Parallel genomic responses to historical climate change and high elevation in East Asian songbirds.

Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel-and whether the level of parallelism is affected by heterozygosity-by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east-west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity-likely the result of late-Pleistocene demographic contraction-than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai-Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.

Field testing of transgenic aspen from large greenhouse screening identifies unexpected winners.

Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.

Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex.

Genetic isolation and morphological differentiation are two important factors in the speciation process that not always act in concert. A rapid morphological change in a lineage can hide its close relationship to another lineage, while slight morphological differentiation between two taxa can give the appearance of a closer relationship than is actually the case. The Dollarbird (Eurystomus orientalis) and the Azure Roller (Eurystomus azureus) is such an example. Today the Dollarbird and the Azure Roller are unanimously considered to constitute two distinct species, but in a recent genetic study it has been shown that the latter taxon, despite being larger and having a distinctly different coloration, is phylogenetically nested within the former. Its precise placement within this complex has not been determined, however. In this study, we investigate the phylogenetic relationships within the Dollarbird/Azure Roller complex. We estimate divergence times and infer phylogenetic relationships using sequence data from 6,475 genome-wide intronic regions, as well as complete mitochondrial genomes, using both concatenation and multispecies coalescence approaches. We find that within the Dollarbird/Azure Roller complex there are several examples of discrepancies between genetic and morphological differentiation. The Dollarbird is currently divided into between nine to twelve subspecies. Some of these subspecies are poorly differentiated, whereas others are morphologically more clearly discernable. Our data suggest that the complex consist of at least seven distinct genetic lineages that do not entirely match the morphological variation within the group. For instance, our results show that the subspecies solomonensis from the Solomon Islands, despite being morphologically very similar to its geographically closest neighbors, in fact is a highly distinct lineage that became isolated more than 700,000 years ago. In contrast, the morphologically distinct Azure Roller, which is currently treated as a distinct species, is nested within the Dollarbird and forms a slightly younger lineage than solomonensis and is the sister group to a clade with Australian and New Guinean Dollarbirds. Our results also show a deep genetic split within the Dollarbirds on the Asian mainland. This stands in contrast to the apparent clinal morphological variation reported for the birds on the Asian mainland. We also find support for the presence of a genetically distinct clade in the Wallacea region. The birds from the Wallacea region has previously been recognized as a distinct subspecies, connectens, but is currently placed in synonymy of other subspecies. Our results are thus at odds with the current division of the Dollarbird/Azure Roller complex into two species. Given that the species status of azureus is undisputed, the apparent genetic isolation of solomonensis and its clear separation from the other lineages suggests that this taxon also warrants species status. Based on the genetic and morphological variation observed within the Dollarbird/Azure Roller complex there is little doubt that even more taxa should regarded as species, but this require further examination.

Design and performance of a dedicated coherent X-ray scanning diffraction instrument at beamline NanoMAX of MAX IV.

The diffraction endstation of the NanoMAX beamline is designed to provide high-flux coherent X-ray nano-beams for experiments requiring many degrees of freedom for sample and detector. The endstation is equipped with high-efficiency Kirkpatrick-Baez mirror focusing optics and a two-circle goniometer supporting a positioning and scanning device, designed to carry a compact sample environment. A robot is used as a detector arm. The endstation, in continued development, has been in user operation since summer 2017.

Complete alignment of a KB-mirror system guided by ptychography.

We demonstrate how the individual mirrors of a high-quality Kirkpatrick-Baez (KB) mirror system can be aligned to each other to create an optimally focused beam, through minimizing aberrations in the phase of the ptychographically reconstructed pupil function. Different sources of misalignment and the distinctive phase artifacts they create are presented via experimental results from the alignment of the KB mirrors at the NanoMAX diffraction endstation. The catalog of aberration artifacts can be used to easily identify which parameter requires further tuning in the alignment of any KB mirror system.

Contrast - a lightweight Python framework for beamline orchestration and data acquisition.

The emergence of fourth-generation synchrotrons is prompting the development of new systems for experimental control and data acquisition. However, as general control systems are designed to cover a wide set of instruments and techniques, they tend to become large and complicated, at the cost of experimental flexibility. Here we present Contrast, a simple Python framework for interacting with beamline components, orchestrating experiments and managing data acquisition. The system is presented and demonstrated via its application at the NanoMAX beamline of the MAX IV Laboratory.

NanoMAX: the hard X-ray nanoprobe beamline at the MAX IV Laboratory.

NanoMAX is the first hard X-ray nanoprobe beamline at the MAX IV laboratory. It utilizes the unique properties of the world's first operational multi-bend achromat storage ring to provide an intense and coherent focused beam for experiments with several methods. In this paper we present the beamline optics design in detail, show the performance figures, and give an overview of the surrounding infrastructure and the operational diffraction endstation.

Knowledge of and support for cancer patient pathways among general practitioners and other physicians - a study from Sweden.

OBJECTIVE: To investigate the expertise in and support of the implemented new method of cancer patient pathways (CPPs) among general practitioners (GPs) and other working physicians in Sweden. DESIGN: A survey in the form of 10 knowledge-based multiple-choice questions (MCQs) and two general questions about CPPs. SETTING: Physicians from two different regions in Sweden answered the survey between December 2018 and January 2019. SUBJECTS: GPs in primary care compared to other physicians. 155 participants completed the survey and the response rate was 65%. MAIN OUTCOME MEASURES: Physicians' self-estimated knowledge of CPPs in general and opinion of CPPs effect on mortality and morbidity. Their scores on 10 different MCQs. Scores were analysed in subgroups related to the physicians medical specialty and experience. RESULTS: A majority of all physicians (63%) felt that they had insufficient knowledge regarding the procedure of CPPs, and the average score from the MCQs was 3.8 out of 10 correct answers. The results showed that GPs performed significantly better than specialists from other disciplines. CONCLUSIONS: The low percentage of correctly answered MCQs shows that the information about the entry part of CPPs needs to be improved. The study demonstrates a support for the system with CPPs because the physicians believed in its' positive effects on morbidity and mortality, however, it also reveals a lack of self-estimated knowledge about the system with CPPs.Key pointsCancer patient pathways (CPPs) is a newly implemented method in Sweden that aims to equalize cancer care and reduce the time to diagnosis and treatment.The proficiency of when to initiate an investigation according to a specific CPP seems low. General practitioners (GPs) performed significantly better on knowledge-based questions than other specialists did.Physicians rated their knowledge as insufficient regarding the procedure of CPPs.A clear majority of physicians believed that CPPs promotes a lower mortality and morbidity in cancer.

Ptychographic characterization of a coherent nanofocused X-ray beam.

The NanoMAX hard X-ray nanoprobe is the first beamline to take full advantage of the diffraction-limited storage ring at the MAX IV synchrotron and delivers a high coherent photon flux for applications in diffraction and imaging. Here, we characterize its coherent and focused beam using ptychographic analysis. We derive beam profiles in the energy range 6-22 keV and estimate the coherent flux based on a probe mode decomposition approach.

Niche filling slows the diversification of Himalayan songbirds.

Speciation generally involves a three-step process--range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.

Focus characterization of the NanoMAX Kirkpatrick-Baez mirror system.

The focusing and coherence properties of the NanoMAX Kirkpatrick-Baez mirror system at the fourth-generation MAX IV synchrotron in Lund have been characterized. The direct measurement of nano-focused X-ray beams is possible by scanning of an X-ray waveguide, serving basically as an ultra-thin slit. In quasi-coherent operation, beam sizes of down to 56 nm (FWHM, horizontal direction) can be achieved. Comparing measured Airy-like fringe patterns with simulations, the degree of coherence |µ| has been quantified as a function of the secondary source aperture (SSA); the coherence is larger than 50% for SSA sizes below 11 µm at hard X-ray energies of 14 keV. For an SSA size of 5 µm, the degree of coherence has been determined to be 87%.

Accurate Hit Estimation for Iterative Screening Using Venn-ABERS Predictors.

Iterative screening has emerged as a promising approach to increase the efficiency of high-throughput screening (HTS) campaigns in drug discovery. By learning from a subset of the compound library, inferences on what compounds to screen next can be made by predictive models. One of the challenges of iterative screening is to decide how many iterations to perform. This is mainly related to difficulties in estimating the prospective hit rate in any given iteration. In this article, a novel method based on Venn-ABERS predictors is proposed. The method provides accurate estimates of the number of hits retrieved in any given iteration during an HTS campaign. The estimates provide the necessary information to support the decision on the number of iterations needed to maximize the screening outcome. Thus, this method offers a prospective screening strategy for early-stage drug discovery.

Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.

The rollers (Coraciidae) constitute a relative small avian family with ca. 12 species distributed in Africa, western and southern Eurasia, and eastern Australia. In this study we examine the phylogenetic relationships of all species currently recognized in the family, including two taxa whose taxonomic status is currently contested. By using shotgun sequencing on degraded DNA from museum study skins we have been able to recover complete mitochondrial genomes as well as 15 nuclear genes for in total 16 taxa. The gene sequences were analyzed both concatenated in a maximum likelihood framework as well in a species tree approach using MP-EST. The different analytical approaches yield similar, highly supported trees and support the current division of the rollers into two genera, Coracias and Eurystomus. The only conflict relates to the placement of the Blue-bellied Roller (C. cyanogaster), where the mitochondrial, and the concatenated nuclear and mitochondrial data set, place this taxon as sister to the other Coracias species, whereas nuclear data and the species tree analysis place it as the sister taxon of C. naevia and C. spatulatus. All analyses place the Eurasian roller (C. garrulus) with the two African species, Abyssinian Roller (C. abyssinica) and Liliac-breasted Roller (C. caudatus), and place this clade as the sister group to the Asian Coracias rollers. In addition, our results support a sister group relationship between the morphologically rather dissimilar Purple Roller (C. naevia) and Racquet-tailed Roller (C. spatulatus) and also support the division of Eurystomus in an African and an Asian clade. However, within the Asian clade the Azure Roller (E. azureus) from Halmahera appears to be nested within the Dollarbird (E. orientalis), indicating that that this taxon is a morphological divergent, but a rather recent offshoot, of the widespread Dollarbird. Similarly, the Purple-winged Roller (C. temminickii) from Sulawesi group together with C. benghalensis affinis from Southeast Asia and these two in turn comprises the sister group to C. benghalensis benghalensis from India and western Asia.

Survival, early growth and impact of damage by late-spring frost and winter desiccation on Douglas-fir seedlings in southern Sweden.

Introduction of non-native species, such as Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), can be a means of mitigating the effects of climate change by meeting the growing demand for biomass and high quality wood. The aim of this study was to investigate early growth, survival and damage from late-spring frost and winter desiccation. A provenance trial with four coastal and three interior provenances of Douglas-fir originating from British Columbia, Canada, was established in Southwest Sweden (56°43'N, 13°08'E). Seedling height, length of the leading shoot, and occurrence of frost damage, were measured after one, three, and six growing seasons. Timing of bud break in spring was also observed. The interior Douglas-fir were more frequently damaged by late-spring frost compared to the coastal Douglas-fir. The interior Douglas-fir still had a higher survival after six growing seasons compared to the coastal variety. All provenances were damaged by winter desiccation, but the provenances originating from the coastal area were more severely damaged. Choice of variety may reduce the risk for either late-spring frost or winter desiccation.

Vibrational stability of a cryocooled horizontal double-crystal monochromator.

The vibrational stability of a horizontally deflecting double-crystal monochromator (HDCM) is investigated. Inherently a HDCM will preserve the vertical beam stability better than a `normal' vertical double-crystal monochromator as the vibrations of a HDCM will almost exclusively affect the horizontal stability. Here both the relative pitch vibration between the first and second crystal and the absolute pitch vibration of the second crystal are measured. All reported measurements are obtained under active cooling by means of flowing liquid nitrogen (LN2). It is found that it is favorable to circulate the LN2 at high pressures and low flow rates (up to 5.9 bar and down to 3 l min(-1) is tested) to attain low vibrations. An absolute pitch stability of the second crystal of 18 nrad RMS, 2-2500 Hz, and a relative pitch stability between the two crystals of 25 nrad RMS, 1-2500 Hz, is obtained under cryocooling conditions that allow for 1516 W to be adsorbed by the LN2 before it vaporizes.

Barriers and enablers to the implementation of Safewards and the alignment to the i-PARIHS framework - A qualitative systematic review.

Inpatient mental healthcare settings should offer safe environments for patients to heal and recover and for staff to provide high-quality treatment and care. However, aggressive patient behaviour, unengaged staff approaches, and the use of restrictive practices are frequently reported. The Safewards model includes ten interventions that aim to prevent conflict and containment. The model has shown promising results but at the same time often presents challenges to successful implementation strategies. The aim of this study was to review qualitative knowledge on staff experiences of barriers and enablers to the implementation of Safewards, from the perspective of implementation science and the i-PARIHS framework. A search of the Web of Science, ASSIA, Cochrane Library, SCOPUS, Medline, Embase, PsycINFO, and CINAHL databases resulted in 10 articles. A deductive framework analysis approach was used to identify barriers and enablers and the alignment to the i-PARIHS. Data most represented by the i-PARIHS were related to the following: local-level formal and informal leadership support, innovation degree of fit with existing practice and values, and recipients' values and beliefs. This indicates that if a ward or organization wants to implement Safewards and direct limited resources to only a few implementation determinants, these three may be worth considering. Data representing levels of external health system and organizational contexts were rare. In contrast, data relating to local (ward)-level contexts was highly represented which may reflect Safewards's focus on quality improvement strategies on a local rather than organizational level.

Scanning WAXS microscopy of regenerated cellulose fibers at mesoscopic resolution.

In this work, regenerated cellulose textile fibers, Ioncell-F, dry-wet spun with different draw ratios, have been investigated by scanning wide-angle X-ray scattering (WAXS) using a mesoscopic X-ray beam. The fibers were found to be homogeneous on the 500 nm length scale. Analysis of the azimuthal angular dependence of a crystalline Bragg spot intensity revealed a radial dependence of the degree of orientation of crystallites that was found to increase with the distance from the center of the fiber. We attribute this to radial velocity gradients during the extrusion of the spin dope and the early stage of drawing. On the other hand, the fiber crystallinity was found to be essentially homogeneous over the fiber cross section.

A complete multilocus species phylogeny of the tits and chickadees (Aves: Paridae).

The avian family Paridae (tits and chickadees) contains c. 55 species distributed in the Palearctic, Nearctic, Afrotropics and Indomalaya. The group includes some of the most well-known and extensively studied avian species, and the evolutionary history, in particular the post-glacial colonization of the northern latitudes, has been comparably well-studied for several species. Yet a comprehensive phylogeny of the whole clade is lacking. Here, we present the first complete species phylogeny for the group based on sequence data from two nuclear introns and one mitochondrial gene for 67 taxa of parids. Our results strongly support the inclusion of the Fire-capped Tit (Cephalopyrus flammiceps), currently placed in the Remizidae, as the most basal member of the Paridae. The Yellow-browed Tit (Sylviparus modestus) and the Sultan Tit (Melanochlora sultanea) constitute the next two sequential branches whereas the remaining tits fall into two large clades, one of which contains the seed hoarding and nest excavating species. The indicated clades within these two groups are largely congruent with recent classifications, but with several unforeseen relationships, such as non-monophyly of the Sombre Tit (Poecile lugubris) and the Marsh Tit (Poecile palustris), as well as non-monophyly of both the African gray and the African black tits. Further, our results support a close relationship between the White-fronted Tit (Parus semilarvatus) and the varied Tit (Poecile varius) as well as a close relationship between the White-naped Tit (Parus nuchalis) and the Yellow-cheeked and Black-lored tits (Parus spilonotus and P. xanthogenys). Finally, Hume's Ground-tit (Pseudopodoces humilis) is found to be closely related to the Green-backed Tit (Parus monticolus) and the Great Tit (Parus major). We propose a new classification that is in accordance with this phylogeny.

Multi-scale characterization of the spatio-temporal interplay between elemental composition, mineral deposition and remodelling in bone fracture healing.

Bone mineralization involves a complex orchestration of physico-chemical responses from the organism. Despite extensive studies, the detailed mechanisms of mineralization remain to be elucidated. This study aims to characterize bone mineralization using an in-vivo long bone fracture healing model in the rat. The spatio-temporal distribution of relevant elements was correlated to the deposition and maturation of hydroxyapatite and the presence of matrix remodeling compounds (MMP-13). Multi-scale measurements indicated that (i) zinc is required for both the initial mineral deposition and resorption processes during mature mineral remodeling; (ii) Zinc and MMP-13 show similar spatio-temporal trends during early mineralization; (iii) Iron acts locally and in coordination with zinc during mineralization, thus indicating novel evidence of the time-events and inter-play between the elements. These findings improve the understanding of bone mineralization by explaining the link between the different constituents of this process throughout the healing time. STATEMENT OF SIGNIFICANCE: Bone mineralization involves a complex orchestration of physico-chemical responses from the organism, the detailed mechanisms of which remain to be elucidated. This study presents a highly novel multi-scale multi-modal investigation of bone mineralization using bone fracture healing as a model system. We present original characterization of tissue mineralization, where we relate the spatio-temporal distribution of important trace elements to a key matrix remodeling compound (MMP-13), the initial deposition and maturation of hydroxyapatite and further remodeling processes. This is the first time that mineralization has been probed down to the nanometric level, and where key mineralization components have been investigated to achieve a comprehensive and mechanistic understanding of the underlying mineralization processes during bone healing.

Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change.

The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.