. The semen was collected from 3 Boer bucks aged at 3 to 5 years old. The semen collection was done once a week with the aid of artificial vagina. The diluents used were young Viridis coconut (5 to 7 months old) and tris aminomethane. The method used was an experiment in a randomized block design with 2 treatments and 10 replicates. The treatments used were T0: tris aminomethane + 10% egg yolk (control) and T1:  young Viridis coconut water + 10% egg yolk. Data were analyzed by analysis of variance using Genstat 18 software. The variables measured were sperm individual motility, viability, and abnormality. The results showed that the sperm individual motility in T1 survived up to 4 days (40.5± 24.3%), the best viability at 5 days (42.0±24.6%),  while the lowest abnormality at 7 days (1.31±0.6). It could be concluded that: 1. Tris aminomethane diluent has higher quality with the storage length up to 9 days, 2. Young Viridis coconut water diluent could preserve liquid semen quality of Boer goat up to 4 days for sperm motility and 5 days for sperm viability.Keywords: diluents, coconut water, viridis variety

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