Miracle-dz/UniFAR-FTUs huggingface dataset:
Functions of Candida albicans cell wall glycosidases Dfg5p and Dcw1p in biofilm formation and HOG MAPK pathway

Background Candida albicans is a commensal fungus that inhabits the oral mucosal surface and causes oral and systemic candidiasis. Oral candidiasis most commonly occurs in patients with AIDS, denture wearers and newborn children. Systemic candidiasis occurs mainly in immunocompromised patients and patients admitted to hospitals for prolonged periods. C. albicans homologous genes, DFG5 and DCW1, encode for two closely related cell wall proteins with putative glycosyltransferase enzyme activity and C-terminal GPI-anchors. Past studies have shown that individual DFG5 and DCW1 mutations are viable but simultaneous deletion of DFG5 and DCW1 in C. albicans results in lethality. However, the exact functions of these cell wall based enzymes, which represent potential drug targets, are not understood. Methods C. albicans DFG5/DCW1 heterologous and conditional double mutant strains were assessed for growth and biofilm formation in comparison to wild type and parental strains. Cell wall and heat stress susceptibility of the mutant and control strains were assessed using agar spotting assays. Growth was assessed under normal and osmotic stress conditions along with light microscopy imaging. Biofilm dry weight and microscopic imaging analysis of biofilms was performed. Hypha formation in response to serum was analyzed using light microscopy imaging. Western blot analysis of mutant strains and control strains was performed to assess Hog1 basal levels and phosphorylation status. Results Analysis of the heterologous mutants indicated that Dfg5p is more important for growth while Dcw1p appeared to play a role in cell wall integrity response. The conditional double mutant was observed to be less resistant to cell wall stress. However, growth of the mutants was similar under control and osmotic stress conditions. The mutants were also able to grow similar to wild type under heat stress. Biofilm formation was reduced in the mutants where DFG5 was deleted or suppressed. Hyphal morphogenesis was reduced although germ tube formation was observed in the biofilms of the mutant strains. Basal Hog1 protein levels were reduced or absent in the DFG5 and DCW1 mutants. However, osmotic stress was able to induce Hog1 protein levels comparable to wild type. Hog1 phosphorylation appeared to be slightly reduced although not significantly. In addition to biofilm assays, serum dose response imaging analysis indicated that hyphae formation in DFG5 and DCW1 mutants was defective. Conclusions These data indicate that DFG5 and DCW1 are required for hyphal morphogenesis and biofilm formation in C. albicans. These functions may be regulated via basal Hog1 MAPK which is required for transcriptional regulation of chitin synthesis.
The posttranslational modification of tubulin undergoes a switch from detyrosination to acetylation as epithelial cells become polarized

Polarity leads to a shift in tubulin modification and microtubule organization. In unpolarized epithelial cells, detyrosinated microtubules point to the spreading edge, but in polarized cells, acetylated microtubules point to the apical domain. In both cases the modified microtubules are oriented to support cargo transport to areas of high need.
The study of clinico-pathological correlation and treatment outcome in acute allograft rejection in the immediate post renal transplant period

Background: The kidney Tx is the treatment of choice for patients with ESRD. However, episodes of AR have a negative impact on short- and long-term graft survival. In spite of immunosuppressive medications, CNI, MMF and steroid, the AR remains a crucial problem for Tx. This analysis was performed to evaluate the changing profile of early AR (during first week of transplant) and its repercussions on graft survival.Methods: This study was an observational cohort study and included 50 renal transplant patients irrespective of age, sex and race who developed bx proven AR within first week of transplant. Three groups were made according to histopathology: ACR, AMR and mixed rejection group. The patients were followed for 6 months thereafter.Results: AR within a week of renal Tx were less symptomatic except decrease in UO. ACR was more common (72%) than AMR and mixed rejections. AMR and Mixed group required more therapeutic modalities than ACR. More patients required HD during AR in AMR and mixed rejection group than ACR. The mean s.cr at 6 months was 1.3,1.5 and 1.6 in ACR, AMR and mixed group respectively. There were more incidences of BK viremia, CMV infection UTI and rejection fronts follow up in AMR and mixed group than ACR group.Conclusions: Acute rejections within a week are less symptomatic and ACR occurred more frequently than AMR and mixed rejection There were more incidences of BKV, CMV and UTI for 6 months follow up in AMR and Mixed rejection group.
Host developmental stage is associated with shifts in the exosphere microbiome of urban-farmed Asian green leafy vegetables

Green leafy vegetables (GLV’s) comprise a significant part of urban South-East Asian (SEA) diets and are intensively farmed in SEA cities, including Singapore. Urban farming practices and urban-adapted vegetable cultivars likely select for specific above- and below-ground microbial communities – microbiomes – that assemble in close proximity to the plant tissues – the exosphere. A healthy exosphere microbiome is important for plant growth and safe human consumption. Using 16S rDNA gene amplicon sequencing compositional analyses, we show here that the exosphere microbiome of two commonly-consumed GLV’s – Choy Sum (Brassica oleracea Alboglabra Group) and Gai Lan (Brassica chinensis var. parachinensis) – dominated by Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Actinobacteria. Shifts in exosphere microbiome composition were strongly associated with plant developmental stage. Finally, microbial taxa consistently detected in the exosphere comprise a small subset, which are predicted to harbour plant-beneficial traits. Significance Among plant crops, GLVs form an integral part of the Asian diet, especially so in Southeast Asia. Some of these GLVs have short life-cycles (∽30-45 days), which makes them suitable for urban farms in terms of cost advantage as short cycle crops are preferred in urban farms. From a food-security perspective, GLVs forms an important target food group and efforts are being made to increase its productivity to meet the increasing food demands. Current farming practices often place lot of importance on chemical fertilizers and nutrient inputs to improve the fertility of non-arable urban lands to increase the crop productivity. Furthermore, farms in urban settings are also associated with anthropogenic inputs and eutrophic conditions. These together, contribute to negative environmental externalities questioning the sustainability and eco-sustenance of urban farming. Microbial based management systems can not only resolve these challenging issues, but can also enhance plant growth, nutrient use efficiency and disease tolerance. However, their use as microbial adjuncts to agricultural practices is currently limited in urban environments, which could possibly be due to the restricted knowledge-base on these urban phytobiomes.
Modulation of Atlantic Basin Tropical Cyclone Activity by the Madden–Julian Oscillation (MJO) from 1905 to 2011

The Madden‐Julian oscillation (MJO) has been demonstrated to play a role in tropical cyclone (TC) activity around the globe in a number of recent studies. While the impact of the MJO on TCs in the Atlantic basinsincethemid-1970shasbeenwelldocumented,anewlydeveloped107-yr-longindexfortheMJOallows for additional analysis of the impacts of the MJO on Atlantic TC activity. TC activity in the Atlantic increases whenMJO-relatedconvectionisenhancedoverAfricaandtheIndianOcean,whileTCactivityintheAtlanticis suppressed whentheMJOenhancesconvectionoverthewesternPacific. Thislong-term recordoftheMJOalso allows for the analysis of how the MJO’s impacts may be modulated by other climate modes, such as the El Nino‐Southern Oscillation (ENSO) over interannual time scales and the Atlantic multidecadal oscillation (AMO) over multidecadal time scales. When climatologically unfavorable conditions such as an El Nino event or a negative AMO phase are present, even TC-favorable MJO conditions are not enough to generate statistically significant increases in TC activity from the long-term average across the Atlantic basin. However, climatologicallyfavorableconditionsduringaLaNinaeventorawarmAMOphaseacttoenhancethemodulation of TC activity over the Atlantic basin by the MJO.
Fast and Accurate Clustering of Single Cell Epigenomes Reveals Cis-Regulatory Elements in Rare Cell Types

Abstract Mammalian tissues are composed of highly specialized cell types defined by distinct gene expression patterns. Identification of cis-regulatory elements responsible for cell-type specific gene expression is essential for understanding the origin of the cellular diversity. Conventional assays to map cis-elements via open chromatin analysis of primary tissues fail to resolve their cell type specificity and lack the sensitivity to identify cis-elements in rare cell types. Single nucleus analysis of transposase-accessible chromatin (ATAC-seq) can overcome this limitation, but current analysis methods begin with pre-defined genomic regions of accessibility and are therefore biased toward the dominant population of a tissue. Here we report a method, Single Nucleus Analysis Pipeline for ATAC-seq (SnapATAC), that can efficiently dissect cellular heterogeneity in an unbiased manner using single nucleus ATAC-seq datasets and identify candidate regulatory sequences in constituent cell types. We demonstrate that SnapATAC outperforms existing methods in both accuracy and scalability. We further analyze 64,795 single cell chromatin profiles from the secondary motor cortex of mouse brain, creating a chromatin landscape atlas with unprecedent resolution, including over 300,000 candidate cis-regulatory elements in nearly 50 distinct cell populations. These results demonstrate a systematic approach for comprehensive analysis of cis-regulatory sequences in the mammalian genomes.
Deformations of Scalar-Flat Anti-Self-Dual metrics and Quotients of Enriques Surfaces

In this article, we prove that a quotient of a K3 surface by a free Z_2+Z_2 action does not admit any metric of positive scalar curvature. This shows that the scalar flat anti self-dual metrics (SF-ASD) on this manifold can not be obtained from a family of metrics for which the scalar curvature changes sign, contrary to the previously known constructions of this kind of metrics on manifolds of b+=0.
BIPARTITE GRAPH SAMPLING METHODS FOR SAMPLING RECOMMENDATION DATA

Sampling is the common practice involved in academic and industry efforts on recommendation algorithm evaluation and selection. Experimental analysis often uses a subset of the entire useritem interaction data available in the operational recommender system, often derived by including all transactions associated with a subset of uniformly randomly selected users. Our paper formally studies the sampling problem for recommendation to understand to what extent population-based algorithm evaluation results correspond with sample-based results using different sampling methods. We use a bipartite graph to represent the key input data of user-item interaction for recommendation algorithms and build on the literature on unipartite graph sampling to develop sampling methods for our context of bipartite graph sampling. We also developed several metrics for assessing the quality of a given sample, including performance recovery and ranking recovery measures for assessing both single-sample and multiple-sample recovery performances. Based on the empirical results from two real-world datasets we provide some general recommendations for sampling for recommendation algorithm evaluation.
The AETG System: An Approach to Testing Based on Combinatiorial Design

This paper describes a new approach to testing that uses combinatorial designs to generate tests that cover the pairwise, triple, or n-way combinations of a system's test parameters. These are the parameters that determine the system's test scenarios. Examples are system configuration parameters, user inputs and other external events. We implemented this new method in the AETG system. The AETG system uses new combinatorial algorithms to generate test sets that cover all valid n-way parameter combinations. The size of an AETG test set grows logarithmically in the number of test parameters. This allows testers to define test models with dozens of parameters. The AETG system is used in a variety of applications for unit, system, and interoperability testing. It has generated both high-level test plans and detailed test cases. In several applications, it greatly reduced the cost of test plan development.
Improving Open Data Usability through Semantics

With the success of Open Data a huge amount of tabular data become available that could potentially be mapped and linked into the Web of (Linked) Data. The use of semantic web technologies would then allow to explore related content and enhanced search functionalities across data portals. However, existing linkage and labeling approaches mainly rely on mappings of textual information to classes or properties in knowledge bases. In this work we outline methods to recover the semantics of tabular Open Data and to identify related content which allows a mapping and automated integration/categorization of Open Data resources and improves the overall usability and quality of Open Data.
SplitsTree: analyzing and visualizing evolutionary data

MOTIVATION Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.
Drosophila TIE-DYE : a combinatorial marking system to visualize and genetically manipulate clones during development in Drosophila melanogaster

INTRODUCTION During the development of an organism, the fate of cells is regulated by both lineage and extracellular signals. Thus, to understand the development of a tissue or an organ there is a need to describe the origin of cells as well as interactions between cells. Additionally, there are modes of regulation affecting organ size determination and tissue homeostasis that can only be appreciated by studying the tissue as a whole rather than by examining the properties of individual cells. Studying these phenomena would be greatly aided by methods that enable tracking the lineage of many cells within an organ and at the same time examining the consequences of local perturbations on the tissue as a whole. Experiments to track cell lineages during development have been performed in many different ways (reviewed by Kretzschmar and Watt, 2012), including the study of gynandromorphs (Sturtevant, 1929; Garcia-Bellido and Merriam, 1969), by using chimeric embryos (Le Douarin and Barq, 1969), and by injecting dyes or enzymes into individual cells in order to label their progeny (Weisblat et al., 1978). More recently, genetic systems that stochastically label cells and all of their progeny have been used to study cell lineages. In addition, by combining systems that direct site-specific recombination with genes encoding multiple fluorescent proteins, it has become possible to label multiple lineages uniquely in a tissue simultaneously as was achieved with the Brainbow system (Livet et al., 2007) in the mouse nervous system. This sparked the creation of multicolor labeling systems in other model organisms, which have been used to map multiple single cell projections in the nervous system (Livet et al., 2007;
A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1

The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na+) transporter, as being a major factor controlling natural variation in leaf Na+ accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na+ in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.
Distinct Expression Pattern of Circulating MiRNA-1, MiRNA-133a and Mirna-133b in STEMI and NSTEMI

Objective: miR-1 miR-133a and miR-133b release into the circulation during the early stages of acute coronary syndrome (ACS). However, their discriminative expression pattern in ST-elevation myocardial infarction (STEMI) and Non-STelevation myocardial infarction (NSTEMI) remains unknown. The present study aims to characterize and compare the circulating miR-1, miR-133a and miR-133b expression levels in peripheral blood samples of ACS patients to determine their discriminative expression pattern of STEMI or NSTEMI. Material and Methods: Peripheral blood samples were taken from 54 patients with ACS (27 STEMI, 27 NSTEMI) and 20 healthy volunteers. The expression levels of miR-1, miR-133a and miR-133b were measured by qRT-PCR. The association of miRNA expressions and characteristics of STEMI and NSTEMI patients were evaluated using a web-based program “RT2 Profiler PCR Array Data Analysis”. Results: The expression levels of miR-1, miR-133a and miR133b were higher in ACS than the control group (P< 0.05). However, the expression pattern of miRNAs differs between STEMI and NSTEMI patients, time-dependently. While miRNA expressions were in positive correlation with CK-MB in STEMI, they were in negative correlation in NSTEMI patients. Conclusion: Our findings suggest that the dynamic expression of miR-1, miR-133a and miR-133b could predict the severity and progression of coronary heart disease in ACS patients. Advanced functional studies and larger cohort validations are required.
On the Z-width limitation due to the vibration modes of haptic interfaces

This paper addresses the effect of internal vibration modes on the stability boundary for haptic rendering. A linear model that includes two vibration modes has been used to characterize one degree-of-freedom of the PHANToM 1.0 haptic interface, and predict the maximum achievable impedances for haptic rendering. The theoretical and experimental results show that the vibration modes of the mechanical interface significantly limit the Z-width of the haptic system.
Inhibition of different histone acetyltransferases (HATs) uncovers transcription-dependent and -independent acetylation-mediated mechanisms in memory formation

Acetylation of histones changes the efficiency of the transcription processes and thus contributes to the formation of long-term memory (LTM). In our comparative study, we used two inhibitors to characterize the contribution of different histone acetyl transferases (HATs) to appetitive associative learning in the honeybee. For one we applied garcinol, an inhibitor of the HATs of the p300 (EP300 binding protein)/CBP (CREB-binding protein) family, and the HATs of the PCAF (p300/CBP-associated factor) family. As comparative agent we applied C646, a specific inhibitor that selectively blocks HATS of the p300/CBP family. Immunochemical analysis reveals differences in histone H3 acetylation in the honeybee brain, in response to the injection of either C646 or garcinol. Behavioral assessment reveals that the two drugs cause memory impairment of different nature when injected after associative conditioning: processes disturbed by garcinol are annihilated by the established transcription blocker actinomycin D and thus seem to require transcription processes. Actions of C646 are unaltered by actinomycin D, and thus seem to be independent of transcription. The outcome of our different approaches as summarized suggests that distinct HATs contribute to different acetylation-mediated processes in memory formation. We further deduce that the acetylation-mediated processes in memory formation comprise transcription-dependent and transcription-independent mechanisms.
Modelling Hotspots for Invasive Alien Plants in India

Identification of invasion hotspots that support multiple invasive alien species (IAS) is a pre-requisite for control and management of invasion. However, till recently it remained a methodological challenge to precisely determine such invasive hotspots. We identified the hotspots of alien species invasion in India through Ecological Niche Modelling (ENM) using species occurrence data from the Global Biodiversity Information Facility (GBIF). The predicted area of invasion for selected species were classified into 4 categories based on number of model agreements for a region i.e. high, medium, low and very low. About 49% of the total geographical area of India was predicted to be prone to invasion at moderate to high levels of climatic suitability. The intersection of anthropogenic biomes and ecoregions with the regions of 'high' climatic suitability was classified as hotspot of alien plant invasion. Nineteen of 47 ecoregions of India, harboured such hotspots. Most ecologically sensitive regions of India, including the 'biodiversity hotspots' and coastal regions coincide with invasion hotspots, indicating their vulnerability to alien plant invasion. Besides demonstrating the usefulness of ENM and open source data for IAS management, the present study provides a knowledge base for guiding the formulation of an effective policy and management strategy for controlling the invasive alien species.