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African weakly electric fish of the mormyrid genus Campylomormyrus generate pulse-type electric organ discharges (EODs) for orientation and communication. Their pulse durations are species-specific and elongated EODs are a derived trait. So far, differential gene expression among tissue-specific transcriptomes across species with different pulses and point mutations in single ion channel genes indicate a relation of pulse duration and electrocyte geometry/excitability. However, a comprehensive assessment of expressed Single Nucleotide Polymorphisms (SNPs) throughout the entire transcriptome of African weakly electric fish, with the potential to identify further genes influencing EOD duration, is still lacking. This is of particular value, as discharge duration is likely based on multiple cellular mechanisms and various genes. Here we provide the first transcriptome-wide SNP analysis of African weakly electric fish species (genus Campylomormyrus) differing by EOD duration to identify candidate genes and cellular mechanisms potentially involved in the determination of an elongated discharge of C. tshokwe. Non-synonymous substitutions specific to C. tshokwe were found in 27 candidate genes with inferred positive selection among Campylomormyrus species. These candidate genes had mainly functions linked to transcriptional regulation, cell proliferation and cell differentiation. Further, by comparing gene annotations between C. compressirostris (ancestral short EOD) and C. tshokwe (derived elongated EOD), we identified 27 GO terms and 2 KEGG pathway categories for which C. tshokwe significantly more frequently exhibited a species-specific expressed substitution than C. compressirostris. The results indicate that transcriptional regulation as well cell proliferation and differentiation take part in the determination of elongated pulse durations in C. tshokwe. Those cellular processes are pivotal for tissue morphogenesis and might determine the shape of electric organs supporting the observed correlation between electrocyte geometry/tissue structure and discharge duration. The inferred expressed SNPs and their functional implications are a valuable resource for future investigations on EOD durations.
The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.
Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress
(2022)
Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.
Previous clinical research found that invasive vagus nerve stimulation (VNS) enhanced word recognition memory in epileptic patients, an effect assumed to be related to the activation of brainstem arousal systems. In this study, we applied non-invasive transcutaneous auricular VNS (tVNS) to replicate and extend the previous work. Using a single-blind, randomized, between-subject design, 60 healthy volunteers received active or sham stimulation during a lexical decision task, in which emotional and neutral stimuli were classified as words or non-words. In a subsequent recognition memory task (1 day after stimulation), participants' memory performance on these words and their subjective memory confidence were tested. Salivary alpha-amylase (sAA) levels, a putative indirect measure of central noradrenergic activation, were also measured before and after stimulation. During encoding, pleasant words were more accurately detected than neutral and unpleasant words. However, no tVNS effects were observed on task performance or on overall sAA level changes. tVNS also did not modulate overall recognition memory, which was particularly enhanced for pleasant emotional words. However, when hit rates were split based on confidence ratings reflecting familiarity- and recollection-based memory, higher recollection-based memory performance (irrespective of emotional category) was observed during active stimulation than during sham stimulation. To summarize, we replicated prior findings of enhanced processing and memory for emotional (pleasant) words. Whereas tVNS showed no effects on word processing, subtle effects on recollection-based memory performance emerged, which may indicate that tVNS facilitates hippocampus-mediated consolidation processes.
Transferability of data-driven models to predict urban pluvial flood water depth in Berlin, Germany
(2023)
Data-driven models have been recently suggested to surrogate computationally expensive hydrodynamic models to map flood hazards. However, most studies focused on developing models for the same area or the same precipitation event. It is thus not obvious how transferable the models are in space. This study evaluates the performance of a convolutional neural network (CNN) based on the U-Net architecture and the random forest (RF) algorithm to predict flood water depth, the models' transferability in space and performance improvement using transfer learning techniques. We used three study areas in Berlin to train, validate and test the models. The results showed that (1) the RF models outperformed the CNN models for predictions within the training domain, presumable at the cost of overfitting; (2) the CNN models had significantly higher potential than the RF models to generalize beyond the training domain; and (3) the CNN models could better benefit from transfer learning technique to boost their performance outside training domains than RF models.
I study deterministic dynamics of chiral active particles in two dimensions. Particles are considered as discs interacting with elastic repulsive forces. An ensemble of particles, started from random initial conditions, demonstrates chaotic collisions resulting in their normal diffusion. This chaos is transient, as rather abruptly a synchronous collisionless state establishes. The life time of chaos grows exponentially with the number of particles. External forcing (periodic or chaotic) is shown to facilitate the synchronization transition.
Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.
Background and Objectives: Low back pain is a worldwide health problem. An early diagnosis is required to develop personalized treatment strategies. The Risk Stratification Index (RSI) was developed to serve the purpose. The aim of this pilot study is to cross-culturally translate the RSI to a French version (RSI-F) and evaluate the test-retest reliability of RSI-F using a French active population. Materials and Methods: The RSI was translated from German to French (RSI-F) based on the guidelines of cross-cultural adaptation of self-report measures. A total of 42 French recreational athletes (age 18–63 years) with non-specific low back pain were recruited and filled in the RSI-F twice. The test-retest reliability was examined using intraclass correlation coefficient (ICC1,2) and Pearson correlation coefficient. Results: Finally, 33 questionnaires were analyzed (14 males and 19 females, age 31 ± 10 years, 9.5 ± 3.2 h/week of training). The test-retest of RSI-F CPI and DISS were excellent (CPI: ICC1,2 = 0.989, p < 0.001; r = 0.989, p < 0.001; DISS: ICC1,2 = 0.991, p < 0.001; r = 0.991, p < 0.001), as well as Korff pain intensity (ICC1,2 = 0.995, p < 0.001; r = 0.995, p < 0.001) and disability (ICC1,2 = 0.998, p < 0.001; r = 0.998, p < 0.001). Conclusion: The RSI-F is linguistically accurate and reliable for use by a French-speaking active population with non-specific low back pain. The RSI-F is considered a tool to examine the evolution of psychosocial factors and therefore the risk of chronicity and the prognostic of pain. Further evaluations, such as internal, external validity, and responsiveness should be evaluated in a larger population.
Broad-spectrum antibiotic combination therapy is frequently applied due to increasing resistance development of infective pathogens. The objective of the present study was to evaluate two common empiric broad-spectrum combination therapies consisting of either linezolid (LZD) or vancomycin (VAN) combined with meropenem (MER) against Staphylococcus aureus (S. aureus) as the most frequent causative pathogen of severe infections. A semimechanistic pharmacokinetic-pharmacodynamic (PK-PD) model mimicking a simplified bacterial life-cycle of S. aureus was developed upon time-kill curve data to describe the effects of LZD, VAN, and MER alone and in dual combinations. The PK-PD model was successfully (i) evaluated with external data from two clinical S. aureus isolates and further drug combinations and (ii) challenged to predict common clinical PK-PD indices and breakpoints. Finally, clinical trial simulations were performed that revealed that the combination of VAN-MER might be favorable over LZD-MER due to an unfavorable antagonistic interaction between LZD and MER.