Computational approaches to motor control

New concepts and computational models that integrate behavioral and neurophysiological observations have addressed several of the most fundamental long-standing problems in motor control. These problems include the selection of particular trajectories among the large number of possibilities, the solution of inverse kinematics and dynamics problems, motor adaptation and the learning of sequential behaviors.     

Frustration‐guided motion planning reveals conformational transitions in proteins

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics‐inspired motion planning procedure called dCC‐RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non‐native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC‐RRT to examine how collective, small‐scale motions of four side‐chains in the active site of cyclophilin A propagate through the protein. dCC‐RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non‐canonical capsid binding site 25 Å away, rationalizing NMR and multi‐temperature crystallography experiments. In all, dCC‐RRT can reveal detailed, all‐atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/ .     

The Development of Multi-epitope Vaccines: Epitope Identification, Vaccine Design and Clinical Evaluation

We have developed efficient methods for epitope identification and vaccine design. Our process for epitope selection based on the combined use of motif analyses, binding assays and immunogenicity evaluations is described. We also describe how the projected population coverage and vaccine design can be optimized. Finally, it is discussed how vaccine potency is evaluated by immunogenicity and antigenicity assays.     

The role of macroinvertebrates for conservation of freshwater systems

Freshwater ecosystems are the most threatened ecosystems worldwide. Argentinian‐protected areas have been established mainly to protect vertebrates and plants in terrestrial ecosystems. In order to create a comprehensive biodiverse conservation plan, it is crucial to integrate both aquatic and terrestrial systems and to include macroinvertebrates. Here, we address this topic by proposing priority areas of conservation including invertebrates, aquatic ecosystems, and their connectivity and land uses. Location: Northwest of Argentina. We modeled the ecological niches of different taxa of macroinvertebrates such as Coleoptera, Ephemeroptera, Hemiptera, Megaloptera, Lepidoptera, Odonata, Plecoptera, Trichoptera, Acari, and Mollusca. Based on these models, we analyzed the contribution of currently established protected areas in the conservation of the aquatic biodiversity and we propose a spatial prioritization taking into account possible conflict regarding different land uses. Our analysis units were the real watersheds, to which were added longitudinal connectivity up and down the rivers. A total of 132 species were modeled in the priority area analyses. The analysis 1 showed that only an insignificant percentage of the macroinvertebrates distribution is within the protected areas in the North West of Argentina. The analyses 2 and 3 recovered similar values of protection for the macroinvertebrate species. The upper part of Bermejo, Salí‐Dulce, San Francisco, and the Upper part of Juramento basins were identified as priority areas of conservation. The aquatic ecosystems need special protection and 10% or even as much as 17% of land conservation is insufficient for species of macroinvertebrates. In turn the protected areas need to combine the aquatic and terrestrial systems and need to include macroinvertebrates as a key group to sustain the biodiversity. In many cases, the land uses are in conflict with the conservation of biodiversity; however, it is possible to apply the connectivity of the watersheds and create multiple‐use modules.     

Potential pitfalls of the PTV concept in dose-to-medium planning optimization

In typical treatment planning of 3D IMRT, the incident energy fluence is optimized to achieve a homogeneous dose distribution to the PTV. The PTV includes the tumour but also healthy tissues that may have a different dose response for the same incident energy fluence, like bony structures included in the PTV (mandibles in head and neck tumours or femoral bones in sarcomas). Dose to medium optimization compensates for this heterogeneous response, leading to a non-homogeneous energy fluence in the PTV and a non-homogeneous dose in the CTV in the presence of geometric errors. We illustrate qualitatively this statement in a cylindrical geometry where the PTV includes a CTV (7 cm diameter) made of water surrounded by ICRU compact bone (1.2 cm thickness); such configuration was chosen to exaggerate the aforementioned effect. Optimization was performed assuming dose equals photon energy fluence times mass energy absorption coefficient. Bone has a 4% lower dose response in a 6 MV flattening filter free spectrum. After optimization either in medium or assuming everything as water composition, the geometry was shifted by 1.2 cm and dose recomputed. As expected, compensating for the under-response of the bone material during optimization in medium leads to an overdosage of the CTV when patient geometric errors are taken into account. Optimization in dose assuming everything as water composition leads to a uniform coverage. Robust optimization or forcing a uniform atomic composition in the PTV margin may resolve this incompatibility between the PTV concept and dose to medium optimization.     

The role a botanical institute can play in the conservation of the terrestrial biodiversity in a developing country

The need to integratein situ conservation into the planning process is outlined, and the importance of vegetation survey to determine conservation priorities and to identify areas suitable forin situ conservation is stressed. A case is presented, drawing on experience gained in Zimbabwe, of how a botanical institute can become an integral part of biological conservation. The institute should consist of a herbarium, a botanical garden, a gene bank and a vegetation survey unit. The function of each section, how they interlink, and how they can be integrated are discussed.     

Land-use changes assessed by overlay or mosaic methods: Which method is best for management planning?

Environmental planning must determine management practices for a given territory based on the landscape processes that have occurred over time and their consequences. Therefore, environmental planning decisions must be based on strong empirical evidence that can be easily understood by all involved parties. Several studies have highlighted the methodological deficiencies that occur when obtaining and interpreting such issues, particularly in heterogeneous landscapes with complex interactions. In this paper, we evaluated two methodological approaches that are used in management planning, land use/cover change (LUCC) and mosaic change (MC) to compare their effectiveness and suitability for supporting decision-making. We applied these methods to the coastal landscape of São Sebastião Island, Brazil, which has undergone many changes in the last 50 years. For two years, land use/cover maps were produced using GIS and assessed according to changes in landscape elements (LUCC) and boundaries (MC). Overall, the LUCC failed to identify sets with similar structural heterogeneities in the landscape. However, the LUCC is easier for stakeholders to understand and apply than the MC. The MC method better presented the evolution of the relationship between the landscape elements and heterogeneity.     

典型矿区植被覆盖度时空分布特征及影响因素

植被状况可以直接或间接地反映采煤对生态环境的影响。以长河井工煤矿、离柳井工煤矿、平朔露天煤矿3个典型矿区为研究区域。以Landsat数据为数据源，基于地形调节植被指数的像元二分模型提取植被覆盖度；采用趋势分析、线性回归斜率、稳定性分析方法，分析了3个典型矿区2001-2016年植被覆盖度的时空变化特征；运用"以时间换空间"的方法，采用相关分析方法对植被覆盖度变化的自然影响因素进行了分析。结果表明：（1）近16年3个典型矿区植被覆盖度呈增加趋势，长河、离柳、平朔矿区的增长速率分别为0.09%/10 a、0.10%/10 a、0.08%/10 a（P > 0.05）。（2）空间上，长河、离柳、平朔矿区植被覆盖度变化不明显比例分别占到66.63%，59.90%，62.25%，呈增加趋势的比例仅分别占28.14%、32.55%、27.81%，而呈减少趋势的比例分别占到5.23%、7.55%、9.94%。长河矿区明显改善的区域位于自然植被和耕作区的北部和东北部，离柳矿区明显改善的区域位于以低植被覆盖度为主的北部，平朔矿区明显改善的区域位于复垦的中西部。（3）不区分植被类型时，3个矿区的植被覆盖度变化与高程、高程与温度的交互作用表现出显著相关性（P < 0.01），与各自然因素的相关性总体表现为长河 > 离柳 > 平朔矿区；区分植被类型时，草地与坡度的相关性不显著（P > 0.05），与降雨量、高程存在显著正相关（P < 0.05）；灌木林与温度相关性不显著，与高程和降雨量的交互作用存在显著正相关；旱地与高程、高程与温度的交互作用存在显著相关性；疏林地与坡向、降雨量与坡向坡度的交互作用均没有表现出相关性；有林地与高程降雨量的交互作用表现出显著正相关性。探讨不同植被类型对自然因素的响应，可为矿区植被结构的选择，矿区复垦提供参考依据。     

Deposition of BaSO4 in the tight junctions of amphibian epithelia causes their opening; apical Ca2+ reverses this effect

Selective deposition of BaSO₄ in the tight junctions (TJs) of frog skins led to profound and reversible functional alterations of these structures, as revealed by changes of tissue conductance (G), clamping current (I), and fluxes of extracellular markers (sulfate (J^SO ₄) and sucrose (J^SUC)). Experiments were performed with nominally Ca²⁺ -free simple salt solutions on the apical side (usually KCl) and Na₂SO₄-Ringer on the inner side of skins. The deposition of BaSO₄ in the TJs was obtained by diffusion and/or migration through the paracellular path of Ba²⁺ from the apical solution and SO ₄ ^2– from the inner solution. A brief presence (2 to 6 min) of apical Ba²⁺ (Ba²⁺ pulse) is followed (i.e., when Ba²⁺ is removed from the apical fluid) by a large increase of G, I, J^SO ₄ and J^SUC, above pre-Ba²⁺ levels. These attain a steady state within 15 to 30 min (overshoot phase), characterizing a conspicuous increase of the paracellular permeability. During the overshoot phase, a second Ba²⁺ pulse blocks the paracellular route while apical Ba²⁺ is present, leading to a new and larger overshoot when the Ba²⁺ pulse is terminated. Addition of apical Ca²⁺ triggers the resealing of the TJs, resulting in a full recovery of G, I, J^SO ₄ and J^SUC. This Ca²⁺ -induced recovery persists when apical Ca²⁺ is removed. The presence of a normal Ca²⁺ concentration in the inner bathing Ringer does not induce the recovery process. Tissues remain viable after being submitted to the Ba²⁺ treatment and the subsequent overshoot. Experiments performed in the urinary bladder of Rana catesbeiana and skins and urinary bladders of Bufo marinus indicate that Ba²⁺ effect can also be elicited in these tissues. The above results seem to report general properties of the TJs. Incidentally, they warn about the use of Ba²⁺ as an ion channel blocker in epithelial membranes in association with SO ₄ ^2– -containing solutions on the contralateral side.This project was supported by grants from Fundação de Amparo à Pesquisa do Estado de São Paulo (91/0293-7 to F.L.V., and 90/1788-1 to A.S.), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (410068/90-0 and 303633-85/BF to F.L.V.). J.A.C. received a doctoral fellowship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/Fundação Universidade do Rio Grande. We thank Dr. Alice T. Ferreira for help in the measurements of free Ca²⁺ concentration.