Applications of a Biomechanical Patient Model for Adaptive Radiation Therapy

Biomechanical patient modeling incorporates physical knowledge of the human anatomy into the image processing that is required for tracking anatomical deformations during adaptive radiation therapy, especially particle therapy. In contrast to standard image registration, this enforces bio-fidelic image transformation. In this thesis, the potential of a kinematic skeleton model and soft tissue motion propagation are investigated for crucial image analysis steps in adaptive radiation therapy. The first application is the integration of the kinematic model in a deformable image registration process (KinematicDIR). For monomodal CT scan pairs, the median target registration error based on skeleton landmarks, is smaller than (1.6 ± 0.2) mm. In addition, the successful transferability of this concept to otherwise challenging multimodal registration between CT and CBCT as well as CT and MRI scan pairs is shown to result in median target registration error in the order of 2 mm. This meets the accuracy requirement for adaptive radiation therapy and is especially interesting for MR-guided approaches. Another aspect, emerging in radiotherapy, is the utilization of deep-learning-based organ segmentation. As radiotherapy-specific labeled data is scarce, the training of such methods relies heavily on augmentation techniques. In this work, the generation of synthetically but realistically deformed scans used as Bionic Augmentation in the training phase improved the predicted segmentations by up to 15% in the Dice similarity coefficient, depending on the training strategy. Finally, it is shown that the biomechanical model can be built-up from automatic segmentations without deterioration of the KinematicDIR application. This is essential for use in a clinical workflow

Mitigation needs adaptation: Tropical forestry and climate change

International audienceThe relationship between tropical forests and global climate change has so far focused on mitigation, while much less emphasis has been placed on how management activities may help forest ecosystems adapt to this change. This paper discusses how tropical forestry practices can contribute to maintaining or enhancing the adaptive capacity of natural and planted forests to global climate change and considers challenges and opportunities for the integration of tropical forest management in broader climate change adaptation. In addition to the use of reduced impact logging to maintain ecosystem integrity, other approaches may be needed, such as fire prevention and management, as well as specific silvicultural options aimed at facilitating genetic adaptation. In the case of planted forests, the normally higher intensity of management (with respect to natural forest) offers additional opportunities for implementing adaptation measures, at both industrial and smallholder levels. Although the integration in forest management of measures aimed at enhancing adaptation to climate change may not involve substantial additional effort with respect to current practice, little action appears to have been taken to date. Tropical foresters and forest-dependent communities appear not to appreciate the risks posed by climate change and, for those who are aware of them, practical guidance on how to respond is largely non-existent. The extent to which forestry research and national policies will promote and adopt management practices in order to assist production forests adapt to climate change is currently uncertain. Mainstreaming adaptation into national development and planning programs may represent an initial step towards the incorporation of climate change considerations into tropical forestry

IT Policy di Perusahaan Pelayaran

Kemajuan teknologi informasi, serta sistem informasi dan ilmu pengetahuannya, telah berkembang pesat dan terus maju di era globalisasi ini. Sistem informasi memegang peranan yang sangat penting dalam mengorganisasikan informasi menjadi informasi dan sebagai alat komunikasi untuk memudahkan komunikasi dengan orang lain. Salah satu yang termasuk dalam komponen sebuah sistem informasi adalah adanya bentuk dari software/perangkat lunak. Maka dari itu, pada penelitian kami kali ini, fokus pembahasan dari tim kami adalah untuk membahas tentang permasalahan software yang dialami oleh perusahaan Pelayaran. Adapun penelitian ini dilakukan dengan tujuan untuk menganalisis bagaimana kondisi penggunaan software accounting yang digunakan oleh perusahaan Pelayaran dari segi aturan dan kondisi kesehariannya, kemudian menemukan solusi terkait masalah program yang bersifat lemot tersebut. Dalam melakukan penelitian ini, Metode penelitian yang kami gunakan adalah dengan mengawali melalui proses studi literatur, lalu mengumpulkan data, kemudian mengolah data, dan pada akhirnya menjadi bentuk analisa dan hasil. Pada pembahasan ini, kami telah mengumpulkan keterangan dari narasumber tentang bagaimana kendala penggunaan software yang sempat dialami. Kegagalan software dikarenakan kegagalan yang terjadi pada perangkat lunak atau software sehingga menyebabkan gangguan atau kerusakan yang dapat membuat pengguna mengalami perlambatan waktu ketika gangguan itu terjadi. Dalam   mengatasi permasalahan ini, hal yang dilakukan adalah dengan cara melakukan uji coba untuk menemukan sumber dari masalah perangkat lunak tersebut dan dengan cepat dilakukannya perbaikan terhadap kegagalan software atau perangkat lunak agar meningkatkan efisiensi ketika menggunakan perangkat lunak. Adapun faktor lain yang mungkin menjadi penyebab dari permasalahan yang terjadi adalah ketika IT Policy dan SOP perusahaan yang tidak dijalankan dengan baik yang kemudian memberikan dampak dari segi kualitas bekerja seorang karyawan

Is local best? Examining the evidence for local adaptation in trees and its scale

Background: Although the importance of using local provenance planting stock for woodland production, habitat conservation and restoration remains contentious, the concept is easy to understand, attractive and easy to ‘sell’. With limited information about the extent and scale of adaptive variation in native trees, discussion about suitable seed sources often emphasises “local” in a very narrow sense or within political boundaries, rather than being based on sound evidence of the scale over which adaptation occurs. Concerns exist over the actual scale (magnitude and spatial scale) of adaptation in trees and the relative dangers of incorrect seed source or restricted seed collection, leading to the establishment of trees with restricted genetic diversity and limited adaptive potential. Tree provenance and progeny field trials in many parts of the world have shown the existence of genotype by environment interaction in many tree species, but have not necessarily looked at whether this is expressed as a home site advantage (i.e. whether provenance performance is unstable across sites, and there is better performance of a local seed source). Methods/design: This review will examine the evidence for local adaptation and its scale in a number of native tree species from different trial sites across the globe (e.g. tropical, Mediterranean, temperate). These trials have been measured and in some cases results published in a range of formats. The data have, however, usually been presented in the form of which provenances grow best at which sites. The review will examine existing data (published and unpublished) in the context of the scale of local adaptation, with the results being presented in two formats: (a) relating survival, performance of provenances (classified by seed zone/provenance region of origin) to seed zone/provenance region of the planting site; (b) plotting survival, performance provenances against the distance (Euclidean/ecological) between the provenance and the trial site.EEA BarilocheFil: Boshier, David. University of Oxford. Department of Plant Sciences; Reino UnidoFil: Broadhurst, Linda. CSIRO National Research Collections Australia (NRCA). Centre for Australian National Biodiversity Research (CANBR); AustraliaFil: Cornelius, Jonathan. International Center for Research in Agroforestry. World Agroforestry Centre; PerúFil: Gallo, Leonardo Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Koskela, Jarkko. FAO; ItaliaFil: Loo, Judy. Bioversity International; ItaliaFil: Petrokofsky, Gillian. University of Oxford. Department of Zoology; Reino UnidosFil: St Clair, Bradley. US Forest Service. Pacific Northwest Research Station; Estados Unido

Is local best? Examining the evidence for local adaptation in trees and its scale

Background: Although the importance of using local provenance planting stock for woodland production, habitat conservation and restoration remains contentious, the concept is easy to understand, attractive and easy to ‘sell’. With limited information about the extent and scale of adaptive variation in native trees, discussion about suitable seed sources often emphasises “local” in a very narrow sense or within political boundaries, rather than being based on sound evidence of the scale over which adaptation occurs. Concerns exist over the actual scale (magnitude and spatial scale) of adaptation in trees and the relative dangers of incorrect seed source or restricted seed collection, leading to the establishment of trees with restricted genetic diversity and limited adaptive potential. Tree provenance and progeny field trials in many parts of the world have shown the existence of genotype by environment interaction in many tree species, but have not necessarily looked at whether this is expressed as a home site advantage (i.e. whether provenance performance is unstable across sites, and there is better performance of a local seed source). Methods/design: This review will examine the evidence for local adaptation and its scale in a number of native tree species from different trial sites across the globe (e.g. tropical, Mediterranean, temperate). These trials have been measured and in some cases results published in a range of formats. The data have, however, usually been presented in the form of which provenances grow best at which sites. The review will examine existing data (published and unpublished) in the context of the scale of local adaptation, with the results being presented in two formats: (a) relating survival, performance of provenances (classified by seed zone/provenance region of origin) to seed zone/provenance region of the planting site; (b) plotting survival, performance provenances against the distance (Euclidean/ecological) between the provenance and the trial site.EEA BarilocheFil: Boshier, David. University of Oxford. Department of Plant Sciences; Reino UnidoFil: Broadhurst, Linda. CSIRO National Research Collections Australia (NRCA). Centre for Australian National Biodiversity Research (CANBR); AustraliaFil: Cornelius, Jonathan. International Center for Research in Agroforestry. World Agroforestry Centre; PerúFil: Gallo, Leonardo Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Koskela, Jarkko. FAO; ItaliaFil: Loo, Judy. Bioversity International; ItaliaFil: Petrokofsky, Gillian. University of Oxford. Department of Zoology; Reino UnidosFil: St Clair, Bradley. US Forest Service. Pacific Northwest Research Station; Estados Unido

FRET-Based Detection of M1 Muscarinic Acetylcholine Receptor Activation by Orthosteric and Allosteric Agonists

Muscarinic acetylcholine receptors (mAChRs) are 7-transmembrane, G protein-coupled receptors that regulate a variety of physiological processes and represent potentially important targets for therapeutic intervention. mAChRs can be stimulated by full and partial orthosteric and allosteric agonists, however the relative abilities of such ligands to induce conformational changes in the receptor remain unclear. To gain further insight into the actions of mAChR agonists, we have developed a fluorescently tagged M(1) mAChR that reports ligand-induced conformational changes in real-time by changes in Förster resonance energy transfer (FRET).Variants of CFP and YFP were inserted into the third intracellular loop and at the end of the C-terminus of the mouse M(1) mAChR, respectively. The optimized FRET receptor construct (M(1)-cam5) was expressed stably in HEK293 cells.The variant CFP/YFP-receptor chimera expressed predominantly at the plasma membrane of HEK293 cells and displayed ligand-binding affinities comparable with those of the wild-type receptor. It also retained an ability to interact with Gα(q/11) proteins and to stimulate phosphoinositide turnover, ERK1/2 phosphorylation and undergo agonist-dependent internalization. Addition of the full agonist methacholine caused a reversible decrease in M(1) FRET (F(EYFP)/F(ECFP)) that was prevented by atropine pre-addition and showed concentration-dependent amplitude and kinetics. Partial orthosteric agonists, arecoline and pilocarpine, as well as allosteric agonists, AC-42 and 77-LH-28-1, also caused atropine-sensitive decreases in the FRET signal, which were smaller in amplitude and significantly slower in onset compared to those evoked by methacholine.The M(1) FRET-based receptor chimera reports that allosteric and orthosteric agonists induce similar conformational changes in the third intracellular loop and/or C-terminus, and should prove to be a valuable molecular reagent for pharmacological and structural investigations of M(1) mAChR activation

Comparison of the Pathogenic Potential of Campylobacter jejuni, C. upsaliensis and C. helveticus and Limitations of Using Larvae of Galleria mellonella as an Infection Model

Campylobacter enteritis in humans is primarily associated with C. jejuni/coli infection. Other species cause campylobacteriosis relatively infrequently; while this could be attributed to bias in diagnostic methods, the pathogenicity of non-jejuni/coli Campylobacter spp. such as C. upsaliensis and C. helveticus (isolated from dogs and cats) is uncertain. Galleria mellonella larvae are suitable models of the mammalian innate immune system and have been applied to C. jejuni studies. This study compared the pathogenicity of C. jejuni, C. upsaliensis, and C. helveticus isolates. Larvae inoculated with either C. upsaliensis or C. helveticus showed significantly higher survival than those inoculated with C. jejuni. All three Campylobacter species induced indistinguishable histopathological changes in the larvae. C. jejuni could be isolated from inoculated larvae up to eight days post-inoculation whereas C. upsaliensis and C. helveticus could only be isolated in the first two days. There was a significant variation in the hazard rate between batches of larvae, in Campylobacter strains, and in biological replicates as random effects, and in species and bacterial dose as fixed effects. The Galleria model is applicable to other Campylobacter spp. as well as C. jejuni, but may be subject to significant variation with all Campylobacter species. While C. upsaliensis and C. helveticus cannot be considered non-pathogenic, they are significantly less pathogenic than C. jejuni

Distinct synaptic transfer functions in same-type photoreceptors

Many sensory systems use ribbon-type synapses to transmit their signals to downstream circuits. The properties of this synaptic transfer fundamentally dictate which aspects in the original stimulus will be accentuated or suppressed, thereby partially defining the detection limits of the circuit. Accordingly, sensory neurons have evolved a wide variety of ribbon geometries and vesicle pool properties to best support their diverse functional requirements. However, the need for diverse synaptic functions does not only arise across neuron types, but also within. Here we show that UV-cones, a single type of photoreceptor of the larval zebrafish eye, exhibit striking differences in their synaptic ultrastructure and consequent calcium to glutamate transfer function depending on their location in the eye. We arrive at this conclusion by combining serial section electron microscopy and simultaneous ‘dual-colour’ two-photon imaging of calcium and glutamate signals from the same synapse in vivo. We further use the functional dataset to fit a cascade-like model of the ribbon synapse with different vesicle pool sizes, transfer rates, and other synaptic properties. Exploiting recent developments in simulation-based inference, we obtain full posterior estimates for the parameters and compare these across different retinal regions. The model enables us to extrapolate to new stimuli and to systematically investigate different response behaviours of various ribbon configurations. We also provide an interactive, easy-to-use version of this model as an online tool. Overall, we show that already on the synaptic level of single-neuron types there exist highly specialised mechanisms which are advantageous for the encoding of different visual features

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future