Planar subgraphs without low-degree nodes

We study the following problem: given a geometric graph G and an integer k, determine if G has a planar spanning subgraph (with the original embedding and straight-line edges) such that all nodes have degree at least k. If G is a unit disk graph, the problem is trivial to solve for k = 1. We show that even the slightest deviation from the trivial case (e.g., quasi unit disk graphs or k = 1) leads to NP-hard problems.Peer reviewe

Differences in size between first and replacement clutches match the seasonal decline in single clutches in Tree Swallows Tachycineta bicolor

© 2016 British Ornithologists' UnionThe seasonal decline in clutch size in birds can be a response to the environmentally conditioned decrease in prospects for offspring or a consequence of a lower physical ability of late-breeding females. To find out which of the explanations apply in Tree Swallows Tachycineta bicolor, we assessed whether replacement clutch size in this species is affected by an individual female's ability to lay a certain number of eggs. To do this, we measured the decline in clutch size as a function of laying date between first and replacement clutches in individuals that re-nested following natural failure, and compared this with the rate of decline in clutch size with laying date for Tree Swallows that laid only a single clutch in that season. Additionally, we assessed whether the clutch size and the rate of its seasonal decline varied across years. We accounted for the truncated and under-dispersed nature of clutch size data by using a Bayesian approach in the analysis. We found little variation in the rate of clutch size decline across years at our breeding site. Accounting for this seasonal decline in clutch size, mean clutch size was similar between single-time breeding females and those that laid replacement clutches, implying that the number of eggs laid on the second attempt by female Tree Swallows is determined by laying date, rather than by the female's physical ability to produce a clutch of a certain size

Crossing and weighted crossing number of near-planar graphs

A nonplanar graph G is near-planar if it contains an edge e such that G − e is planar. The problem of determining the crossing number of a near-planar graph is exhibited from different combinatorial viewpoints. On the one hand, we develop min-max formulas involving efficiently computable lower and upper bounds. These min-max results are the first of their kind in the study of crossing numbers and improve the approximation factor for the approximation algorithm given by Hliněny and Salazar (Graph Drawing GD’06). On the other hand, we show that it is NP-hard to compute a weighted version of the crossing number for near-planar graphs

Musculoskeletal symptoms of the upper extremities and the neck: A cross-sectional study on prevalence and symptom-predicting factors at visual display terminal (VDT) workstations

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to determine the prevalence and the predictors of musculoskeletal symptoms in the upper extremities and neck at visual display terminal (VDT) workstations.</p> <p>Methods</p> <p>In a cross-sectional study 1,065 employees working at VDT > 1 h/d completed a standardised questionnaire. Workstation conditions were documented in a standardised checklist, and a subgroup of 82 employees underwent a physical examination.</p> <p>Results</p> <p>Using the Nordic Questionnaire, the 12-month prevalence of symptoms of the neck, shoulder region, hand/wrist, or elbow/lower arm was 55%, 38%, 21%, and 15% respectively. The duration of VDT work had a significant impact on the frequency of neck symptoms in employees performing such work > 6 h/d.</p> <p>Conclusion</p> <p>With regard to musculoskeletal symptoms of the upper extremities, preventive measures at VDT workstations should be focused on neck and shoulder symptoms (e.g. ergonomic measures, breaks to avoid sitting over long periods).</p

Expanding The Genetic Code

Karsten L, Bergen D, Drake C, et al. Expanding The Genetic Code. Bielefeld University; 2017.We worked in many different scientific fields to find suitable ways for the translational incorporate of non-canonical amino acids into proteins. Repurposing existing codons or incorporating new bases are two possible ways. We realized both ways to expand the genetic code of Escherichia coli. The repurposing of a codon for the incorporation of a non-canonical amino acid (ncAA) is possible using the rarely used amber stop codon UAG or other rarely used codons like the leucine codon CUA. To incorporate a non-canonical amino acid using these codons, an orthogonal tRNA/aminoacyl-tRNA synthetase (tRNA/aaRS) pair is necessary, which can charge the ncAA to the tRNA. We designed and synthetized the novel ncAA Nγ‑2‑cyanobenzothiazol‑6‑yl‑L‑asparagine (CBT-asparagine). This ncAA has the chemical ability of perform a highly specific covalent binding reaction, which we wanted to incorporate into our target protein. Therefore, we created a library of aaRS with random mutagenized amino acid binding sites and a selection system to select for the aaRS that specifically incorporates the ncAA. In parallel to the libary and selection based approach, we modeled the aaRS which could incorporate our new amino acid CBT-asparagine. We demonstrated that both ways are suitable for the evolution of aaRS. Although incorporation of ncAAs through the amber codon works, there are challenges associated with this approach. The repurposing of codons leads to the decrease of the growth rate of E. coli and it is only feasible to incorporate up to two different ncAAs. Therefore, we took a new way to incorporate ncAAs. The incorporation of an unnatural base pair into the DNA generates 64 new codons. Our first challenge was the uptake of the unnatural base from the media, because E.coli has no nucleoside triphosphate transporter and is not able to synthetize the bases itself. We cloned a nucleoside triphosphate transporter that enables the uptake of both bases from the media. Furthermore, we analyzed the transcriptome of the plant Croton tiglium, which produces the unnatural base isoG. The transcriptome revealed an enzyme for the biosynthesis, which was cloned and characterized for the biosynthesis of isoG in E. coli. To detect the unnatural base we developed two orthogonal systems. A restriction experiment based on the software tool M.A.X. and an adaption of the Oxford Nanopore sequencing, which were combined into one software suite. To demonstrate the possibilities offered by the incorporation of ncAAs, we developed a toolbox containing five different tools. We chose seven different ncAAs for these five tools and demonstrated interesting applications for them. These ncAAs can be used for various approaches in basic research, medicine and manufacturing. Furthermore, with our submitted parts, every iGEM team can incorporate these ncAAs into their target proteins. Regarding our project, two of the ncAAs that are part of our toolbox perform an autocatalytic reaction upon irradiation with ultraviolet light. Therefore, we decided to build our own LED panel that allows us to perform experiments with these non‑canonical amino acids under reproducible irradiation conditions

Extending Epigenesis: From Phenotypic Plasticity to the Bio-Cultural Feedback

The paper aims at proposing an extended notion of epigenesis acknowledging an actual causal import to the phenotypic dimension for the evolutionary diversification of life forms. Section 1 offers introductory remarks on the issue of epigenesis contrasting it with ancient and modern preformationist views. In Section 2 we propose to intend epigenesis as a process of phenotypic formation and diversification a) dependent on environmental influences, b) independent of changes in the genomic nucleotide sequence, and c) occurring during the whole life span. Then, Section 3 focuses on phenotypic plasticity and offers an overview of basic properties (like robustness, modularity and degeneracy) that allows biological systems to be evolvable – i.e. to have the potentiality of producing phenotypic variation. Successively (Section 4), the emphasis is put on environmentally-induced modification in the regulation of gene expression giving rise to phenotypic variation and diversification. After some brief considerations on the debated issue of epigenetic inheritance (Section 5), the issue of culture (kept in the background of the preceding sections) is considered. The key point is that, in the case of humans and of the evolutionary history of the genus Homo at least, the environment is also, importantly, the cultural environment. Thus, Section 6 argues that a bio-cultural feedback should be acknowledged in the “epigenic” processes leading to phenotypic diversification and innovation in Homo evolution. Finally, Section 7 introduces the notion of “cultural neural reuse”, which refers to phenotypic/neural modifications induced by specific features of the cultural environment that are effective in human cultural evolution without involving genetic changes. Therefore, cultural neural reuse may be regarded as a key instance of the bio-cultural feedback and ultimately of the extended notion of epigenesis proposed in this work

Occupation and SARS-CoV-2 infection risk among 108 960 workers during the first pandemic wave in Germany

OBJECTIVE: The aim of this study was to identify the occupational risk for a SARS-CoV-2 infection in a nationwide sample of German workers during the first wave of the COVID-19 pandemic (1 February-31 August 2020). METHODS: We used the data of 108 960 workers who participated in a COVID follow-up survey of the German National Cohort (NAKO). Occupational characteristics were derived from the German Classification of Occupations 2010 (Klassifikation der Berufe 2010). PCR-confirmed SARS-CoV-2 infections were assessed from self-reports. Incidence rates (IR) and incidence rate ratios (IRR) were estimated using robust Poisson regression, adjusted for person-time at risk, age, sex, migration background, study center, working hours, and employment relationship. RESULTS: The IR was 3.7 infections per 1000 workers [95% confidence interval (CI) 3.3-4.1]. IR differed by occupational sector, with the highest rates observed in personal (IR 4.8, 95% CI 4.0-5.6) and business administration (IR 3.4, 95% CI 2.8-3.9) services and the lowest rates in occupations related to the production of goods (IR 2.0, 95% CI 1.5-2.6). Infections were more frequent among essential workers compared with workers in non-essential occupations (IRR 1.95, 95% CI 1.59-2.40) and among highly skilled compared with skilled professions (IRR 1.36, 95% CI 1.07-1.72). CONCLUSIONS: The results emphasize higher infection risks in essential occupations and personal-related services, especially in the healthcare sector. Additionally, we found evidence that infections were more common in higher occupational status positions at the beginning of the pandemic

Children’s residential exposure to selected allergens and microbial indicators: endotoxins and (1→3)-β-D-glucans

Objectives: The study was aimed at assessment of exposure to endotoxins, (1→3)-β-D-glucans and mite, cockroach, cat, dog allergens present in settled dust in premises of children as agents which may be significantly correlated with the occurrence of allergic symptoms and diseases in children. Materials and Methods: The study covered 50 homes of one- or two-year-old children in Poland. Samples of settled dust were taken from the floor and the child's bed. The levels of (1→3)-β-D-glucans (floor), endotoxins (floor) and allergens of mite, cat, dog and cockroach (floor and bed) were analyzed. Results: Average geometric concentrations (geometric standard deviation) of endotoxins, (1→3)-β-D-glucans, Der p1, Fel d1, Can f1 and Bla g1 in children homes were on the floor 42 166.0 EU/g (3.2), 20 478.4 ng/g (2.38), 93.9 ng/g (6.58), 119.8 ng/g (13.0), 288.9 ng/g (3.4), 0.72 U/g (4.4) and in their beds (only allergens) 597.8 ng/g (14.2), 54.1 ng/g (4.4), 158.6 ng/g (3.1) 0.6 U/g (2.9), respectively. When the floor was covered with the carpet, higher concentrations of endotoxins, (1→3)-β-D-glucans and allergens (each type) were found in the settled dust (p < 0.05). The trend was opposite in case of allergens (except dog) analyzed from bed dust and significantly higher concentrations were found in the rooms with smooth floor (p < 0.05). Conclusions: Among the analyzed factors only the type of floor significantly modified both the level of biological indicators and allergens. The results of this study could be the base for verifying a hypothesis that carpeting may have a protective role against high levels of cockroach, dog and cat allergens