The Footprint Sorting Problem

Phylogenetic footprints are short pieces of noncoding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints in their order along the genomes. It is complicated by the fact that not all footprints are collinear:  they may cross each other. The problem thus becomes the identification of the crossing footprints, the sorting of the remaining collinear cliques, and finally the insertion of the noncollinear ones at “reasonable” positions. We show that solving the footprint sorting problem requires the solution of the “Minimum Weight Vertex Feedback Set Problem”, which is known to be NP-complete and APX-hard. Nevertheless good approximations can be obtained for data sets of interest. The remaining steps of the sorting process are straightforward:  computation of the transitive closure of an acyclic graph, linear extension of the resulting partial order, and finally sorting w.r.t. the linear extension. Alternatively, the footprint sorting problem can be rephrased as a combinatorial optimization problem for which approximate solutions can be obtained by means of general purpose heuristics. Footprint sortings obtained with different methods can be compared using a version of multiple sequence alignment that allows the identification of unambiguously ordered sublists. As an application we show that the rat has a slighly increased insertion/deletion rate in comparison to the mouse genome

A convergent spectroscopy-based approach for Vcmax across leaf age and growth environments.

Abstract OOS 2-2

Does Amazon forest leaf phenology mediate transpiration seasonality and hence, ecoclimate teleconnections?

Abstract OOS 11-5

Age-dependent leaf function and consequences for carbon uptake of leaves, branches, and the canopy during the dry season in an Amazon evergreen forest.

Abstract COS 124-3

Multiple sequence alignment with user-defined constraints at GOBICS

Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do

Consensus statement: loneliness in older adults, the 21st century social determinant of health?

© Author(s) (or their employer(s)) 2020. Objective The purpose of this consensus statement is to determine the state of the field of loneliness among older people, highlighting key issues for researchers, policymakers and those designing services and interventions. Methods In December 2018, an international meeting on loneliness was held in Belfast with leaders from across the USA and Europe. A summary of the conclusions reached at this event is presented following a consensus-building exercise conducted both during this event after each presentation as well as after the event through the drafting, reviewing and agreement of this statement by all authors for over 6 months. Results This meeting resulted in an agreement to produce a consensus statement on key issues including definitions of loneliness, measurement, antecedents, consequences and interventions. Discussion There has been an exponential growth in research on loneliness among older adults. However, differing measurements and definitions of loneliness mean the incidence and prevalence, associated risk factors and health consequences are often conflicting or confusing especially for those developing policy and services

Photochemistry Of Monochloro Complexes Of Copper(ii) In Methanol Probed By Ultrafast Transient Absorption Spectroscopy

Ultrafast transient absorption spectra in the deep to near UV range (212-384 nm) were measured for the [Cu-II(MeOH)(5)Cl](+) complexes in methanol following 255-nm excitation of the complex into the ligand-to-metal charge-transfer excited state. The electronically excited complex undergoes sub-200 fs radiationless decay, predominantly via back electron transfer, to the hot electronic ground state followed by fast vibrational relaxation on a 0.4-4 Ps time scale. A minor photochemical channel is Cu-Cl bond dissociation, leading to the reduction of copper(H) to copper(I) and the formation of MeOH center dot Cl charge-transfer complexes. The depletion of ground-state [Cu-II(MeOH)(5)Cl](+) perturbs the equilibrium between several forms of copper(II) complexes present in solution. Complete re-equilibration between [Cu-II(MeOH)(5)Cl](+) and [Cu-II(MeOH)(4)Cl-2] is established on a 10-500 ps time scale, slower than methanol diffusion, suggesting that the involved ligand exchange mechanism is dissociative

Impact of the COVID-19 Pandemic on Loneliness and Social Isolation: A Multi-Country Study

Copyright: © 2021 by the authors. The COVID-19 global pandemic and subsequent public health social measures have challenged our social and economic life, with increasing concerns around potentially rising levels of social isolation and loneliness. This paper is based on cross-sectional online survey data (available in 10 languages, from 2 June to 16 November 2020) with 20,398 respondents from 101 different countries. It aims to help increase our understanding of the global risk factors that are associated with social isolation and loneliness, irrespective of culture or country, to support evidence-based policy, services and public health interventions. We found the prevalence of severe loneliness was 21% during COVID-19 with 6% retrospectively reporting severe loneliness prior to the pandemic. A fifth were defined as isolated based on their usual connections, with 13% reporting a substantial increase in isolation during COVID-19. Personal finances and mental health were overarching and consistently cross-cutting predictors of loneliness and social isolation, both before and during the pandemic. With the likelihood of future waves of COVID-19 and related restrictions, it must be a public health priority to address the root causes of loneliness and social isolation and, in particular, address the needs of specific groups such as carers or those living alone