First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages.

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

Tracking Chromosomal Origins in the Northern Italy System of Metacentric Races of the House Mouse.

The Western European house mouse is chromosomally diverse, with diploid karyotypes ranging from the standard 40 telocentric chromosomes down to 22 chromosomes. Karyotypes are modified through Robertsonian (Rb) fusion of 2 telocentrics into a single metacentric, occurring repeatedly with fixation, and whole-arm reciprocal translocations (WARTs) generating additional novel karyotypes. Over 100 metacentric populations (chromosomal races) have been identified, geographically clustered into "systems." Chromosomal races within systems often hybridise, and new races may emerge through this hybridisation ("zonal raciation"). We wished to determine the degree to which chromosomal races in a system have evolved independently or share common ancestry. Recombination between chromosomes from hybridising chromosomal races can erase the signals associated with a particular metacentric of interest, making inferences challenging. However, reduced recombination near the centromeres of chromosomal race-specific metacentrics makes centromere-adjacent markers ideal for solving this problem. For the Northern Italy System (NIS), we used microsatellite markers near the centromere to test previous hypotheses about evolutionary relationships of 5 chromosomal races. We chose markers from chromosomes 1, 3, 4, and 6, all of which comprise one arm of a metacentric in at least 2 of these NIS metacentric populations. We used estimates of FST and RST, as well as principal components analyses and neighbour-joining phylogenetic analyses, to infer evolutionary relationships between these 5 chromosomal races and neighbouring mice with the standard karyotype. We showed that the metacentric populations form a single grouping distinct from the standard populations, consistent with their common origin and consistent with a parsimonious sequence of chromosomal rearrangements to explain the relationship of the chromosomal races. That origin and evolution of the chromosomal races in the system would have involved Rb fusions, explaining the occurrence of chromosomal races with diploid numbers as low as 22. However, WARTs and zonal raciation have also been inferred, and the rare occurrence of chromosome 1 in different metacentrics in closely related chromosomal races is almost certainly explained by a WART. Our results with centromeric microsatellites are consistent with the above scenarios, illustrating, once again, the value of markers in the centromeric region to test evolutionary hypotheses in house mouse chromosomal systems.

Low-resolution description of the conformational space for intrinsically disordered proteins.

Intrinsically disordered proteins (IDP) are at the center of numerous biological processes, and attract consequently extreme interest in structural biology. Numerous approaches have been developed for generating sets of IDP conformations verifying a given set of experimental measurements. We propose here to perform a systematic enumeration of protein conformations, carried out using the TAiBP approach based on distance geometry. This enumeration was performed on two proteins, Sic1 and pSic1, corresponding to unphosphorylated and phosphorylated states of an IDP. The relative populations of the obtained conformations were then obtained by fitting SAXS curves as well as Ramachandran probability maps, the original finite mixture approach RamaMix being developed for this second task. The similarity between profiles of local gyration radii provides to a certain extent a converged view of the Sic1 and pSic1 conformational space. Profiles and populations are thus proposed for describing IDP conformations. Different variations of the resulting gyration radius between phosphorylated and unphosphorylated states are observed, depending on the set of enumerated conformations as well as on the methods used for obtaining the populations.

Simulation and compensation of thermal lensing in optical systems.

High-power optical systems are used in a number of industrial applications. One difficulty in designing such systems is that the beam itself is a significant source of heat, which changes the optical properties of the system. To reduce this effect, we propose a new thermal lensing compensation technique based on a detailed analysis of the optical properties of the high-power optical system. To this end, we have developed a new ray tracing simulation technique that accurately models optical propagation through inhomogeneous, anisotropic, and deformed media. This model enables the performance of systems in physically realistic situations to be evaluated efficiently. Experimental comparisons were conducted to validate the simulation. We found excellent agreement between the simulation and the measured data. We have validated the simulation technique for a single lens setup and a complex optical scanner system.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

Evaluating Benefits, Costs, and Social Value as Predictors of Gratitude.

Although much is known about cooperation, the internal decision rules that regulate motivations to initiate and maintain cooperative relationships have not been thoroughly explored. Here, we focus on how acts of benefit delivery and perceptions of social value inform gratitude, an emotion that promotes cooperation. We evaluated alternate information-processing models to determine which inputs and internal representations best account for the intensity with which people report experiencing gratitude. Across two experiments (Ns = 257 and 208), we tested 10 models that consider multiple variables: the magnitude of benefits conferred on beneficiaries, the magnitude of costs incurred by benefactors, beneficiaries' perception of how much benefactors value their welfare, and beneficiaries' value for the welfare of their benefactors. Across both studies, only beneficiaries' change in social valuation for their benefactors consistently predicted gratitude. Results point to the need for further research and contribute to the growing literature linking cooperation, social emotions, and social valuation.

Typhoid fever in travellers: estimating the risk of acquisition by country.

BACKGROUND: Typhoid fever is a notifiable disease within Australia. Although studies in endemic regions give an indication of acquisition risk, many countries lack reliable data, and little is known of the absolute or relative risk in Australian travellers. By combining notified case data with travel statistics provided by the Australian Bureau of Statistics, the aim of this study was to give an indication of risk for typhoid acquisition among Australian travellers. METHODS: Australian typhoid notifications between 1st January 2010 and 30th June 2017 were grouped by country of acquisition and age category (<15 or ≥15 years). Australian travel data were used to inform time at risk and incidence rate of Australian typhoid notifications pertaining to country and region of acquisition. Salmonella Paratyphi infections, though notifiable, were excluded as the focus was vaccine preventable illness. Data from New South Wales and Victoria were used to examine the incidence in those acquiring infection in their country of birth (COB) against travellers who did not. RESULTS: Nine hundred twenty-three cases of typhoid were notified over the period of review, 96% of which were acquired overseas. The greatest determinant of risk was travel destination, with countries in south Asia associated with highest crude incidence rate (252 per 100 000 person-years), particularly Bangladesh. Younger age and immigrants returning to their COB were generally associated with higher risk of acquisition. CONCLUSIONS: The risk of typhoid fever in Australian travellers to endemic regions is considerable. Immigrants returning to their COB appear to be at higher risk and it is likely that this risk extends to their traveling dependents. These findings help clinicians and public health officials to plan and advise pre-travel vaccination strategies with at-risk individuals and groups. Additional sociodemographic data collection with Australian typhoid notifications would enhance the surveillance of differing international travel risk groups leaving Australia.

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx.

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species' evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies' current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

Review on Experimental and Theoretical Investigations of Ultra-Short Pulsed Laser Ablation of Metals with Burst Pulses.

Laser processing with ultra-short double pulses has gained attraction since the beginning of the 2000s. In the last decade, pulse bursts consisting of multiple pulses with a delay of several 10 ns and less found their way into the area of micromachining of metals, opening up completely new process regimes and allowing an increase in the structuring rates and surface quality of machined samples. Several physical effects such as shielding or re-deposition of material have led to a new understanding of the related machining strategies and processing regimes. Results of both experimental and numerical investigations are placed into context for different time scales during laser processing. This review is dedicated to the fundamental physical phenomena taking place during burst processing and their respective effects on machining results of metals in the ultra-short pulse regime for delays ranging from several 100 fs to several microseconds. Furthermore, technical applications based on these effects are reviewed.

Experimental evidence that apologies promote forgiveness by communicating relationship value.

Robust evidence supports the importance of apologies for promoting forgiveness. Yet less is known about how apologies exert their effects. Here, we focus on their potential to promote forgiveness by way of increasing perceptions of relationship value. We used a method for directly testing these causal claims by manipulating both the independent variable and the proposed mediator. Namely, we use a 2 (Apology: yes vs. no) × 2 (Value: high vs. low) concurrent double-randomization design to test whether apologies cause forgiveness by affecting the same causal pathway as relationship value. In addition to supporting this causal claim, we also find that apologies had weaker effects on forgiveness when received from high-value transgressors, suggesting that the forgiveness-relevant information provided by apologies is redundant with relationship value. Taken together, these findings from a rigorous methodological paradigm help us parse out how apologies promote relationship repair.

African and Asian leopards are highly differentiated at the genomic level.

Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.

The complete mitochondrial genome of the meerkat (Suricata suricatta) and its phylogenetic relationship with other feliform species.

The meerkat, Suricata suricatta, is a highly social member of the mongoose family (Herpestidae) and the only extant species of the genus Suricata. We present the first complete mitochondrial genome of the meerkat, assembled with a seed-and-extend algorithm using three closely related species as references. Phylogenetic analyses using 22 mitochondrial genome sequences confirm the position of meerkat within the Herpestidae family and the Feliformia, a suborder of Carnivora, with high support values. This position is in good agreement with formerly conducted studies based on a small number of mitochondrial and nuclear gene fragments. Our complete mitochondrial genome represents a valuable resource for further phylogenetic studies, especially of the underrepresented members of the Herpestidae family.

Case Report: Neurocysticercosis Acquired in Australia.

Neurocysticercosis (NCC) is a disease caused by infection of the central nervous system with the larval stage of the tapeworm Taenia solium. This disease is endemic in many parts of the world, including Africa, Asia, and Latin America, where animal husbandry practices are common such that pigs reared for human consumption ingest feces from humans infected with T. solium. Neurocysticercosis is rarely acquired in economically affluent regions, including North America, Central Europe, Japan, and Australasia, and in countries where pork consumption is discouraged by religious or social practices. In these countries, NCC is usually diagnosed in immigrants or returning travelers who have spent time in endemic regions. Here, we report a case of NCC in a 25-year-old woman presenting with worsening visual symptoms in association with headache, diagnosed previously as a migraine with visual aura. This person had always lived in Australia and had never traveled overseas to a country endemic for T. solium. The unusual features of the clinical presentation and epidemiology are highlighted to raise physicians' awareness that attention needs to be paid to the risk of autochthonous infection occurring in non-endemic countries.

Dissociable mappings of tonic and phasic pupillary features onto cognitive processes involved in mental arithmetic.

Pupil size modulations have been used for decades as a window into the mind, and several pupillary features have been implicated in a variety of cognitive processes. Thus, a general challenge facing the field of pupillometry has been understanding which pupil features should be most relevant for explaining behavior in a given task domain. In the present study, a longitudinal design was employed where participants completed 8 biweekly sessions of a classic mental arithmetic task for the purposes of teasing apart the relationships between tonic/phasic pupil features (baseline, peak amplitude, peak latency) and two task-related cognitive processes including mental processing load (indexed by math question difficulty) and decision making (indexed by response times). We used multi-level modeling to account for individual variation while identifying pupil-to-behavior relationships at the single-trial and between-session levels. We show a dissociation between phasic and tonic features with peak amplitude and latency (but not baseline) driven by ongoing task-related processing, whereas baseline was driven by state-level effects that changed over a longer time period (i.e. weeks). Finally, we report a dissociation between peak amplitude and latency whereby amplitude reflected surprise and processing load, and latency reflected decision making times.

Forgiveness takes place on an attitudinal continuum from hostility to friendliness: Toward a closer union of forgiveness theory and measurement.

Researchers commonly conceptualize forgiveness as a rich complex of psychological changes involving attitudes, emotions, and behaviors. Psychometric work with the measures developed to capture this conceptual richness, however, often points to a simpler picture of the psychological dimensions in which forgiveness takes place. In an effort to better unite forgiveness theory and measurement, we evaluate several psychometric models for common measures of forgiveness. In doing so, we study people from the United States and Japan to understand forgiveness in both nonclose and close relationships. In addition, we assess the predictive utility of these models for several behavioral outcomes that traditionally have been linked to forgiveness motives. Finally, we use the methods of item response theory, which place person abilities and item responses on the same metric and, thus, help us draw psychological inferences from the ordering of item difficulties. Our results highlight models based on correlated factors models and bifactor (S-1) models. The bifactor (S-1) model evinced particular utility: Its general factor consistently predicts variation in relevant criterion measures, including 4 different experimental economic games (when played with a transgressor), and also suffuses a second self-report measure of forgiveness. Moreover, the general factor of the bifactor (S-1) model identifies a single psychological dimension that runs from hostility to friendliness while also pointing to other sources of variance that may be conceived of as method factors. Taken together, these results suggest that forgiveness can be usefully conceptualized as prosocial change along a single attitudinal continuum that ranges from hostility to friendliness. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

National cost savings from an ambulatory program for low-risk febrile neutropenia patients in Australia.

Objective The management of low-risk febrile neutropenia (FN) patients through ambulatory programs has demonstrated comparative safety and effectiveness to in-patient strategies. However, there is limited evidence of benefits of changing practice, particularly on a national scale. The aim of this study was to estimate costs and benefits of the program over a 10-year time horizon. Methods A comparative cost analysis from a health system perspective was performed, comparing costs and length of stay (LOS) of patients enrolled in an ambulatory program to a historical cohort who did not receive the program. Generalised linear models were used for analysis and bootstrapped to account for uncertainty. National data of identified FN admissions were used to inform future projections, with varying proportions of low-risk patients and eligibility for the ambulatory program. Results The overall LOS for patients in ambulatory cohort was 1.9 days shorter (95% confidence interval (CI) 1.0-2.8 days), a 50% reduction in in-patient bed-days. Although patients in the ambulatory cohort incurred additional costs due to care received outside hospital (mean (± s.d.) A$828.03 ± 124.30), the mean total cost incurred remained substantially lower than that of the historical cohort (A$2979 lower; 95% CI A$772-5391). On a national scale, this could translate into A$62.7 million in costs averted and 41347 bed-days saved over 10 years if the low-risk prediction rate and eligibility for ambulatory programs remained at currently observed rates. Conclusions The wider implementation of a safe and effective ambulatory program to manage low-risk FN patients can result in significant return-on-investment for the healthcare system by eliminating avoidable costs due to unnecessary lengthy hospital admissions. What is known about the topic? There is strong evidence demonstrating out-patient treatment of low-risk FN patients to be an effective and cost-effective strategy compared with continued in-patient hospitalisation. What does this paper add? This study demonstrates the sustainability of the ambulatory program in ensuring cost benefits and in-patient beds through real-life implementation data. It also provides evidence of the substantial cost and bed-days potentially averted when the cost savings and difference in LOS are estimated on a national scale over a 10-year time horizon. What are the implications for practitioners? The management of low-risk FN patients through ambulatory or out-patient programs is a safe and effective approach. There is strong evidence demonstrating the likely cost savings and considerable bed-days saved, which can be reallocated to meet other medical demands.

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes.

Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.

Non-invasive faecal sampling reveals spatial organization and improves measures of genetic diversity for the conservation assessment of territorial species: Caucasian lynx as a case species.

The Caucasian lynx, Lynx lynx dinniki, has one of the southernmost distributions in the Eurasian lynx range, covering Anatolian Turkey, the Caucasus and Iran. Little is known about the biology and the genetic status of this subspecies. To collect baseline genetic, ecological and behavioural data and benefit future conservation of L. l. dinniki, we monitored 11 lynx territories (396 km2) in northwestern Anatolia. We assessed genetic diversity of this population by non-invasively collecting 171 faecal samples and trapped and sampled 12 lynx individuals using box traps. We observed high allelic variation at 11 nuclear microsatellite markers, and found no signs of inbreeding despite the potential isolation of this population. We obtained similar numbers of distinct genotypes from the two sampling sources. Our results indicated that first order female relatives occupy neighbouring territories (female philopatry) and that territorial male lynx were highly unrelated to each other and to female territorial lynx, suggesting long distance male dispersal. Particular male and female resident territorial lynx and their offspring (kittens and subadults) were more likely to be trapped than resident floaters or dispersing (unrelated) lynx. Conversely, we obtained more data for unrelated lynx and higher numbers of territorials using non-invasive sampling (faeces). When invasive and non-invasive samples were analysed separately, the spatial organisation of lynx (in terms of female philopatry and females and males occupying permanent ranges) affected measures of genetic diversity in such a way that estimates of genetic diversity were reduced if only invasive samples were considered. It appears that, at small spatial scales, invasive sampling using box traps may underestimate the genetic diversity in carnivores with permanent ranges and philopatry such as the Eurasian lynx. As non-invasive sampling can also provide additional data on diet and spatial organisation, we advocate the use of such samples for conservation genetic studies of vulnerable, endangered or data deficient territorial species.

Shedding Light on a Secretive Tertiary urodelean Relict: Hynobiid salamanders (Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental and Transcriptomic Data.

The Hyrcanian Forests present a unique Tertiary relict ecosystem, covering the northern Elburz and Talysh Ranges (Iran, Azerbaijan), a poorly investigated, unique biodiversity hotspot with many cryptic species. Since the 1970s, two nominal species of Urodela, Hynobiidae, Batrachuperus (later: Paradactylodon) have been described: Paradactylodon persicus from northwestern and P. gorganensis from northeastern Iran. Although P. gorganensis has been involved in studies on phylogeny and development, there is little data on the phylogeography, systematics, and development of the genus throughout the Hyrcanian Forests; genome-wide resources have been entirely missing. Given the huge genome size of hynobiids, making whole genome sequencing hardly affordable, we aimed to publish the first transcriptomic resources for Paradactylodon from an embryo and a larva (9.17 Gb RNA sequences; assembled to 78,918 unigenes). We also listed 32 genes involved in vertebrate sexual development and sex determination. Photographic documentation of the development from egg sacs across several embryonal and larval stages until metamorphosis enabled, for the first time, comparison of the ontogeny with that of other hynobiids and new histological and transcriptomic insights into early gonads and timing of their differentiation. Transcriptomes from central Elburz, next-generation sequencing (NGS) libraries of archival DNA of topotypic P. persicus, and GenBank-sequences of eastern P. gorganensis allowed phylogenetic analysis with three mitochondrial genomes, supplemented by PCR-amplified mtDNA-fragments from 17 museum specimens, documenting <2% uncorrected intraspecific genetic distance. Our data suggest that these rare salamanders belong to a single species P. persicus s.l. Humankind has a great responsibility to protect this species and the unique biodiversity of the Hyrcanian Forest ecosystems.

Sequencing Library Preparation from Degraded Samples for Non-illumina Sequencing Platforms.

Efficient methods for building genomic sequencing libraries from degraded DNA have been in place for Illumina sequencing platforms for some years now, but such methods are still lacking for other sequencing platforms. Here, we provide a protocol for building genomic libraries from degraded DNA (archival or ancient sample material) for sequencing on the Ion Torrent™ high-throughput sequencing platforms. In addition to a reduction in time and cost in comparison to commercial kits, this protocol removes purification steps prior to library amplification, an important consideration for work involving historical samples. Libraries prepared using this method are appropriate for either shotgun sequencing or enrichment-based downstream approaches.