Doc2RDFa: Semantic Annotation for Web Documents

Ever since its conception, the amount of data published on the worldwide web has been rapidly growing to the point where it has become an important source of both general and domain specific information. However, the majority of documents published online are not machine readable by default. Many researchers believe that the answer to this problem is to semantically annotate these documents, and thereby contribute to the linked "Web of Data". Yet, the process of annotating web documents remains an open challenge. While some efforts towards simplifying this process have been made in the recent years, there is still a lack of semantic content creation tools that integrate well with information worker toolsets. Towards this end, we introduce Doc2RDFa, an HTML rich text processor with the ability to automatically and manually annotate domain-specific Content

PLoS One

ObjectivesTo identify the reasons patients miss taking their antiretroviral therapy (ART) and the proportion who miss their ART because of symptoms; and to explore the association between symptoms and incomplete adherence.MethodsSecondary analysis of data collected during a cross-sectional study that examined ART adherence among adults from 18 purposefully selected sites in Tanzania, Uganda, and Zambia. We interviewed 250 systematically selected patients per facility ( 6518 years) on reasons for missing ART and symptoms they had experienced (using the HIV Symptom Index). We abstracted clinical data from the patients\u2019 medical, pharmacy, and laboratory records. Incomplete adherence was defined as having missed ART for at least 48 consecutive hours during the past 3 months.ResultsTwenty-nine percent of participants reported at least one reason for having ever missed ART (1278/4425). The most frequent reason was simply forgetting (681/1278 or 53%), followed by ART-related hunger or not having enough food (30%), and symptoms (12%). The median number of symptoms reported by participants was 4 (IQR: 2\u20137). Every additional symptom increased the odds of incomplete adherence by 12% (OR: 1.1, 95% CI: 1.1\u20131.2). Female participants and participants initiated on a regimen containing stavudine were more likely to report greater numbers of symptoms.ConclusionsSymptoms were a common reason for missing ART, together with simply forgetting and food insecurity. A combination of ART regimens with fewer side effects, use of mobile phone text message reminders, and integration of food supplementation and livelihood programmes into HIV programmes, have the potential to decrease missed ART and hence to improve adherence and the outcomes of ART programmes.2016PEPFAR/United States26788919PMC4720476703

Tailoring modal properties of inhibited-coupling guiding fibers by cladding modification

Understanding cladding properties is crucial for designing microstructured optical fibers. This is particularly acute for Inhibited-Coupling guiding fibers because of the reliance of their core guidance on the core and cladding mode-field overlap integral. Consequently, careful planning of the fiber cladding parameters allows obtaining fibers with optimized characteristics such as low loss and broad transmission bandwidth. In this manuscript, we report on how one can tailor the modal properties of hollow-core photonic crystal fibers by adequately modifying the fiber cladding. We show that the alteration of the position of the tubular fibers cladding tubes can alter the loss hierarchy of the modes in these fibers, and exhibit salient polarization propriety. In this context, we present two fibers with different cladding structures which favor propagation of higher order core modes \u2013 namely LP11 and LP21 modes. Additionally, we provide discussions on mode transformations in these fibers and show that one can obtain uncommon intensity and polarization profiles at the fiber output. This allows the fiber to act as a mode intensity and polarization shaper. We envisage this novel concept can be useful for a variety of applications such as hollow core fiber based atom optics, atom-surface physics, sensing and nonlinear optics

Genes Associated With Psychrotolerant Bacillus cereus Group Isolates

The Bacillus cereus group comprises 18 different species, including human pathogens as well as psychrotolerant strains that are an important cause of fluid milk spoilage. To enhance our understanding of the genetic markers associated with psychrotolerance (defined here as > 1 log10 increase in cfu/mL after 21 days incubation at 6°C) among dairy-associated B. cereus group isolates, we used genetic (whole genome sequencing) and phenotypic methods [growth in Skim Milk Broth (SMB) and Brain Heart Infusion (BHI) broth] to characterize 23 genetically-distinct representative isolates from a collection of 503 dairy-associated isolates. Quality threshold clustering identified three categories of psychrotolerance: (i) 14 isolates that were not psychrotolerant in BHI or SMB, (ii) 6 isolates that were psychrotolerant in BHI but not in SMB, and (iii) 2 isolates that were psychrotolerant in BHI and SMB. One isolate, which was psychrotolerant in BHI broth but was just below the cut-off of >1 log10 cfu/mL increase in SMB was not assigned to a cluster. A maximum likelihood phylogeny constructed with core genome single nucleotide polymorphisms classified all psychrotolerant isolates (i.e., psychrotolerant in BHI) into clade VI (representing B. mycoides/weihenstephanensis). Analysis of correlations between gene ortholog presence or absence patterns and psychrotolerance identified 206 orthologous gene clusters that were significantly overrepresented among psychrotolerant strains, including two clusters of cold shock proteins, which were identified in 8/9 and 7/9 psychrotolerant isolates. Gene ontology analyses revealed 36 gene ontology terms that were overrepresented in psychrotolerant isolates, including putrescine catabolic processes and putrescine transmembrane transporter activity. Lastly, Hidden Markov Model searches identified three protein family motifs, including cold shock domain proteins and fatty acid hydroxylases that were significantly associated with psychrotolerance in BHI broth. Analyses of CspA sequences revealed a positive association between psychrotolerant strains and a previously identified “psychrotolerant” CspA sequence. Overall, our data highlight genetic and phenotypic differences in psychrotolerance among B. cereus group dairy-associated isolates and show that psychrotolerance is dependent on the growth medium. We also identified a number of gene targets that could be used for specific detection or control of psychrotolerant B. cereus group isolates

Genetic determinants of fungi-induced ROS production are associated with the risk of invasive pulmonary aspergillosis

© 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Reactive oxygen species (ROS) are an essential component of the host defense against fungal infections. However, little is known about how common genetic variation affects ROS-mediated antifungal host defense. In the present study, we investigated the genetic factors that regulate ROS production capacity in response to the two human fungal pathogens: Candida albicans and Aspergillus fumigatus. We investigated fungal-stimulated ROS production by immune cells isolated from a population-based cohort of approximately 200 healthy individuals (200FG cohort), and mapped ROS-quantitative trait loci (QTLs). We identified several genetic loci that regulate ROS levels (P < 9.99 × 10-6), with some of these loci being pathogen-specific, and others shared between the two fungi. These ROS-QTLs were investigated for their influence on the risk of invasive pulmonary aspergillosis (IPA) in a disease relevant context. We stratified hematopoietic stem-cell transplant (HSCT) recipients based on the donor's SNP genotype and tested their impact on the risk of IPA. We identified rs4685368 as a ROS-QTL locus that was significantly associated with an increased risk of IPA after controlling for patient age and sex, hematological malignancy, type of transplantation, conditioning regimen, acute graft-versus-host-disease grades III-IV, and antifungal prophylaxis. Collectively, this data provides evidence that common genetic variation can influence ROS production capacity, and, importantly, the risk of developing IPA among HSCT recipients. This evidence warrants further research for patient stratification based on the genetic profiling that would allow the identifications of patients at high-risk for an invasive fungal infection, and who would benefit the most from a preventive strategy.This study was supported by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 847507 (HDM-FUN). MGN was supported by an ERC Advanced grant (833247) and a Spinoza grant of the Netherlands Association for Scientific Research. VK was supported by a Research Grant [2017] of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and Hypatia tenure track grant. AC was supported by the Fundação para a Ciência e a Tecnologia (FCT) (UIDB/50026/2020 and UIDP/50026/2020), the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) (NORTE-01-0145-FEDER-000039), and the “la Caixa” Foundation (ID 100010434) and FCT under the agreement LCF/PR/HR17/52190003. CC was supported by FCT (CEECIND/04058/2018 and PTDC/SAU-SER/29,635/2017) and the Gilead Research Scholars Program – Antifungals. SMG was the recipient of a PhD fellowship funded by FCT (SFRH/BD/136,814/2018). MSG was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft - DFG) Emmy Noether Program (project no. 434385622/GR 5617/1-1).info:eu-repo/semantics/publishedVersio

A family of unsymmetrical hydroxyl-substituted BEDT-TTF donors: syntheses, structures and preliminary thin film studies

Three new unsymmetrical hydroxyl-functionalized donors H1–H3 closely related to hydroxymethyl-BEDT-TTF have been synthesised and characterised. Cyclic voltammetry studies showed that the compounds exhibit reversible two one-electron redox processes typical for BEDT-TTF derivatives. X-ray diffraction studies of H1 and H2 reveal π-stacking interactions between pairs of donors that are organized into distinct H-bonded square motifs and DFT calculations indicate that the HOMO is located on the central 1,3-dithiole rings. Protection of the hydroxyl group with acetyl in 13 eliminates co-facial S...S interactions between the dimers to accommodate the bulkier side chains, but short edge-to-edge S...S contacts offer an alternative pathway for electron mobility. Chemical oxidation of H1 and HMET 2 with I2 afforded single crystals of two 1 : 1 charge transfer salts, 18 and 19. The molecules pack as dimers with close π-stacking interactions between pairs of radical cations whose crystal structures are further stabilized via an interplay of S...S and S...I contacts. Iodine-doped surface conducting polystyrene blend films of H3 deposited on a silica substrate exhibit quasiconducting properties, but afford no OFET response when fabricated into devices. Visible-NIR studies of a doped polystyrene blend film of H3 cast on a glass substrate show absorption bands at λ =9 50 and 3000 nm, consistent with mixed valence states due to the presence of charge-transfer species on the surface of the films

Investigation of structure-directing interactions within copper(i)thiocyanate complexes through X-ray analyses and non-covalent interaction (NCI) theoretical approach

Herein, we reported the synthesis of copperIJI) thiocyanate complexes with ortho-pyridinyl carbohydrazones containing a thiophene (L1) or a furyl ring (L2) as a mixture of two different crystals for each compound, linkage isomers of C1N, [CuIJNCS)IJL1)PPh3] and C1S, [Cu(SCN)(L1)PPh3], for L1, whereas monomeric and polymeric structures C2N, [Cu(NCS)(L2)PPh3], and C2P, [–(NCS)Cu(L2)–]n, for L2. Crystallographic information and theoretical calculations, mainly noncovalent interaction reduced density gradient (NCI-RDG) analyses, were pursued to generate a profound understanding of the structure-directing interactions in these complexes. The supramolecular assemblies are first driven by cooperative π⋯π interactions and hydrogen bonds followed by CH⋯π, S⋯S and S⋯π linkages. In the case of the linkage isomers, intermolecular interactions may have a significant role in the formation of the less stable S-bound isomer C1S

MIDA boronates are hydrolysed fast and slow by two different mechanisms

MIDA boronates (N-methylimidodiacetic boronic acid esters) serve as an increasingly general platform for small-molecule construction based on building blocks, largely because of the dramatic and general rate differences with which they are hydrolysed under various basic conditions. Yet the mechanistic underpinnings of these rate differences have remained unclear, which has hindered efforts to address the current limitations of this chemistry. Here we show that there are two distinct mechanisms for this hydrolysis: one is base mediated and the other neutral. The former can proceed more than three orders of magnitude faster than the latter, and involves a rate-limiting attack by a hydroxide at a MIDA carbonyl carbon. The alternative 'neutral' hydrolysis does not require an exogenous acid or base and involves rate-limiting B-N bond cleavage by a small water cluster, (H2O)n. The two mechanisms can operate in parallel, and their relative rates are readily quantified by (18)O incorporation. Whether hydrolysis is 'fast' or 'slow' is dictated by the pH, the water activity and the mass-transfer rates between phases. These findings stand to enable, in a rational way, an even more effective and widespread utilization of MIDA boronates in synthesis

Creating a conceptual framework to improve the re‐usability of open geographic data in cities

Open data has a profound effect on the working environment within which information is created and shared at all levels. At the local government level, open data initiatives have resulted in higher transparency in policy, a greater engagement between decision‐makers and citizens, and have changed the culture about how data analysis and evidence are used to support local governance. This article, based on data collected through an on‐line survey, participatory workshops with data user communities in four cities (in Colombia and Spain), and interviews with Valencia good‐government office, identifies four elements for a conceptual framework to improve the re‐usability of open geographic data in cities. The essential elements defined in this research are the definition of data user communities and their needs, the creation of the community of reuse, user‐focused metadata, and reuse‐focused legal terms. The definition of these indicators provides a framework for authorities to re‐shape their current open data strategy to include data user requirements. At the end of this article, a roadmap for future research and implementation is presented, considering some reflections on the conceptual framework