Glottocodes: identifiers linking families, languages and dialects

Glottocodes constitute the backbone identification system for the language, dialect and family inventory Glottolog(https://glottolog.org). In this paper, we summarize the motivation and history behind the system of glottocodes and describe theprinciples and practices of data curation, technical infrastructure and update/version-tracking systematics. Since our understandingof the target domain—the dialects, languages and language families of the entire world—is continually evolving, changesand updates are relatively common. The resulting data is assessed in terms of the FAIR (Findable, Accessible, Interoperable,Reusable) Guiding Principles for scientific data management and stewardship. As such the glottocode-system responds to animportant challenge in the realm of Linguistic Linked Data with numerous NLP applications.1. Introduction 2. Motivation and History 3. Glottolog data curation 3.1. Glottolog data is findable 3.2. Glottolog data is accessible 3.3. Glottolog data is interoperable 3.4. Glottolog data is reusable 4. Policies governing glottocode assignment 5. Glottolog versioning 6. Conclusio

Lymph node tissue kallikrein-related peptidase 6 mRNA: a progression marker for colorectal cancer

BACKGROUND: A most important characteristic feature for poor prognosis in colorectal cancer (CRC) is the presence of lymph node metastasis. Determination of carcinoembryonic antigen (CEA) mRNA levels in lymph nodes has proven powerful for quantification of disseminated tumour cells. Here, we investigate the utility of human tissue kallikrein-related peptidase 6 (KLK6) mRNA as a progression biomarker to complement CEA mRNA, for improved selection of patients in need of adjuvant therapy and intensified follow-up after surgery. METHODS: Lymph nodes of pTNM stage I-IV CRC-(166 patients/503 lymph nodes) and control (23/108) patients were collected at surgery and analysed by quantitative RT-PCR. RESULTS: Lymph node KLK6 positivity was an indicator of poor outcome (hazard ratio 3.7). Risk of recurrence and cancer death increased with KLK6 lymph node levels. Patients with KLK6 lymph node levels above the 90th percentile had a hazard ratio of 6.5 and 76 months shorter average survival time compared to patients with KLK6 negative nodes. The KLK6 positivity in lymph nodes with few tumour cells, that is, low CEA mRNA levels, also indicated poor prognosis (hazard ratio 2.8). CONCLUSION: In CRC patients, lymph node KLK6 positivity indicated presence of aggressive tumour cells associated with poor prognosis and high risk of tumour recurrence. British Journal of Cancer (2012) 107, 150-157. doi: 10.1038/bjc.2012.220 www.bjcancer.com Published online 14 June 2012 (C) 2012 Cancer Research U

Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells

Class switch recombination (CSR) is a region-specific, transcriptionally regulated, nonhomologous recombinational process that is initiated by activation-induced cytidine deaminase (AID). The initial lesions in the switch (S) regions are subsequently processed and resolved, leading to recombination of the two targeted S regions. The mechanisms by which repair and ligation of the broken DNA ends occurs is still elusive. Recently, a small number of patients lacking DNA ligase IV, a critical component of the nonhomologous end joining (NHEJ) machinery, have been identified. We show that these patients display a considerably increased donor/acceptor homology at Sμ–Sα junctions compared with healthy controls. In contrast, Sμ–Sγ junctions show an increased frequency of insertions but no increase in junctional homology. These altered patterns of junctional resolution may be related to differences in the homology between the Sμ and the downstream isotype S regions, and could reflect different modes of switch junction resolution when NHEJ is impaired. These findings link DNA ligase IV, and thus NHEJ, to CSR

Predictive markers for humoral influenza vaccine response in patients with common variable immunodeficiency (CVID)

BACKGROUND: A subgroup of patients with common variable immunodeficiencies (CVID) responds to vaccination. The aim of the study was to try to identify predictive markers for those who developed a humoral immune response after influenza vaccination. METHODS: 48 patients with CVID (29 females, 19 males, mean age 59.4 years) were vaccinated with the A(H1N1) influenza vaccine Pandemrix® and boosted after one month. Blood samples were collected prior to each vaccination and two months later. Patients with a 4-fold titer increase of the hemagglutinin inhibition test (≥ 1:40) were considered responders and compared to non-responders for clinical, immunological and genetic markers. RESULTS: Eight (16.7%) patients responded to the vaccination. A significantly higher proportion of the responders, who showed a Euroclass SmB-Trnorm21norm profile (p=0.03) with a post-germinal center B cell pattern (p=0.04) in blood, suffered from enteropathies (p=0.04) as compared to non-responders. Bronchiectasis on the other hand, was exclusively found among non-responders (n=7), as was autoimmune cytopenia (n=5). Non-responders with a Euroclass SmB-21lowTrnorm profile (p=0.02), had a significantly higher prevalence of progressive antibody deficiency (p=0.048) and, at diagnosis, a higher mean serum IgM level (p=0.03), a lower mean serum IgG1 level (p=0.007), an expansion of absolute counts of cytotoxic CD8+ T-cells (p=0.033) and an increased proportion of memory CD8+ T-cells (p=0.044) in blood. CVID associated HLA markers were not detected in non-responders (p=0.03). CONCLUSION: About one-fifth of the CVID patients achieved protective antibody levels after A(H1N1) vaccination and selected clinical and immunological markers were identified that may predict a positive outcome of influenza vaccination

Simultaneous visualization of language endangerment and language description

The world harbors a diversity of some 6,500 mutually unintelligible languages.As has been increasingly observed by linguists, many minority languages are be-coming endangered and will be lost forever if not documented. Urgently indeed,many efforts are being launched to document and describe languages. This under-taking naturally has the priority toward the most endangered and least describedlanguages. For the first time, we combine world-wide databases on language de-scription (Glottolog) and language endangerment (ElCat, Ethnologue, UNESCO)and provide two online interfaces, GlottoScope and GlottoVis, to visualize thesetogether. The interfaces are capable of browsing, filtering, zooming, basic statis-tics, and different ways of combining the two measures on a world map back-ground. GlottoVis provides advanced techniques for combining cluttered dotson a map. With the tools and databases described we seek to increase the overallknowledge of the actual state language endangerment and description worldwid

Photochemically induced isomerisation in ruthenium polypyridyl complexes

The synthesis and characterisation of a series of ruthenium polypyridyl complexes containing pyridyltriazole ligands in different coordination modes are described. The electrochemical and electronic properties of the compounds are reported and discussed with respect to the coordination mode of the pyridyltriazole ligand. Upon photolysis of the complex containing the 1-methyl-3-(pyridin-2-yl)-1,2,4-triazole ligand irreversible ligand isomerisation is observed

Involvement of Artemis in nonhomologous end-joining during immunoglobulin class switch recombination

DNA double-strand breaks (DSBs) introduced in the switch (S) regions are intermediates during immunoglobulin class switch recombination (CSR). These breaks are subsequently recognized, processed, and joined, leading to recombination of the two S regions. Nonhomologous end-joining (NHEJ) is believed to be the principle mechanism involved in DSB repair during CSR. One important component in NHEJ, Artemis, has however been considered to be dispensable for efficient CSR. In this study, we have characterized the S recombinational junctions from Artemis-deficient human B cells. Sμ–Sα junctions could be amplified from all patients tested and were characterized by a complete lack of “direct” end-joining and a remarkable shift in the use of an alternative, microhomology-based end-joining pathway. Sμ–Sγ junctions could only be amplified from one patient who carries “hypomorphic” mutations. Although these Sμ–Sγ junctions appear to be normal, a significant increase of an unusual type of sequential switching from immunoglobulin (Ig)M, through one IgG subclass, to a different IgG subclass was observed, and the Sγ–Sγ junctions showed long microhomologies. Thus, when the function of Artemis is impaired, varying modes of CSR junction resolution may be used for different S regions. Our findings strongly link Artemis to the predominant NHEJ pathway during CSR