Using Links to prototype a Database Wiki

Both relational databases and wikis have strengths that make them attractive for use in collaborative applications. In the last decade, database-backed Web applications have been used extensively to develop valuable shared biological references called curated databases. Databases offer many advantages such as scalability, query optimization and concurrency control, but are not easy to use and lack other features needed for collaboration. Wikis have become very popular for early-stage biocuration projects because they are easy to use, encourage sharing and collaboration, and provide built-in support for archiving, history-tracking and annotation. However, curation projects often outgrow the limited capabilities of wikis for structuring and efficiently querying data at scale, necessitating a painful phase transition to a database-backed Web application. We perceive a need for a new class of general-purpose system, which we call a Database Wiki, that combines flexible wiki-like support for collaboration with robust database-like capabilities for structuring and querying data. This paper presents DBWiki, a design prototype for such a system written in the Web programming language Links. We present the architecture, typical use, and wiki markup language design for DBWiki and discuss features of Links that provided unique advantages for rapid Web/database application prototyping

Mesoscopic Luttinger Liquid Theory in an Aharonov-Bohm Ring

A careful study on the mesoscopic PC in a Luttinger liquid ring is carried out. It is shown that discreteness plays an important role in calculating the PC caused by the magnetic flux. At zero temperature, the current is shown to be independent of the interaction even when $g=g_2-g_4$ is not zero. The current becomes enhanced at finite temperatures comparing to the non-interacting case, when the parameter g is positive.Comment: 4 pages, 2 figures. Version to appear in PR

Organization of chromatin and histone modifications at a transcription site

According to the transcription factory model, localized transcription sites composed of immobilized polymerase molecules transcribe chromatin by reeling it through the transcription site and extruding it to form a surrounding domain of recently transcribed decondensed chromatin. Although transcription sites have been identified in various cells, surrounding domains of recently transcribed decondensed chromatin have not. We report evidence that transcription sites associated with a tandem gene array in mouse cells are indeed surrounded by or adjacent to a domain of decondensed chromatin composed of sequences from the gene array. Formation of this decondensed domain requires transcription and topoisomerase IIα activity. The decondensed domain is enriched for the trimethyl H3K36 mark that is associated with recently transcribed chromatin in yeast and several mammalian systems. Consistent with this, chromatin immunoprecipitation demonstrates a comparable enrichment of this mark in transcribed sequences at the tandem gene array. These results provide new support for the pol II factory model, in which an immobilized polymerase molecule extrudes decondensed, transcribed sequences into its surroundings

Quantitative comparison of camera technologies for cost-effective super-resolution optical fluctuation imaging (SOFI)

Van den Eynde R, Sandmeyer A, Vandenberg W, et al. Quantitative comparison of camera technologies for cost-effective super-resolution optical fluctuation imaging (SOFI). Journal of Physics: Photonics. 2019;1(4): 044001

Vulnerabilities to flood hazards among rural households in India

Flooding constitutes the most predominant natural disaster in India. The degree and causes of vulnerability to flood risk vary by society, geographical region and over time. The rural people of India are highly vulnerable to flood hazards due to high dependence on natural resources for livelihood and poor socio-economic situations. The information regarding the degree of vulnerability of these people is limited. In order to formulate improved adaption policies and effective programmes to reduce vulnerability, it is crucial to quantify the vulnerability of rural households affected by floods at a regional level. Our study provides insight into the vulnerability of rural households affected by floods in India. We use primary data of 220 flood-prone rural households of Odisha state in India for analysis. The vulnerability is analysed using the Livelihood Vulnerability Index and the Socio-economic Vulnerability Index. Our results show that these households are vulnerable to flood in more than one dimension. Sociodemographic characteristics such as a low literacy rate, a high dependency ratio and a weak housing structure increase these residents’ vulnerability. Access to social networks and social institutions plays a significant role in uplifting poor rural households. Our study concludes that the vulnerability of a household is governed by both non-climatic factors and the incidence of floods. The findings of our study may be considered in developing policies and programmes that will reduce the flood risk. The recommendations we suggested in this study can be applied in other south Asian counties with similar socio-economic profiles

Quantifying household vulnerability triggered by drought: evidence from rural India

Drought is a complex, slow-onset phenomenon that imposes serious challenges on human beings and ecosystems. The vulnerability associated with drought may vary at different social, geographical and temporal scales. These differences emphasize the need for regional-level vulnerability assessments, which in turn helps to formulate efficient adaptation policies and strategies that are suitable for the region to mitigate the drought risk. The objective of this paper is to quantify the livelihood and socio-economic vulnerability of rural households that are affected by drought in rural India. The Livelihood Vulnerability Index and Socioeconomic Vulnerability Index were applied to analyse the vulnerability of rural households. A sample size of 157 rural households from the state of Odisha in India was surveyed in 2015. Socio-demographic characteristics such as low literacy rates, high dependency ratios and weak housing structures make people more vulnerable, whereas access to social networks plays a significant role in supporting poor rural households. The research concludes that the impacts of drought make people who are already vulnerable due to poverty, inequality and marginalization even more vulnerable. The outcomes of this study may be considered in formulating effective coping strategies and policies that may help mitigate the drought risk. The findings and recommendations of this study will find applicability in other rural, natural resource-dependent countries with similar socio-economic profiles such as other south Asian countries

Photosynthetic Adaptation to Length of Day Is Dependent on S-Sulfocysteine Synthase Activity in the Thylakoid Lumen

Abstract Arabidopsis (Arabidopsis thaliana) chloroplasts contain two O-acetyl-serine(thiol)lyase (OASTL) homologs, OAS-B, which is an authentic OASTL, and CS26, which has S-sulfocysteine synthase activity. In contrast with OAS-B, the loss of CS26 function resulted in dramatic phenotypic changes, which were dependent on the light treatment. We have performed a detailed characterization of the photosynthetic and chlorophyll fluorescence parameters in cs26 plants compared with those of wild-type plants under short-day growth conditions (SD) and long-day growth conditions (LD). Under LD, the photosynthetic characterization, which was based on substomatal CO2 concentrations and CO2 concentration in the chloroplast curves, revealed significant reductions in most of the photosynthetic parameters for cs26, which were unchanged under SD. These parameters included net CO2 assimilation rate, mesophyll conductance, and mitochondrial respiration at darkness. The analysis also showed that cs26 under LD required more absorbed quanta per driven electron flux and fixed CO2. The nonphotochemical quenching values suggested that in cs26 plants, the excess electrons that are not used in photochemical reactions may form reactive oxygen species. A photoinhibitory effect was confirmed by the background fluorescence signal values under LD and SD, which were higher in young leaves compared with mature ones under SD. To hypothesize the role of CS26 in relation to the photosynthetic machinery, we addressed its location inside of the chloroplast. The activity determination and localization analyses that were performed using immunoblotting indicated the presence of an active CS26 enzyme exclusively in the thylakoid lumen. This finding was reinforced by the observation of marked alterations in many lumenal proteins in the cs26 mutant compared with the wild type.</jats:p

Linking Food Security with Household’s Adaptive Capacity and Drought Risk: Implications for Sustainable Rural Development

In spite of green revolution and rapid economic growth, India’s vast population still suffers from hunger and poverty, especially in the rural areas. Moreover, drought adversely affects India’s economy by declining agricultural production and purchasing power. It also escalates rural unemployment which ultimately affects household food security. Our study investigated the food security of drought prone rural households in a broader context by linking the dimensions of food security with dimensions of climate change vulnerability. We used the primary data of 157 drought prone rural households of Odisha state in India for analysis. This study employed polychoric principal component analysis to construct an aggregate food security index. An ordered probit model was used to estimate the determinants of food security. The FSI showed that three-fourth of the respondents were facing food security issues with varying degrees. The estimates of ordered probit model indicated that joint family, education, migration and health insurance are key variables that determine food security, whereas drought adversely affected food security of rural households. Overarching strategies are required to effectively address food security issues in the wake of increased drought risk. This study provides an insight for policy makers in India and in similar south Asian countries who must consider food security in the light of drought

The CORDEX.be initiative as a foundation for climate services in Belgium

The CORDEX.be project created the foundations for Belgian climate services by producing high-resolution Belgian climate information that (a) incorporates the expertise of the different Belgian climate modeling groups and that (b) is consistent with the outcomes of the international CORDEX ("COordinated Regional Climate Downscaling Experiment") project. The key practical tasks for the project were the coordination of activities among different Belgian climate groups, fostering the links to specific international initiatives and the creation of a stakeholder dialogue. Scientifically, the CORDEX.be project contributed to the EURO-CORDEX project, created a small ensemble of High-Resolution (H-Res) future projections over Belgium at convection-permitting resolutions and coupled these to seven Local Impact Models. Several impact studies have been carried out. The project also addressed some aspects of climate change uncertainties. The interactions and feedback from the stakeholder dialogue led to different practical applications at the Belgian national level

KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons

Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABAB receptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins