Understanding and applying biological resilience, from genes to ecosystems.

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions.

Research Infrastructure Contact Zones: a framework and dataset to characterise the activities of major biodiversity informatics initiatives.

Background: The landscape of biodiversity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional biodiversity informatics space, while others operate across a broad front, but differ from others by data type(s) handled, their geographic scope and the life cycle phase(s) of the data they support. In an effort to characterise the various dimensions of the biodiversity informatics landscape, we developed a framework and dataset to survey these dimensions for ten organisations (DiSSCo, GBIF, iBOL, Catalogue of Life, iNaturalist, Biodiversity Heritage Library, GeoCASe, LifeWatch, eLTER ELIXIR), relative to both their current activities and long-term strategic ambitions.

Low Entropy Future Boundary Conditions.

A number of ways to detect future, low-entropy, boundary conditions are considered. The most important of these is the use of slowly-decaying isotopes and the observation (or prediction) of galactic dynamics. There is the expectation that future developments in experimental or observational technique will yield positive results.

Natural variations in AAVHSC16 significantly reduce liver tropism and maintain broad distribution to periphery and CNS.

Adeno-associated viruses derived from human hematopoietic stem cells (AAVHSCs) are naturally occurring AAVs. Fifteen AAVHSCs have demonstrated broad biodistribution while displaying differences in transduction. We examine the structure-function relationships of these natural amino acid variations on cellular binding.

Apparent Power Laws Can Occur without Criticality.

Power laws often lead to the conclusion that self-organized criticality is at work. This is not the case, and power laws can also occur away from criticality or can occur for other reasons.

A molecular-based identification resource for the arthropods of Finland.

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species.

Causality Is an Effect, II.

Causality follows the thermodynamic arrow of time, where the latter is defined by the direction of entropy increase. After a brief review of an earlier version of this article, rooted in classical mechanics, we give a quantum generalization of the results. The quantum proofs are limited to a gas of Gaussian wave packets.

The Finnish Biodiversity Information Facility as a best-practice model for biodiversity data infrastructures.

Biodiversity informatics has advanced rapidly with the maturation of major biodiversity data infrastructures (BDDIs), such as the Global Biodiversity Information Facility sharing unprecedented data volumes. Nevertheless, taxonomic, temporal and spatial data coverage remains unsatisfactory. With an increasing data need, the global BDDIs require continuous inflow from local data mobilisation, and national BDDIs are being developed around the world.

Translocation of an arctic seashore plant reveals signs of maladaptation to altered climatic conditions.

Ongoing anthropogenic climate change alters the local climatic conditions to which species may be adapted. Information on species' climatic requirements and their intraspecific variation is necessary for predicting the effects of climate change on biodiversity. We used a climatic gradient to test whether populations of two allopatric varieties of an arctic seashore herb ( ssp.

Wildlife collection for scientific purposes.

Illegal transfer of wildlife has 2 main purposes: trade and scientific research. Trade is the most common, whereas scientific research is much less common and unprofitable, yet still important. Biopiracy in science is often neglected despite that many researchers encounter it during their careers.

The Observable Representation.

The observable representation (OR) is an embedding of the space on which a stochastic dynamics is taking place into a low dimensional Euclidean space. The most significant feature of the OR is that it respects the dynamics. Examples are given in several areas: the definition of a phase transition (including metastable phases), random walks in which the OR recovers the original space, complex systems, systems in which the number of extrema exceed convenient viewing capacity, and systems in which successful features are displayed, but without the support of known theorems.

A benchmark dataset of herbarium specimen images with label data.

Background: More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets.

Bacterial resistance to antibodies: a model evolutionary study.

The tangled nature model of evolution (reviewed in the main text) is adapted for use in the study of antibody resistance acquired by horizontal gene transfer. Exchanges of DNA and the acquisition of resistant gene sequences are considered. For the parameters used, resistant strains rapidly proliferate and dominate, although initial intense antibiotic treatment can occasionally prevent this.

Punctuated equilibrium as an emergent process and its modified thermodynamic characterization.

We address evolutionary dynamics and consider under which conditions the ecosystem interaction network allows punctuated equilibrium (i.e., alternation between hectic and quasi-stable phases).

Resident Rounds Part III: Case Report: Fatal Cryptococcal Panniculitis in a Lung Transplant Recipient.

Cryptococcal panniculitis is a rare entity previously reported in only 13 solid organ transplant (SOT) recipients. Cutaneous cryptococcosis in SOT recipients warrants extensive systemic workup and treatment as if central nervous system (CNS) disease is present. It should be included in the differential diagnosis of panniculitis in the immunocompromised host, as early diagnosis and treatment are critical.

Low temperature delayed recombination and trap tunneling.

Delayed recombination of charge carriers at an activator is a significant problem for fast scintillators and is usually associated with thermal effects. However, experimental results have shown that this phenomenon can occur even at the lowest temperatures. We here provide evidence in support of the idea that this is due to quantum tunneling between activator and nearby traps, and provide analytic estimates relating the energy levels and locations of those traps to the observed delayed recombination.

Coming to terms with the concept of moving species threatened by climate change - a systematic review of the terminology and definitions.

Intentional moving of species threatened by climate change is actively being discussed as a conservation approach. The debate, empirical studies, and policy development, however, are impeded by an inconsistent articulation of the idea. The discrepancy is demonstrated by the varying use of terms, such as assisted migration, assisted colonisation, or managed relocation, and their multiple definitions.

Dissipation, interaction, and relative entropy.

Many thermodynamic relations involve inequalities, with equality if a process does not involve dissipation. In this article we provide equalities in which the dissipative contribution is shown to involve the relative entropy (also called the Kullback-Leibler divergence). The processes considered are general time evolutions in both classical and quantum mechanics, and the initial state is sometimes thermal, sometimes partially so.

Cluster identification based on correlations.

The problem addressed is the identification of cooperating agents based on correlations created as a result of the joint action of these and other agents. A systematic method for using correlations beyond second moments is developed. The technique is applied to a didactic example, the identification of alphabet letters based on correlations among the pixels used in an image of the letter.

Efficiency of a thermodynamic motor at maximum power.

Several recent theories address the efficiency of a macroscopic thermodynamic motor at maximum power and question the so-called Curzon-Ahlborn (CA) efficiency. Considering the entropy exchanges and productions in an n-sources motor, we study the maximization of its power and show that the controversies are partly due to some imprecision in the maximization variables. When power is maximized with respect to the system temperatures, these temperatures are proportional to the square root of the corresponding source temperatures, which leads to the CA formula for a bithermal motor.

Constrained maximal power in small engines.

Efficiency at maximum power is studied for two simple engines (three- and five-state systems). This quantity is found to be sensitive to the variable with respect to which the maximization is implemented. It can be wildly different from the well-known Curzon-Ahlborn bound (one minus the square root of the temperature ratio), or can be even closer than previously realized.

Stochastic thermodynamics and sustainable efficiency in work production.

We propose a novel definition of efficiency, valid for motors in a nonequilibrium stationary state exchanging heat and possibly other resources with an arbitrary number of reservoirs. This definition, based on a rational estimation of all irreversible effects associated with power production, is adapted to the concerns of sustainable development. Under conditions of maximum power production the new efficiency has for upper bound 1/2 in situations relevant for mesoscopic systems.