Breeding schemes: what are they, how to formalize them, and how to improve them?

Open Access Journal; Published online: 21 Jan 2022Formalized breeding schemes are a key component of breeding program design and a gateway to conducting plant breeding as a quantitative process. Unfortunately, breeding schemes are rarely defined, expressed in a quantifiable format, or stored in a database. Furthermore, the continuous review and improvement of breeding schemes is not routinely conducted in many breeding programs. Given the rapid development of novel breeding methodologies, it is important to adopt a philosophy of continuous improvement regarding breeding scheme design. Here, we discuss terms and definitions that are relevant to formalizing breeding pipelines, market segments and breeding schemes, and we present a software tool, Breeding Pipeline Manager, that can be used to formalize and continuously improve breeding schemes. In addition, we detail the use of continuous improvement methods and tools such as genetic simulation through a case study in the International Institute of Tropical Agriculture (IITA) Cassava east-Africa pipeline. We successfully deploy these tools and methods to optimize the program size as well as allocation of resources to the number of parents used, number of crosses made, and number of progeny produced. We propose a structured approach to improve breeding schemes which will help to sustain the rates of response to selection and help to deliver better products to farmers and consumers

Short term non-invasive ventilation post-surgery improves arterial blood-gases in obese subjects compared to supplemental oxygen delivery - a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>In the immediate postoperative period, obese patients are more likely to exhibit hypoxaemia due to atelectasis and impaired respiratory mechanics, changes which can be attenuated by non-invasive ventilation (NIV). The aim of the study was to evaluate the duration of any effects of early initiation of short term pressure support NIV vs. traditional oxygen delivery via venturi mask in obese patients during their stay in the PACU.</p> <p>Methods</p> <p>After ethics committee approval and informed consent, we prospectively studied 60 obese patients (BMI 30-45) undergoing minor peripheral surgery. Half were randomly assigned to receive short term NIV during their PACU stay, while the others received routine treatment (supplemental oxygen via venturi mask). Premedication, general anaesthesia and respiratory settings were standardized. We measured arterial oxygen saturation by pulse oximetry and blood gas analysis on air breathing. Inspiratory and expiratory lung function was measured preoperatively (baseline) and at 10 min, 1 h, 2 h, 6 h and 24 h after extubation, with the patient supine, in a 30 degrees head-up position. The two groups were compared using repeated-measure analysis of variance (ANOVA) and t-test analysis. Statistical significance was considered to be P < 0.05.</p> <p>Results</p> <p>There were no differences at the first assessment. During the PACU stay, pulmonary function in the NIV group was significantly better than in the controls (p < 0.0001). Blood gases and the alveolar to arterial oxygen partial pressure difference were also better (p < 0.03), but with the addition that overall improvements are of questionable clinical relevance. These effects persisted for at least 24 hours after surgery (p < 0.05).</p> <p>Conclusion</p> <p>Early initiation of short term NIV during in the PACU promotes more rapid recovery of postoperative lung function and oxygenation in the obese. The effect lasted 24 hours after discontinuation of NIV. Patient selection is necessary in order to establish clinically relevant improvements.</p> <p>Trial Registration#</p> <p>DRKS00000751; <url>http://www.germanctr.de</url></p

Analysis of agronomic categories in different soil texture classification systems

Different soil texture classification systems are used in Poland. The system most widely used in agriculture is named after Polish Soil Science Society (PSSS) and is described in the soil classification norm BN-78/9180-11 (BN1978 standard). The last edition of soil classification system and soil texture classes published by PSSS in 2008 (PSSS 2008 classification) is different from BN1978 standard. The aim of this paper is a quantitative and qualitative comparison of the compatibility of agronomic categories created according to the old textural classes (BN1978 standard) and the new textural classes (PSSS 2008 classification). The representative set of soil samples (n=316) for arable mineral soils in Poland were divided into agronomic categories according to these two soil classification systems. The agronomic categories, which comply with soil classification systems PSSS 1978 are widely used in agricultural advisory. The results of the study showed differences in the amount of soil samples classified for the corresponding agronomic category. The study also showed discrepancies in the fine particle (<0.02 mm) and colloidal fraction (<0.002 mm) content in the corresponding categories. The differences may affect the assessment of soil fertility in nutrients(abundance) such as potassium, magnesium and of soil liming needs, as well as appropriate determination of fertiliser doses

Visible and near-infrared spectroscopy as a tool for soil classification and soil profile description

This paper presents preliminary results of the use of visible and near-infrared (VIS -NIR) spectroscopy for soil classification and soil profile examination. Three experiments involving (1) three different soil types (Albic Luvisol, Gleyic Phaeozem, Brunic Arenosol), (2) three artificial micro-plots with similar texture (loamy sand, Gleyic Phaeozem) but different soil organic carbon (SOC) content and (3) a soil profile (Fluvisol) have been investigated using VIS -NIR spectroscopy. Results indicated that VIS -NIR is a promising technique for preliminary soil description and can classify soils according to soil properties (especially SOC ) and horizons. Instead of complex chemical and physical analyses involved in routine soil profile classification, VIS-NIR spectroscopy is suggested as a useful, rapid, and inexpensive tool for soil profile investigation

Usefulness of pulse oximetry using the SET technology in critically ill adult patients

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What Glues a Homodimer Together Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein Protein Interface of the tRNA Modifying Enzyme Tgt

Shigella bacteria constitute the causative agent of bacillary dysentery, an acute inflammatory disease causing the death of more than one million humans per year. A null mutation in the tgt gene encoding the tRNA modifying enzyme tRNA guanine transglycosylase Tgt was found to drastically decrease the pathogenicity of Shigella bacteria, suggesting the use of Tgt as putative target for selective antibiotics. The enzyme is only functionally active as a homodimer; thus, interference with the formation of its protein protein interface is an attractive opportunity for therapeutic intervention. To better understand the driving forces responsible for the assembly, stability, and formation of the homodimer, we studied the properties of the residues that establish the dimer interface in detail. We performed site directed mutagenesis and controlled shifts in the monomer dimer equilibrium ratio in solution in a concentration dependent manner by native mass spectrometry and used crystal structure analysis to elucidate the geometrical modulations resulting from mutational variations. The wild type enzyme exhibits nearly exclusive dimer geometry. A patch of four aromatic amino acids, embedded into a ring of hydrophobic residues and further stabilized by a network of H bonds, is essential for the stability of the dimer s contact. Accordingly, any perturbance in the constitution of this aromatic patch by nonaromatic residues reduces dimer stability significantly, with some of these exchanges resulting in a nearly exclusively monomeric state. Apart from the aromatic hot spot, the interface comprises an extended loop helix motif that exhibits remarkable flexibility. In the destabilized mutated variants, the loop helix motif adopts deviating conformations in the interface region, and a number of water molecules, penetrating into the interface, are observe