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Paleogenomes reveal a complex evolutionary history of late Pleistocene bison in Northeastern China
(2022)
Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere.
Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive.
Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China.
Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP).
In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B).
Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.
A special class of English words with tense vowel/diphthong nuclei and liquid codas receive variable syllable count judgments (one and over-one syllables).
Tilsen and Cohn (2016) showed that differences in judgments correlate with differences in production, supporting their hypothesis that meta-phonological judgments and speech motor control share a common representation.
In the present study, we further propose that syllable count judgments are related to subsegmental representation in the rime, and are independent of acoustic duration.
We test the hypothesis by comparing English and German, chosen for their similar word structures and vowel length contrast, and their crucial difference in the gestural specification of coda liquids.
In English, coda liquids have an earlier vocalic gesture relative to the consonantal one, while in German, both gestures are simultaneous.
We stipulated that sesquisyllabic (over-one) judgments are related to the count of sequentially-timed vocalic gestures in the rime. The difference in the coda liquid composition between the two languages predicts that sesquisyllables should not emerge in German.
Our predictions were confirmed by the results of parallel production (acoustic) and syllable count judgment experiments in English and German.
We propose a model accounting for these results, and we discuss its typological implications and its limitations.
During a survey of aquatic fungi from Anzali Lagoon in Iran, several fungal specimens were isolated from freshwater habitats. Morphological evidence and comparing sequencing based on rDNA (ITS and LSU) and protein-coding genes (TEF1 and TUB2) showed that some isolates belong to undescribed fungal species.
These isolates belong to Arthrobotrys and Sarocladium, two ascomycetes genera. Arthrobotrys hyrcanus, sp. nov., differs from closely related species such as A. dianchiensis by its larger conidia and septation of primary conidia. Sarocladium pseudokiliense, sp. nov., was similar to S. kiliense, but distinguished by its conidial shape and the absence of adelophialides and chlamydospores.
Morphological descriptions, illustrations and multilocus phylogenetic analysis for both new species are provided.
Devising optimal interventions for constraining stochastic systems is a challenging endeavor that has to confront the interplay between randomness and dynamical nonlinearity.
Existing intervention methods that employ stochastic path sampling scale poorly with increasing system dimension and are slow to converge.
Here we propose a generally applicable and practically feasible methodology that computes the optimal interventions in a noniterative scheme.
We formulate the optimal dynamical adjustments in terms of deterministically sampled probability flows approximated by an interacting particle system.
Applied to several biologically inspired models, we demonstrate that our method provides the necessary optimal controls in settings with terminal, transient, or generalized collective state constraints and arbitrary system dynamics.
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal enzymes that catalyze the oxyfunctionalization of non-activated hydrocarbons, making them valuable biocatalysts. Despite the increasing interest in UPOs that has led to the identification of thousands of putative UPO genes, only a few of these have been successfully expressed and characterized.
There is currently no universal expression system in place to explore their full potential. Cell-free protein synthesis has proven to be a sophisticated technique for the synthesis of difficult-to-express proteins.
In this work, we aimed to establish an insect-based cell-free protein synthesis (CFPS) platform to produce UPOs. CFPS relies on translationally active cell lysates rather than living cells.
The system parameters can thus be directly manipulated without having to account for cell viability, thereby making it highly adaptable.
The insect-based lysate contains translocationally active, ER-derived vesicles, called microsomes.
These microsomes have been shown to allow efficient translocation of proteins into their lumen, promoting post-translational modifications such as disulfide bridge formation and N-glycosylations.
In this study the ability of a redox optimized, vesicle-based, eukaryotic CFPS system to synthesize functional UPOs was explored. The influence of different reaction parameters as well as the influence of translocation on enzyme activity was evaluated for a short UPO from Marasmius rotula and a long UPO from Agrocybe aegerita.
The capability of the CFPS system described here was demonstrated by the successful synthesis of a novel UPO from Podospora anserina, thus qualifying CFPS as a promising tool for the identification and evaluation of novel UPOs and variants thereof.
Quantifying the influence of pollen aging on the adhesive
properties of Hypochaeris radicata pollen
(2022)
Simple Summary Pollination is the transfer of pollen from a plant's male part (anther) to the corresponding female part (stigma). It is a fundamental biological process that ensures plant reproduction. Most studies investigate pollination from a biological perspective, but the underlying physical processes are poorly understood. Many plants rely on insects to transport pollen and the forces with which pollen adhere to insects and floral surfaces are fundamental for successful pollination.
We quantified pollen adhesion by measuring the forces necessary to detach Hypochaeris radicata (catsear, a common insect-pollinated plant) pollen from glass and studied for the first time how the adhesion forces change with pollen aging.
Our results show that newly formed adhesion bonds between H. radicata pollen and glass are stronger for fresh pollen than for old ones. On the other hand, when H. radicata pollen age in contact with glass, the adhesion between pollen and glass strengthens over time. These effects are probably caused by the viscous liquid covering most pollen (pollenkitt) changing its viscoelastic properties as it dries.
Although pollination is one of the most crucial biological processes that ensures plant reproduction, its mechanisms are poorly understood. Especially in insect-mediated pollination, a pollen undergoes several attachment and detachment cycles when being transferred from anther to insect and from insect to stigma. The influence of the properties of pollen, insect and floral surfaces on the adhesion forces that mediate pollen transfer have been poorly studied.
Here, we investigate the adhesive properties of Hypochaeris radicata pollen and their dependence on pollen aging by quantifying the pull-off forces from glass slides using centrifugation and atomic force microscopy. We found that the properties of the pollenkitt-the viscous, lipid liquid on the surface of most pollen grains-influences the forces necessary to detach a pollen from hydrophilic surfaces.
Our results show that aged H. radicata pollen form weaker adhesions to hydrophilic glass than fresh ones. On the other hand, when a pollen grain ages in contact with glass, the adhesion between the two surfaces increases over time.
This study shows for the first time the pollen aging effect on the pollination mechanism.
Volatile organic compounds (VOCs) are involved in microbial interspecies communication and in the mode of action of various antagonistic interactions. They are important for balancing host-microbe interactions and provide the basis for developing biological control strategies to control plant pathogens.
We studied the interactions between the bacterial antagonist Serratia plymuthica HRO-C48 and three fungal plant pathogens Rhizoctonia solani, Leptosphaeria maculans and Verticillium longisporum. Significant differences in fungal growth inhibition by the Serratia-emitted VOCs in pairwise dual culture assays and changes in the transcriptome of the bacterium and in the volatilomes of both interacting partners were observed. Even though the rate of fungal growth inhibition by Serratia was variable, the confrontation of the bacterium with the VOCs of all three fungi changed the levels of expression of the genes involved in stress response, biofilm formation, and the production of antimicrobial VOCs. Pairwise interacting microorganisms switched between defense (downregulation of gene expression) and attack (upregulation of gene expression and metabolism followed by growth inhibition of the interacting partner) modes, subject to the combinations of microorganisms that were interacting.
In the attack mode HRO-C48 significantly inhibited the growth of R. solani while simultaneously boosting its own metabolism; by contrast, its metabolism was downregulated when HRO-C48 went into a defense mode that was induced by the L. maculans and V. longisporum VOCs. L. maculans growth was slightly reduced by the one bacterial VOC methyl acetate that induced a strong downregulation of expression of genes involved in almost all metabolic functions in S. plymuthica.
Similarly, the interaction between S. plymuthica and V. longisporum resulted in an insignificant growth reduction of the fungus and repressed the rate of bacterial metabolism on the transcriptional level, accompanied by an intense volatile dialogue. Overall, our results indicate that VOCs substantially contribute to the highly break species-specific interactions between pathogens and their natural antagonists and thus deserving of increased consideration for pathogen control.
Floodplain wetlands are critical for sustaining various ecological and hydrological functions in a riverine environment. Severe anthropogenic alterations and human occupation of floodplains have threatened these wetlands in several parts of the world. A major handicap in designing sustainable restoration and monitoring strategies for these wetlands is the lack of scientific process-based understanding and information on the basin-scale controls of their degradation. Here, we offer a novel approach to integrate the connectivity of the wetlands with the surrounding landscape along with other attributes such as stream density, hydrometeorological parameters, and groundwater dynamics to explain their degradation and then to prioritise them for restoration and monitoring.
We hypothesise that the best possible connectivity scenario for the existence of a wetland would be if (a) the wetland has a high connectivity with its upslope area, and (b) the wetland has a low connectivity with its downslope region.
The first condition ensures the flow of water into the wetland and the second condition allows longer water residence time in the wetland. Accordingly, we define four connectivity-based wetland health scenarios-good, no impact, bad, and worst.
We have implemented the proposed method in 3226 wetlands in the Ramganga Basin in north India. Further, we have applied specific selection criteria, such as distance from the nearest stream and stream density, to prioritise the wetlands for restoration and monitoring.
We conclude that the connectivity analysis offers a quick process-based assessment of wetlands' health status and serves as an important criterion to prioritise the wetlands for developing appropriate management strategies.
Dark field scattering microscopy can create large hyperspectral data sets that contain a wealth of information on the properties and the molecular environment of noble metal nanoparticles.
For a quick screening of samples of microscopic dimensions that contain many different types of plasmonic nanostructures, we propose a multivariate analysis of data sets of thousands to several hundreds of thousands of scattering spectra.
By using non-negative matrix factorization for decomposing the spectra, components are identified that represent individual plasmon resonances and relative contributions of these resonances to particular microscopic focal volumes in the mapping data sets. Using data from silver and gold nanoparticles in the presence of different molecules, including gold nanoparticle-protein agglomerates or silver nanoparticles forming aggregates in the presence of acrylamide, plasmonic properties are observed that differ from those of the original nanoparticles.
For the case of acrylamide, we show that the plasmon resonances of the silver nanoparticles are ideally suited to support surface enhanced Raman scattering (SERS) and the two-photon excited process of surface enhanced hyper Raman scattering (SEHRS). Both vibrational tools give complementary information on the in situ formed polyacrylamide and the molecular composition at the nanoparticle surface.
In this increasingly data-rich world, visual recordings of human behavior are often unable to be shared due to concerns about privacy.
Consequently, data sharing in fields such as behavioral science, multimodal communication, and human movement research is often limited.
In addition, in legal and other non-scientific contexts, privacy-related concerns may preclude the sharing of video recordings and thus remove the rich multimodal context that humans recruit to communicate.
Minimizing the risk of identity exposure while preserving critical behavioral information would maximize utility of public resources (e.g., research grants) and time invested in audio-visual research.
Here we present an open-source computer vision tool that masks the identities of humans while maintaining rich information about communicative body movements. Furthermore, this masking tool can be easily applied to many videos, leveraging computational tools to augment the reproducibility and accessibility of behavioral research.
The tool is designed for researchers and practitioners engaged in kinematic and affective research. Application areas include teaching/education, communication and human movement research, CCTV, and legal contexts.
Objective:
Hypertension has long been recognized as one of the most important predisposing factors for cardiovascular diseases and mortality.
In recent years, machine learning methods have shown potential in diagnostic and predictive approaches in chronic diseases.
Electronic health records (EHRs) have emerged as a reliable source of longitudinal data. The aim of this study is to predict the onset of hypertension using modern deep learning (DL) architectures, specifically long short-term memory (LSTM) networks, and longitudinal EHRs.
Materials and Methods:
We compare this approach to the best performing models reported from previous works, particularly XGboost, applied to aggregated features.
Our work is based on data from 233 895 adult patients from a large health system in the United States. We divided our population into 2 distinct longitudinal datasets based on the diagnosis date.
To ensure generalization to unseen data, we trained our models on the first dataset (dataset A "train and validation") using cross-validation, and then applied the models to a second dataset (dataset B "test") to assess their performance.
We also experimented with 2 different time-windows before the onset of hypertension and evaluated the impact on model performance.
Results:
With the LSTM network, we were able to achieve an area under the receiver operating characteristic curve value of 0.98 in the "train and validation" dataset A and 0.94 in the "test" dataset B for a prediction time window of 1 year. Lipid disorders, type 2 diabetes, and renal disorders are found to be associated with incident hypertension.
Conclusion:
These findings show that DL models based on temporal EHR data can improve the identification of patients at high risk of hypertension and corresponding driving factors. In the long term, this work may support identifying individuals who are at high risk for developing hypertension and facilitate earlier intervention to prevent the future development of hypertension.
The mechanisms underlying increased dual-task costs in the comparison of modality compatible stimulus -response mappings (e.g., visual-manual, auditory-vocal) and modality incompatible mappings (e.g., visual -vocal, auditory-manual) remain elusive.
To investigate whether additional control mechanisms are at work in simultaneously processing two modality incompatible mappings, we applied a transfer logic between both types of dual-task mappings in the context of a mental fatigue induction.
We expected an increase in dual-task costs for both modality mappings after a fatigue induction with modality compatible tasks. In contrast, we expected an additional, selective increase in modality incompatible dual-task costs after a fatigue induction with modality incompatible tasks.
We tested a group of 45young individuals (19-30 years) in an online pre-post design, in which participants were assigned to one of three groups. The two fatigue groups completed a 90-min time-on -task intervention with a dual task comprising either compatible or incompatible modality mappings.
The third group paused for 90 min as a passive control group. Pre and post-session contained single and dual tasks in both modality mappings for all participants. In addition to behavioral performance measurements, seven subjective items (effort, focus, subjective fatigue, motivation, frustration, mental and physical capacity) were analyzed.
Mean dual-task performance during and after the intervention indicated a practice effect instead of the presumed fatigue effect for all three groups. The modality incompatible intervention group showed a selective performance improvement for the modality incompatible mapping but no transfer to the modality compatible dual task. In contrast, the compatible intervention group showed moderately improved performance in both modality map-pings.
Still, participants reported increased subjective fatigue and reduced motivation after the fatigue inter-vention.
This dynamic interplay of training and fatigue effects suggests that high control demands were involved in the prolonged performance of a modality incompatible dual task, which are separable from modality compatible dual-task demands.
Hepatobiliary involvement is a hallmark in cystic fibrosis (CF), as the causative CF Transmembrane Conductance Regulator (CFTR) defect is expressed in the biliary tree. However, bile acid (BA) compositions in regard to pancreatic insufficiency, which is present at an early stage in about 85% of CF patients, have not been satisfactorily understood.
We assess the pattern of serum BAs in people with CF (pwCF) without CFTR modulator therapy in regard to pancreatic insufficiency and the CFTR genotype.
In 47 pwCF, 10 free and 12 taurine- and glycine-conjugated BAs in serum were prospectively assessed.
Findings were related to genotype, pancreatic insufficiency prevalence (PIP)-score, and hepatic involvement indicated by serum liver enzymes, as well as clinical and ultrasound criteria for CF-related liver disease.
Serum concentrations of total primary BAs and free cholic acid (CA) were significantly higher in pwCF with higher PIP-scores (p = 0.025, p = 0.009, respectively). Higher total BAs were seen in pwCF with PIP-scores >= 0.88 (p = 0.033) and with pancreatic insufficiency (p = 0.034).
Free CA was higher in patients with CF-related liver involvement without cirrhosis, compared to pwCF without liver disease (2.3-fold, p = 0.036). pwCF with severe CFTR genotypes, as assessed by the PIP-score, reveals more toxic BA compositions in serum. Subsequent studies assessing changes in BA homeostasis during new highly effective CFTR-modulating therapies are of high interest.
International migration patterns, at the global level, can to a large extent be explained through economic factors in origin and destination countries.
On the other hand, it has been shown that global climate change is likely to affect economic development over the coming decades.
Here, we demonstrate how these future climate impacts on national income levels could alter the global migration landscape.
Using an empirically calibrated global migration model, we investigate two separate mechanisms. The first is through destination-country income, which has been shown consistently to have a positive effect on immigration.
As countries' income levels relative to each other are projected to change in the future both due to different rates of economic growth and due to different levels of climate change impacts, the relative distribution of immigration across destination countries also changes as a result, all else being equal.
Second, emigration rates have been found to have a complex, inverted U-shaped dependence on origin-country income.
Given the available migration flow data, it is unclear whether this dependence-found in spatio-temporal panel data-also pertains to changes in a given migration flow over time. If it does, then climate change will additionally affect migration patterns through origin countries' emigration rates, as the relative and absolute positions of countries on the migration "hump" change.
We illustrate these different possibilities, and the corresponding effects of 3 degrees C global warming (above pre-industrial) on global migration patterns, using climate model projections and two different methods for estimating climate change effects on macroeconomic development.
We present the extension of the Kalmag model, proposed as a candidate for IGRF-13, to the twentieth century.
The dataset serving its derivation has been complemented by new measurements coming from satellites, ground-based observatories and land, marine and airborne surveys.
As its predecessor, this version is derived from a combination of a Kalman filter and a smoothing algorithm, providing mean models and associated uncertainties. These quantities permit a precise estimation of locations where mean solutions can be considered as reliable or not.
The temporal resolution of the core field and the secular variation was set to 0.1 year over the 122 years the model is spanning.
Nevertheless, it can be shown through ensembles a posteriori sampled, that this resolution can be effectively achieved only by a limited amount of spatial scales and during certain time periods.
Unsurprisingly, highest accuracy in both space and time of the core field and the secular variation is achieved during the CHAMP and Swarm era. In this version of Kalmag, a particular effort was made for resolving the small-scale lithospheric field.
Under specific statistical assumptions, the latter was modeled up to spherical harmonic degree and order 1000, and signal from both satellite and survey measurements contributed to its development.
External and induced fields were jointly estimated with the rest of the model. We show that their large scales could be accurately extracted from direct measurements whenever the latter exhibit a sufficiently high temporal coverage.
Temporally resolving these fields down to 3 hours during the CHAMP and Swarm missions, gave us access to the link between induced and magnetospheric fields. In particular, the period dependence of the driving signal on the induced one could be directly observed.
The model is available through various physical and statistical quantities on a dedicated website at https://ionocovar.agnld.uni-potsdam.de/Kalmag/.
Time and angle-resolved time-of-flight electron spectroscopy for functional materials science
(2022)
Electron spectroscopy with the unprecedented transmission of angle-resolved time-of-flight detection, in combination with pulsed X-ray sources, brings new impetus to functional materials science.
We showcase recent developments towards chemical sensitivity from electron spectroscopy for chemical analysis and structural information from photoelectron diffraction using the phase transition properties of 1T-TaS2.
Our development platform is the SurfaceDynamics instrument located at the Femtoslicing facility at BESSY II, where femtosecond and picosecond X-ray pulses can be generated and extracted.
The scientific potential is put into perspective to the current rapidly developing pulsed X-ray source capabilities from Lasers and Free-Electron Lasers.
Faults and fractures can be permeable pathways for focused fluid flow in structurally controlled ore-forming hydrothermal systems.
However, quantifying their role in fluid flow on the scale of several kilometers with numerical models typically requires high-resolution meshes.
This study introduces a modified numerical representation of m-scale fault zones using lower-dimensional elements (here, one-dimensional [1D] elements in a 2D domain) to resolve structurally controlled fluid flow with coarser mesh resolutions and apply the method to magmatic-hydrothermal ore-forming systems.
We modeled horizontal and vertical structure-controlled magmatic-hydrothermal deposits to understand the role of permeability and structure connectivity on ore deposition.
The simulation results of vertically extended porphyry copper systems show that ore deposition can occur along permeable vertical structures where ascending, overpressured magmatic fluids are cooled by downflowing ambient fluids. Structure permeability and fault location control the distribution of ore grades.
In highly permeable structures, the mineralization can span up to 3 km vertically, resulting in heat-pipe mechanisms that promote the ascent of a magmatic vapor phase to an overlying structurally controlled epithermal system.
Simulations for the formation of subhorizontal vein-type deposits suggest that the major control on fluid flow and metal deposition along horizontal structures is the absence of vertical structures above the injection location but their presence at greater distances.
Using a dynamic permeability model mimicking crack-seal mechanisms within the structures leads to a pulsating behavior of fracture-controlled hydrothermal systems and prevents the inflow of ambient fluids under overpressured conditions.
Floods affect more people than any other natural hazard; thus flood warning and disaster management are of utmost importance.
However, the operational hydrological forecasts do not provide information about affected areas and impact but only discharge and water levels at gauges.
We show that a simple hydrodynamic model operating with readily available data is able to provide highly localized information on the expected flood extent and impacts, with simulation times enabling operational flood warning.
We demonstrate that such an impact forecast would have indicated the deadly potential of the 2021 flood in western Germany with sufficient lead time.
This study aimed to validate the Norwegian version of the Basic Psychological Need Satisfaction and Frustration Scale (BPNSFS) and to examine its relations with indicators of well-being and ill-being. Additionally, despite the vast number of studies employing the BPNSFS, norms related to the BPNSFS are currently lacking.
Therefore, we also aimed to provide normative data for this scale. Data were collected among a representative sample of 326 participants (M age = 42.90 years, SD = 14.76; range 18-70) in Norway, of which 49.7% was female.
Results yielded evidence for a six-factor structure (i.e., combining satisfaction/frustration with the type of need) and showed the subscales to be highly reliable. Subsequent structural equation modeling showed that both need satisfaction and need frustration related strongly to vitality, life satisfaction, and internalizing symptoms, but in opposite ways. Norm scores were provided, thereby differentiating between women and men and different age groups.
These findings support the use of the Norwegian BPNSFS and provide researchers and professionals with normative data on the most widely used tool to assess individuals' satisfaction and frustration of the basic psychological needs for autonomy, competence, and relatedness.
In this work we present windlidar data for the research village Ny-Alesund located on Svalbard in the European Arctic (78.923 degrees N, 11.928 degrees F) from 2013 to 2021.
The data have a resolution of 50 m and 10 min with an overlapping height of about 150 m.
The maximum range depends on the meteorologic situation. Up to 1000 m altitude the data availability is better than 71%.
We found that the highest wind speeds occur in November and December, the lowest ones in June and July, up to 500 m altitude the wind is channelled strongly in ESE to NW direction parallel to the fjord axis and the synoptic conditions above 1000 m altitude already dominate.
While the fraction of windy days (v > 10 m/s) varies significantly from month to month, there is no overall trend of the wind visible in our data set.
We define gusts and jets by the requirement of wind maxima v > 2 m/s above and below a wind maximum. In total, more than 24,000 of these events were identified (corresponding to 6% of the time), of which 223 lasted for at least 100 min ("Long Jets"). All of these events are fairly equally distributed over the months relatively to the available data.
Further, gusts and jets follow different distributions (in terms of altitude or depths) and occur more frequently for synoptic flow from roughly a southerly direction. Jets do not show a clear correlation between occurrence and synoptic flow. Gusts and jets are not related to cloud cover.
We conclude that the atmosphere from 400 m to 1000 m above Ny-Alesund is dominated by a turbulent wind shear zone, which connects the micrometeorology in the atmospheric boundary layer (ABL) with the synoptic flow.