Principles of nonlinear regression modeling

Summary Five principles govern the selection of nonlinear regression models for bacterial growth. Examples are given of the various ways in which researchers have approached the problems of nonlinear regression modeling together with some discussion of linear modeling.Reference to a brand or firm name does not constitute endorsement by the US Department of Agriculture over others of a similar nature not mentioned.     

Elevated CO2 and the mineral content of herbaceous and woody plants

The CO₂ enrichment effects (300–650 µmol mol^-1) on mineral concentration (N, P, K, Ca, Mg, Mn, Fe, Zn), absolute total mineral contents per individual and of whole stands of four herbaceous (Trifolium repens L.,Trifolium pratense L.,Lolium perenne L.,Festuca pratensis HUDS.) and two woody species (Acer pseudo-platanus L.,Fagus sylvatica L.) were investigated.In general, the mineral concentration of the plant tissues decreased (all six species: N>Ca>K>Mg) with the exception of P. Mn and Fe were only determined for the tree species. Both decreased in concentration (Mn>Fe). Zn was only analysed forTrifolium pratense andFestuca pratensis and decreased significantly in the grass.Despite of decreases in concentrations of as much as 20% in some cases there were increases in absolute amounts per individual and, therefore, in the whole vegetation up to 25% because of the enhanced dry matter accumulation at elevated CO₂ supply.Dedicated to Prof. Dr. R. Bornkamm, TU-Berlin, on behalf of his 60th birthday     

Behaviour of suspended and sedimentary organic matter in the deltaic areas of the Gulf of Lions (Mediterranean Sea)

The behaviour of organic matter has been approached in two fluvio-marine areas of the Gulf of Lions in the Northwestern Mediterranean Sea: deltas of the Rhône and Têt rivers. Elemental analysis, pyrolysis-gas chromatography-mass spectrometry (main classes of organic compounds) and high performance liquid chromatography (phenolic compounds) enabled to show the fractioning processes and the differentiation of water layers from the river mouth to the open sea. Transitory horizontal and vertical geochemical gradients appeared in the water column. They were more marked in surficial sediments. They underlined the effects of the river inputs which were characterized by high phenol contents. The increase of the marine character towards the open sea was shown by increasing nitrogen-containing compounds. In the Rhône delta, the distribution of the suspended material and organic compounds emphasized the occurrence of a multi-layered water system. In the surficial layers the suspended organic matter was in a little degraded state. On the contrary, the bottom nepheloid contained altered organo-mineral complexes enriched in resistant organic compounds. In the deeper areas of the Lacaze-Duthiers Canyon, in front of the Têt prodelta, the abundance of phytoplanktonic material in the euphotic zone was emphasized by the increase of both nitrogen-containing compounds and aminosugars. In the deeper layers, the suspended material transported by advective currents showed a detrital characteri.e. enriched in clays and in degraded organic matter. The observations carried out in the Rhône delta, the Têt prodelta and the Lacaze-Duthiers Canyon underlined the importance of the general transfer system of suspended material from East to West enhanced by the Liguro-Provençal current.     

Protocol for Development of American Association of Clinical Endocrinology Clinical Practice Guidelines and Consensus Statements: Summary of Methodology,Process, and Policy – 2023 Update

ObjectiveThis 2023 updated protocol summarizes the American Association of Clinical Endocrinology’s (AACE’s) new framework for the development of clinical practice guidelines and other guidance documents that includes changes to methodology, processes, and policies.MethodsAACE has critically reviewed its development processes for guidance documents over the last several years against the National Academy of Medicine Standards for Developing Trustworthy Clinical Practice Guidelines and the Council of Medical Specialty Societies Principles for Development of Specialty Society Clinical Guidelines to determine areas for improvement.ResultsThe new AACE framework for development of guidance documents incorporates many changes, including a revised conflicts of interest (COI) policy; strengthened commitment to collection of disclosures and management of relevant COI during development; open calls to membership for authors; new requirements for authors; new diversity, equity, and inclusion (DEI) policy; new empanelment process that incorporates consideration of DEI; and adoption of the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology to increase the quality of evidence assessment and standardize recommendation grades and statements, among other improvements.ConclusionsAACE has revised its policies and adopted a completely new methodology for guideline development in support of the mission to elevate the practice of clinical endocrinology to improve patient care. With the use of an evidence-based medicine framework and by continually assessing and improving its processes for development of guidance, AACE strives to deliver trustworthy, unbiased, and up-to-date information that ensures clinician and patient confidence in AACE content. Further, AACE hopes that these enhancements foster a more collaborative approach to development and increase engagement with the worldwide medical community to improve global health.     

Wax as a Mechanism for Protection against Photoinhibition — A Study of Cotyledon orbiculata

The leaves of the Crassulacean acid metabolism plant Cotyledon orbiculata have a waxy coating which is highly reflective but can be easily removed by brushing. This provided an ideal system in which to investigate the role of epidermal wax as a possible photoprotectant. Removal of the wax, prior to exposure to natural sunlight, resulted in substantial decreases in F_v/F_m and in severe cases evidence of photoinhibitory damage, as indicated by a rise in F_o. Leaves from which wax had been removed also showed higher conversion of violaxanthin to zeaxanthin than waxed leaves. Recovery of brushed leaves over a 12 day period was correlated with an increase in the total pool of xanthophyll cycle components. This study suggests that the presence of highly reflective wax on the epidermis may confer significant photoprotection to plants exposed to high solar radiation environments.     

切除上胚轴对绿豆子叶衰老逆转及其核酸和蛋白质代谢的效应

在绿豆子叶衰老达到不归点(萌发后5～6d)前切除上胚轴可使开始衰老的子叶中核酸和蛋白质含量回升,衰老短期逆转。衰老不归点后的子叶中核酸和蛋白质变化的主要特征是:丧失了较多的核主带DNA、25S、18S rRNA以及大部分可溶性蛋白质组分,一种小分子DNA 组分完全消失。不归点前切除上胚轴可使上述核酸和蛋白质组分明显增加,表明子叶衰老的逆转可能与这些重要功能物质的回升有关。在切除上胚轴的茎顶涂抹IAA,能阻止子叶核酸和蛋白质回升,也消除了切除上胚轴对子叶裹老的逆转作用。     

北部湾茅尾海无瓣海桑红树林地上生物量反演——基于XGBoost机器学习算法

无瓣海桑是广西从自治区外引进的外来红树林树种,采用定量化算法精确估算无瓣海桑地上生物量对红树林生态修复以及海洋蓝碳监测提供经验和方法。论文以广西茅尾海自然保护区无瓣海桑红树林为研究对象,以野外实测无瓣海桑红树林地上生物量数据和Sentinel-1/2卫星提取的后向散射数据、波段数据、植被指数数据和纹理指数数据为数据源,通过分析各遥感因子与实测红树林地上生物量之间的重要性关系,采用极端梯度提升(XGBoost)机器学习算法对比了不同的变量组合对模型精度的影响,最后基于优选的变量组合反演了无瓣海桑红树林的地上生物量。结果表明：(1)研究区无瓣海桑红树林实测树高范围为1.55—13.58m,平均值为8.37m,胸径范围为0.7—41cm,平均值为15.62cm;(2)通过XGBoost算法优选的21个特征变量组合模型拟合效果较好,其模型在测试阶段R²=0.7237,RMSE=21.70Mg/hm²。XGBoost算法反演研究区无瓣海桑地上生物量介于19.14—138.46Mg/hm²之间,平均值为51.92Mg/hm^...     

Stein and Moore Award address. The molten globule intermediate of apomyoglobin and the process of protein folding.

The molten globule model for the beginning of the folding process, which originated with Kuwajima's studies of alpha-lactalbumin (Kuwajima, K., 1989, Proteins Struct. Funct. Genet. 6, 87-103, and references therein), states that, for those proteins that exhibit equilibrium molten globule intermediates, the molten globule is a major kinetic intermediate near the start of the folding pathway. Pulsed hydrogen-deuterium exchange measurements confirm this model for apomyoglobin (Jennings, P.A. & Wright, P.E., in prep.). The energetics of the acid-induced unfolding transition, which have been determined by fitting a minimal three-state model (N<-->I<-->U; N = native, I = molten globule intermediate, U = unfolded) show that I is more stable than U at neutral pH (Barrick, D. & Baldwin, R.L., 1993, Biochemistry 32, in press), which provides an explanation for why I is formed from U at the start of folding. Hydrogen exchange rates measured by two-dimensional NMR for individual peptide NH protons, taken together with the CD spectrum of I, indicate that moderately stable helices are present in I at the locations of the A, G, and H helices of native myoglobin (Hughson, F.M., Wright, P.E., & Baldwin, R.L., 1990, Science 249, 1544-1548). Directed mutagnesis experiments indicate that the interactions between the A, G, and H helices in I are loose (Hughson, F.M., Barrick, D., & Baldwin, R.L., 1991, Biochemistry 30, 4113-4118), which can explain why I is formed rapidly from U at the start of folding.(ABSTRACT TRUNCATED AT 250 WORDS)     

Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.