Lichtmeetprotocol : lichtmetingen in onderzoekskassen meet LED en SON-T belichting

Gedurende de laatste jaren is er in lichtonderzoek projecten een nieuw fenomeen ontstaan, t.w. de introductie van LEDs als assimilatie belichting in de glastuinbouw. Naar aanleiding daarvan heeft LNV en Productschap Tuinbouw in het kader van Kas als Energiebron opdracht gegeven aan WUR Glastuinbouw om een protocol te schrijven voor het meten van licht in SON-T en LED belichtingsystemen in onderzoekskassen. WUR Glastuinbouw heeft dit meetprotocol opgesteld in samenwerking met Plant Dynamics en WU Tuinbouwproductieketens. Dit protocol is vervolgens besproken en vastgesteld in een platform met Philips, Lemnis Lighting, Hortilux, KEMA en TNO

A pilot study on the use of tracking technology: Feasibility, acceptability, and benefits for people in early stages of dementia and their informal caregivers

Objectives: Caregivers and clinicians may be confronted with the dilemma whether to allow people in early stages of dementia to go outside independently with the risk of getting lost, or to limit their autonomy and mobility. Newly available technology may offer a solution. This pilot study is focused on the feasibility, acceptability, and effectiveness of a three-month use of Global Positioning System (GPS) by care receivers and caregivers. Method: Numbers and percentages of participants with positive responses to self-report questions were calculated. Differences between the pre- and post-test scores of role-overload and worry were tested with paired t-tests and effect-sizes were calculated. Results: Of the 33 dyads of care receivers and caregivers, 28 remained in the study (dropout rate 15%). The majority of the caregivers was able to use the technology and integrate the use into their daily routines and would recommend the use of GPS. Almost half of the participants with dementia experienced more freedom and were less worried when they were outside unaccompanied, a quarter mentioned that they were more outside independently and a fifth that they had less conflicts with their caregiver after three months. Caregivers showed a trend to feel less worried, especially caregivers who could reach their relative using the telephone connection. No changes in caregivers feelings of role-overload were found. Conclusion: The GPS device used in this study seems to be promising for people in early stages of dementia and their informal caregivers. A next step is to carry out a randomized controlled trial. © 2012 Taylor and Francis Group, LLC

Application of Artificial Neural Networks in Pharmacokinetics

Drug development is a long and expensive process. It is often not until potential drug candidates are administered to humans that accurate quantification of their pharmacokinetic characteristics is achieved. The goal of developing quantitative structure-pharmacokinetic relationships (QSPkRs) is to relate the molecular structure of a chemical entity with its pharmacokinetic characteristics. In this thesis artificial neural networks (ANNs) were used to construct in silico predictive QSPkRs for various pharmacokinetic parameters using different drug data sets. Drug pharmacokinetic data for all studies were taken from the literature. Information for model construction was extracted from drug molecular structure. Numerous theoretical descriptors were generated from drug structure ranging from simple constitutional and functional group counts to complex 3D quantum chemical numbers. Subsets of descriptors were selected which best modeled the target pharmacokinetic parameter(s). Using manual selective pruning, QSPkRs for physiological clearances, volumes of distribution, and fraction bound to plasma proteins were developed for a series of beta-adrenoceptor antagonists. All optimum ANN models had training and cross-validation correlations close to unity, while testing was performed with an independent set of compounds. In most cases the ANN models developed performed better than other published ANN models for the same drug data set. The ability of ANNs to develop QSPkRs with multiple target outputs was investigated for a series of cephalosporins. Multilayer perceptron ANN models were constructed for prediction of half life, volume of distribution, clearances (whole body and renal), fraction excreted in the urine, and fraction bound to plasma proteins. The optimum model was well able to differentiate compounds in a qualitative manner while quantitative predictions were mostly in agreement with observed literature values. The ability to make simultaneous predictions of important pharmacokinetic properties of a compound made this a valuable model. A radial-basis function ANN was employed to construct a quantitative structure-bioavailability relationship for a large, structurally diverse series of compounds. The optimum model contained descriptors encoding constitutional through to conformation dependent solubility characteristics. Prediction of bioavailability for the independent testing set were generally close to observed values. Furthermore, the optimum model provided a good qualitative tool for differentiating between drugs with either low or high experimental bioavailability. QSPkR models constructed with ANNs were compared with multilinear regression models. ANN models were shown to be more effective at selecting a suitable subset of descriptors to model a given pharmacokinetic parameter. They also gave more accurate predictions than multilinear regression equations. This thesis presents work which supports the use of ANNs in pharmacokinetic modeling. Successful QSPkRs were constructed using different combinations of theoretically-derived descriptors and model optimisation techniques. The results demonstrate that ANNs provide a valuable modeling tool that may be useful in drug discovery and development

Comparative genomics among members of the Streptococcus bovis/Streptococcus equinus complex

Background: Today, only one streptococcal species, i.e. Streptococcus thermophilus is recognized as food-grade. Interestingly, other streptococci like Streptococcus macedonicus and Streptococcus infantarius belonging to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) are also found in food matrices. However, these species are phylogenetically related to Streptococcus gallolyticus and Streptococcus pasteurianus that have been linked to endocarditis, bacteremia and colon cancer. Objectives: To compare the available genomes of the members of the SBSEC in order to shed light onto their evolution and phylogenetic relation and to assess in silico their pathogenic potential. Methods: Comparative genomics analysis including full chromosome and CDS alignments, whole genome phylogeny and evaluation of gene content (e.g. core genome, singletons, etc.) was performed with appropriate bioinformatics tools. Conclusions: Despite the fact that the four species of the SBSEC were found tightly related based on whole genome phylogeny, there were two different patterns of evolution among them. Streptococcus pasteurianus, S. macedonicus and S. infantarius seem to have undergone a reductive evolution process that resulted in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to S. gallolyticus. In addition, S. pasteurianus, S. macedonicus and S. infantarius seem to have lost several genes previously linked to the ability of S. gallolyticus to survive in the gastrointestinal tract of herbivores and to its pathogenicity. Our findings indicate differences in the ecological niche and the pathogenic potential among the four species

Diversidade nucleotídica de genes envolvidos na biossíntese de ácidos clorogênicos de cafeeiros.

Os ácidos clorogênicos (CGAs) são compostos químicos importantes de Coffea spp. para a qualidade da bebida, pois eles interferem na adstringência e podem alterar o aroma e sabor da bebida. Aproximadamente 310.000 ESTs de Coffea estão disponíveis e possibilitam o acesso à variabilidade nucleotídica da planta e o desenvolvimento de marcadores moleculares ligados à qualidade da bebida para as principais enzimas da via de biossíntese dos CGAs: PAL, C4H, 4CL, CQT e C3?H. Neste trabalho foram detectados polimorfismos dos tipos SNP, INDEL ou SSR dentro das sequências nucleotídidicas disponíveis no Projeto Genoma Café e no NCBI. As sequências de ESTs de CGAs foram clusterizadas pelo programa Codon Code Aligner, assim como a detecção de polimorfismos e validação dos mesmos (qualidade de cromatograma). Foram identificadas seis isoformas para PAL, uma para C4H, seis para 4CL, duas para CQT e duas para C3?H. Os contigs formados apresentaram um total de 248 polimorfismos (236 SNPs e 12 INDELs), sendo 201 na região codante (127 não sinônimos e 74 sinônimos). A frequência dos polimorfismos foi maior nas regiões UTRs (1pol/54pb), em relação à codante (1pol/81pb). A análise das sequências de C. arabica permitiu a identificação de 2 subgrupos diferentes de sequências, referentes aos seus genomas ancestrais (C. canephora e C. eugenioides). Foi observada a presença de 67,4% dos polimorfismos entre os grupos ancestrais e 32,6% dentro dos grupos em C. arabica. Esses resultados vêm permitindo definir genes tanto para estudos de expressão de homeólogos de CGAs como para o desenvolvimento de marcadores moleculares para o mapeamento genético

RUST: Latent Neural Scene Representations from Unposed Imagery

Inferring the structure of 3D scenes from 2D observations is a fundamental challenge in computer vision. Recently popularized approaches based on neural scene representations have achieved tremendous impact and have been applied across a variety of applications. One of the major remaining challenges in this space is training a single model which can provide latent representations which effectively generalize beyond a single scene. Scene Representation Transformer (SRT) has shown promise in this direction, but scaling it to a larger set of diverse scenes is challenging and necessitates accurately posed ground truth data. To address this problem, we propose RUST (Really Unposed Scene representation Transformer), a pose-free approach to novel view synthesis trained on RGB images alone. Our main insight is that one can train a Pose Encoder that peeks at the target image and learns a latent pose embedding which is used by the decoder for view synthesis. We perform an empirical investigation into the learned latent pose structure and show that it allows meaningful test-time camera transformations and accurate explicit pose readouts. Perhaps surprisingly, RUST achieves similar quality as methods which have access to perfect camera pose, thereby unlocking the potential for large-scale training of amortized neural scene representations.Comment: CVPR 2023 Highlight. Project website: https://rust-paper.github.io

Comparative genomics of Streptococcus macedonicus ACA-DC 198 against related species within the Streptococcus bovis/Streptococcus equinus complex

Apart from Streptococcus thermophilus other streptococci that can be found growing in milk belong to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Interestingly, Streptococcus macedonicus, which is a member of SBSEC, has been suggested to be adapted to milk and to be nonpathogenic. However, the species is phylogenetically related to Streptococcus gallolyticus and Streptococcus pasteurianus (formerly known as S. bovis biotypes I and II.2, respectively), which in turn are considered pathogenic, since they have been implicated in endocarditis and colon cancer in humans. Comparative analysis of the S. macedonicus genome with the complete genomes of its related streptococci (including that of S. infantarius, which is also a dairy isolate) indicated that a significant portion of the genomic organization has been conserved overall. Following a gene presence/absence strategy, we determined that S. macedonicus shows a reduced capacity to reside in the gastrointestinal tract of ruminants when compared to S. gallolyticus since it misses important genes for metabolizing complex carbohydrates of plant origin and for detoxifying this environment. S. macedonicus also lacks several pathogenicity traits found in S. gallolyticus. For example from the three pilus gene clusters (pil1, pil2, pil3), which may mediate the binding of S. gallolyticus to the extracellular matrix, S. macedonicus carries only one (i.e. the pil3). Gene gain events are also evident in the S. macedonicus genome sometimes originating from dairy bacteria, like the acquisition of the lactococcal plasmid pSMA198. Functional analysis of the S. macedonicus genome is necessary to further assess its pathogenic and technological potential

Polimorfismos nucleotidicos de genes envolvidos nas características químicas do grão de café. Complementaridade das estratégias in silico e in vivo.

A compreensão das bases genéticas da composição química do grão de café é indispensável para a gestão dos programas de melhoramento que têm como objetivo a qualidade da bebida. O desenvolvimento da genômica permite hoje a identificação de genes candidatos que são potencialmente envolvidos nessas características. Entretanto, a utilização destas novas ferramentas para o melhoramento depende da capacidade de identificar dentro de todos esses candidatos,, os que controlam a variabilidade das características entre genótipos. Essa identificação envolve o teste das relações entre os polimorfismos dos genes e a variabilidade fenotípica. A avaliação da diversidade nucleotídica pode ser feita de duas maneiras: usando as informações disponíveis nos bancos de dados EST (estratégia in silico) ou por seqüênciamento direto de genótipos de interesse (estratégia in vivo). O objetivo desse estudo foi avaliar o potencial da estratégia de analise de polimorfismos in silico para o café baseado nos bancos de dados disponíveis. Foram estudadas as vias da biossíntese da sacarose e dos diterpenos, compostos com efeitos na qualidade da bebida e na saúde humana, respectivamente. Essa busca permitiu a identificação de 1.1 polimorfismos para cada 100 bp para os 14 genes estudados. Uma avaliação da diversidade nucleotídica in vivo para alguns desses genes (via da biossíntese da sacarose) permitiu comparar essas duas estratégias. A estratégia in silico é complementar à estratégia in vivo permitindo uma avaliação geral dos níveis de polimorfismos dos genes numa larga escala em todo o genoma com um baixo custo