Miracle-dz/UniFAR-FTUs huggingface dataset:
A Compendium of in vitro Germination Media for Pollen Research

The correct choice of in vitro pollen germination media (PGM) is crucial in basic and applied pollen research. However, the methodological gaps (e.g., strong focus of current research on model species and cultivated plants along with the lack of general rules for developing a PGM) makes experimenting with pollen difficult. We closed these gaps by compiling a compendium of optimized in vitro PGM recipes from more than 1800 articles published in English, German, and Russian from 1926 to 2019. The compendium includes 1572 PGM recipes successfully used to germinate pollen grains or produce pollen tubes in 816 species representing 412 genera and 114 families (both monocots and dicots). Among the 110 components recorded from the different PGM recipes, sucrose (89% of species), H3BO3 (77%), Ca2+ (59%), Mg2+ (44%), and K+ (39%) were the most commonly used PGM components. PGM pH was reported in 35% of all studies reviewed. Also, we identified some general rules for creating PGM for various groups of species differing in area of research (wild and cultivated species), phylogenetic relatedness (angiosperms vs. gymnosperms, dicots vs. monocots), pollen physiology (bi- and tri-cellular), biochemistry (starchy vs. starchless pollen grains), and stigma properties (dry vs. wet), and compared the component requirements. Sucrose, calcium, and magnesium concentrations were significantly different across most categories indicating that pollen sensitivity to sugar and mineral requirements in PGM is highly group-specific and should be accounted for when composing new PGM. This compendium is an important data resource on PGM and can facilitate future pollen research.
Comparative Transcriptome Analysis of Salt Stress-Induced Leaf Senescence in Medicago truncatula

Leaves are the most critical portion of forage crops such as alfalfa (Medicago sativa). Leaf senescence caused by environmental stresses significantly impacts the biomass and quality of forages. To understand the molecular mechanisms and identify the key regulator of the salt stress-induced leaf senescence process, we conducted a simple and effective salt stress-induced leaf senescence assay in Medicago truncatula, which was followed by RNA-Seq analysis coupled with physiological and biochemical characterization. By comparing the observed expression data with that derived from dark-induced leaf senescence at different time points, we identified 3,001, 3,787, and 4,419 senescence-associated genes (SAGs) for salt stress-induced leaf senescence on day 2, 4, and 6, respectively. There were 1546 SAGs shared by dark and salt stress treatment across the three time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the 1546 SAGs were mainly related to protein and amino acids metabolism, photosynthesis, chlorophyll metabolism, and hormone signaling during leaf senescence. Strikingly, many different transcription factors (TFs) families out of the 1546 SAGs, including NAC, bHLH, MYB, and ERF, were associated with salt stress-induced leaf senescence processes. Using the transient expression system in Nicotiana benthamiana, we verified that three functional NAC TF genes from the 1546 SAGs were related to leaf senescence. These results clarify SAGs under salt stress in M. truncatula and provide new insights and additional genetic resources for further forage crop breeding.
Potential of Pulse Flours as Partial Meat Replacers in Heat-Treated Emulsion-Type Meat Sausages

Reformulation approaches in the meat industry are required to promote nutritional improvement, health functionality, and reduce environmental impact. A relevant approach among these is to reduce the amount of meat in meat products. Reduced-meat products should maintain or improve the sensory characteristics and nutritive value compared to conventional meat products. Among meat products, heat-treated emulsion-meat sausages are widely consumed and especially suitable for reformulation approaches. Due to its high protein content, with high functionally and biological value, pulse flour has a high potential to be used as meat replacer. Most studies regarding the replacement of meat with pulses have been made on fresh meat preparations where amounts of up to 15% of pulse flour did not negatively affect sensory quality while increased yield and firmness. However, studies using pulse flour in emulsion-type sausages are scarce. Further research is warranted to optimize the reformulation of these meat products using flour pulses. The topics to be addressed are the following: effects of pulse type, pulse pretreatments, such as soaking or germination, pulse flour treatments before incorporation into the meat mix, combination of pulses with other proper ingredients, and heat treatment intensity on the pulse antinutrient inactivation and the technological and edible quality traits of the pulse-containing sausages.
Effects of Pain-Reporting Education Program on Children's Pain Reports—Results From a Randomized Controlled Post-operative Pediatric Pain Trial

Objective: Accurate assessment of patients' pain is an essential part of adequate analgesic treatment. Although reporting pain is a complex task, limited-to-no instructions are provided to pediatric patients regarding this process. Our goal in this randomized parallel-group clinical trial (Clinicaltrial.gov study protocol number NCT04306679) was to evaluate if a training program designed to improve children's ability to understand and use pain scales in a post-surgical setting would affect their pain scores. Methods: Eligible children (aged 8–17), hospitalized for elective surgery and their parents were randomized into two groups. Pre-surgery the intervention group underwent a multi-media program aimed to teach and train how to report pain. The control group received standard pre-surgical instructions. Post-surgery, the children reported their pain on 4 pain scales. The primary outcome was the concordance between children's pain intensity scores reported on four pain scales, both in terms of within-child standard deviation and absolute difference. Results: Ninety-six children met inclusion criteria and completed the study. The trained subjects' pain reports had significantly (p = 0.002) lower within-subject standard deviation (0.41 ± 0.31) than the control group (0.67 ± 0.46). In line, regarding absolute difference, the concordance of children's pain reports was twice better in the trained group (mean difference of 0.43 ± 0.40) than in the control group (0.88 ± 0.70) (p < 0.001). Discussion: Our results suggests that children's ability to report pain is a skill that can be improved. Future studies should test the potential clinical impacts of educational interventions aimed to improve pain assessment in children and adults.
Multi-Pharmacology of Berberine in Atherosclerosis and Metabolic Diseases: Potential Contribution of Gut Microbiota

Atherosclerosis (AS), especially atherosclerotic cardiovascular diseases (ASCVDs), and metabolic diseases (such as diabetes, obesity, dyslipidemia, and nonalcoholic fatty liver disease) are major public health issues worldwide that seriously threaten human health. Exploring effective natural product-based drugs is a promising strategy for the treatment of AS and metabolic diseases. Berberine (BBR), an important isoquinoline alkaloid found in various medicinal plants, has been shown to have multiple pharmacological effects and therapeutic applications. In view of its low bioavailability, increasing evidence indicates that the gut microbiota may serve as a target for the multifunctional effects of BBR. Under the pathological conditions of AS and metabolic diseases, BBR improves intestinal barrier function and reduces inflammation induced by gut microbiota-derived lipopolysaccharide (LPS). Moreover, BBR reverses or induces structural and compositional alterations in the gut microbiota and regulates gut microbe-dependent metabolites as well as related downstream pathways; this improves glucose and lipid metabolism and energy homeostasis. These findings at least partly explain the effect of BBR on AS and metabolic diseases. In this review, we elaborate on the research progress of BBR and its mechanisms of action in the treatment of AS and metabolic diseases from the perspective of gut microbiota, to reveal the potential contribution of gut microbiota to the multifunctional biological effects of BBR.
Branchiomeric Muscle Development Requires Proper Retinoic Acid Signaling

The first and second branchiomeric (branchial arch) muscles are craniofacial muscles that derive from branchial arch mesoderm. In mammals, this set of muscles is indispensable for jaw movement and facial expression. Defects during embryonic development that result in congenital partial absence of these muscles can have significant impact on patients’ quality of life. However, the detailed molecular and cellular mechanisms that regulate branchiomeric muscle development remains poorly understood. Herein we investigated the role of retinoic acid (RA) signaling in developing branchiomeric muscles using mice as a model. We administered all-trans RA (25 mg/kg body weight) to Institute of Cancer Research (ICR) pregnant mice by gastric intubation from E8.5 to E10.5. In their embryos at E13.5, we found that muscles derived from the first branchial arch (temporalis, masseter) and second branchial arch (frontalis, orbicularis oculi) were severely affected or undetectable, while other craniofacial muscles were hypoplastic. We detected elevated cell death in the branchial arch mesoderm cells in RA-treated embryos, suggesting that excessive RA signaling reduces the survival of precursor cells of branchiomeric muscles, resulting in the development of hypoplastic craniofacial muscles. In order to uncover the signaling pathway(s) underlying this etiology, we focused on Pitx2, Tbx1, and MyoD1, which are critical for cranial muscle development. Noticeably reduced expression of all these genes was detected in the first and second branchial arch of RA-treated embryos. Moreover, elevated RA signaling resulted in a reduction in Dlx5 and Dlx6 expression in cranial neural crest cells (CNCCs), which disturbed their interactions with branchiomeric mesoderm cells. Altogether, we discovered that embryonic craniofacial muscle defects caused by excessive RA signaling were associated with the downregulation of Pitx2, Tbx1, MyoD1, and Dlx5/6, and reduced survival of cranial myogenic precursor cells.
Transport of Moving Duck Flocks in Indonesia and Vietnam: Management Practices That Potentially Impact Avian Pathogen Dissemination

Highly pathogenic avian influenza (HPAI) virus is endemic in Indonesia and Vietnam, where “moving” duck production is commonly practiced. Questionnaire surveys were conducted with transporters of “moving” duck flocks in Indonesia (N = 55) and Vietnam (N = 43). The main purpose of transportation was to transport duck flocks between rice paddies used for scavenging. Trucks were commonly utilized for transport in both countries (Indonesia: 98.2%, 54/55; Vietnam: 37.2%, 16/43), while boats were only used in Vietnam (62.8%, 27/43). Transporters in Vietnam moved larger flocks and traveled over longer distances. Deaths of ducks due to diseases were reported in both countries (Indonesia: 16.4%, 9/55; Vietnam: 4.7%, 2/43; p = 0.11). Throwing away of carcasses was the primary method of disposal of dead birds in Indonesia (60.0%, 33/55), but was not practiced in Vietnam (p < 0.001), while more transporters in Vietnam (34.9%, 15/43) buried carcasses compared to Indonesia (6.8%, 4/55; p = 0.001). Consumption of carcasses (20.9%, 9/43), sale of dead ducks (14.0%, 6/43) and processing of ducks for fish feed (9.3%, 4/43) was conducted in Vietnam, but not in Indonesia. Vehicles were predominantly cleaned in rivers and stored outside in Vietnam, while cleaning and storage was usually conducted in houses/garages in Indonesia. In conclusion, we identified management practices that potentially impact transmission of avian pathogens, such as HPAI virus. In Indonesia, unsafe management practices were related to multipurpose usage of transport vehicles and disposal of birds in the environment, while in Vietnam, they were related to the mixing of birds during transport, the processing of dead carcasses and the storage and cleaning of transport vehicles.
Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role

The structure of eukaryotic genes is generally a combination of exons interrupted by intragenic non-coding DNA regions (introns) removed by RNA splicing to generate the mature mRNA. A fraction of genes, however, comprise a single coding exon with introns in their untranslated regions or are intronless genes (IGs), lacking introns entirely. The latter code for essential proteins involved in development, growth, and cell proliferation and their expression has been proposed to be highly specialized for neuro-specific functions and linked to cancer, neuropathies, and developmental disorders. The abundant presence of introns in eukaryotic genomes is pivotal for the precise control of gene expression. Notwithstanding, IGs exempting splicing events entail a higher transcriptional fidelity, making them even more valuable for regulatory roles. This work aimed to infer the functional role and evolutionary history of IGs centered on the mouse genome. IGs consist of a subgroup of genes with one exon including coding genes, non-coding genes, and pseudogenes, which conform approximately 6% of a total of 21,527 genes. To understand their prevalence, biological relevance, and evolution, we identified and studied 1,116 IG functional proteins validating their differential expression in transcriptomic data of embryonic mouse telencephalon. Our results showed that overall expression levels of IGs are lower than those of MEGs. However, strongly up-regulated IGs include transcription factors (TFs) such as the class 3 of POU (HMG Box), Neurog1, Olig1, and BHLHe22, BHLHe23, among other essential genes including the β-cluster of protocadherins. Most striking was the finding that IG-encoded BHLH TFs fit the criteria to be classified as microproteins. Finally, predicted protein orthologs in other six genomes confirmed high conservation of IGs associated with regulating neural processes and with chromatin organization and epigenetic regulation in Vertebrata. Moreover, this study highlights that IGs are essential modulators of regulatory processes, such as the Wnt signaling pathway and biological processes as pivotal as sensory organ developing at a transcriptional and post-translational level. Overall, our results suggest that IG proteins have specialized, prevalent, and unique biological roles and that functional divergence between IGs and MEGs is likely to be the result of specific evolutionary constraints.
Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination

Grain yield, which is one of the most important traits in rice breeding, is controlled in part by panicle branching patterns. Numerous genes involved in the control of panicle architecture have been identified through mutant and QTL characterization. Previous studies suggested the importance of several AP2/ERF transcription factor-encoding genes in the control of panicle development, including the AINTEGUMENTA/PLETHORA-like (euANT/PLT) genes. The ANT gene was specifically considered to be a key regulator of shoot and floral development in Arabidopsis thaliana. However, the likely importance of paralogous euANT/PLT genes in the regulation of meristem identities and activities during panicle architecture development has not to date been fully addressed in rice. In this study, we observed that the rice euANT/PLT genes displayed divergent temporal expression patterns during the branching stages of early panicle development, with spatial localization of expression in meristems for two of these genes. Moreover, a functional analysis of rice ANT-related genes using genome editing revealed their importance in the control of panicle architecture, through the regulation of axillary meristem (AM) establishment and meristem fate transition. Our study suggests that the paralogous euANT/PLT genes have become partially diversified in their functions, with certain opposing effects, since they arose from ancestral gene duplication events, and that they act in regulating the branching of the rice panicle.
Inactivation of Prefrontal Cortex Delays Emergence From Sevoflurane Anesthesia

Studies aimed at investigating brain regions involved in arousal state control have been traditionally limited to subcortical structures. In the current study, we tested the hypothesis that inactivation of prefrontal cortex, but not two subregions within parietal cortex—somatosensory barrel field and medial/lateral parietal association cortex—would suppress arousal, as measured by an increase in anesthetic sensitivity. Male and female Sprague Dawley rats were surgically prepared for recording electroencephalogram and bilateral infusion into prefrontal cortex (N = 13), somatosensory barrel field (N = 10), or medial/lateral parietal association cortex (N = 9). After at least 10 days of post-surgical recovery, 156 μM tetrodotoxin or saline was microinjected into one of the cortical sites. Ninety minutes after injection, rats were anesthetized with 2.5% sevoflurane and the time to loss of righting reflex, a surrogate for loss of consciousness, was measured. Sevoflurane was stopped after 45 min and the time to return of righting reflex, a surrogate for return of consciousness, was measured. Tetrodotoxin-mediated inactivation of all three cortical sites decreased (p < 0.05) the time to loss of righting reflex. By contrast, only inactivation of prefrontal cortex, but not somatosensory barrel field or medial/lateral parietal association cortex, increased (p < 0.001) the time to return of righting reflex. Burst suppression ratio was not altered following inactivation of any of the cortical sites, suggesting that there was no global effect due to pharmacologic lesion. These findings demonstrate that prefrontal cortex plays a causal role in emergence from anesthesia and behavioral arousal.
Neuro-Steered Music Source Separation With EEG-Based Auditory Attention Decoding And Contrastive-NMF

We propose a novel informed music source separation paradigm, which can be referred to as neuro-steered music source separation. More precisely, the source separation process is guided by the user’s selective auditory attention decoded from his/her EEG response to the stimulus. This high-level prior information is used to select the desired instrument to isolate and to adapt the generic source separation model to the observed signal. To this aim, we leverage the fact that the attended instrument’s neural encoding is substantially stronger than the one of the unattended sources left in the mixture. This "contrast" is extracted using an attention decoder and used to inform a source separation model based on non-negative matrix factorization named Contrastive-NMF. The results are promising and show that the EEG information can automatically select the desired source to enhance and improve the separation quality.
Online Classification of Dynamic Multilayer-Network Time Series in Riemannian Manifolds

This work exploits Riemannian manifolds to introduce a geometric framework for online state and community classification in dynamic multilayer networks where nodes are annotated with time series. A bottom-up approach is followed, starting from the extraction of Riemannian features from nodal time series, and reaching up to on- line/sequential classification of features via geodesic distances and angular information in the tangent spaces of a Riemannian manifold. As a case study, features in the Grassmann manifold are generated by fitting a kernel autoregressive-moving-average model to the nodal time series of the multilayer network. The paper highlights also numerical tests on synthetic and real brain-network data, where it is shown that the proposed geometric framework outperforms state-of- the-art deep-learning models in classification accuracy, especially in cases where the number of training data is small with respect to the number of the testing ones.
Application-Layer DDOS Attacks with Multiple Emulation Dictionaries

We consider the problem of identifying the members of a botnet under an application-layer (L7) DDoS attack, where a target site is flooded with a large number of requests that emulate legitimate users’ patterns. This challenging problem has been recently addressed with reference to two simplified scenarios, where either all bots pick requests from the same emulation dictionary (total overlap), or they are divided in separate clusters corresponding to distinct emulation dictionaries (no overlap at all). However, over real networks these two extreme conditions are difficult to realize, and the intermediate situation is observed where the emulation patterns of distinct bots belong to partially overlapped dictionaries. This intermediate situation introduces significant sophistication in the bot identification problem. In order to address this issue, we provide an analytical characterization of the pairwise cluster interaction, which is exploited to devise an identification rule to discriminate legitimate users from bots and to identify the individual bot clusters.
Improving The Robustness Of Right Whale Detection In Noisy Conditions Using Denoising Autoencoders And Augmented Training

The aim of this paper is to examine denoising autoencoders (DAEs) for improving the detection of right whales recorded in harsh marine environments. Passive acoustic recordings are taken from autonomous surface vehicles (ASVs) and are subject to noise from sources such as shipping and offshore construction. To mitigate the noise we apply DAEs and consider how best to train the classifier by augmenting clean training data with examples contaminated by noise. Evaluations find that the DAE improves detection accuracy and is particularly effective when the classifier is trained on data that has itself been denoised rather than using a clean model. Further, testing on unseen noises is also effective particularly for noises that exhibit similar character to noises seen in training.
Label-Guided Dictionary Pair Learning for ECG Biometric Recognition

ECG biometric recognition has received plenty of attention in biometrics area. In recent years, various classical sparse representation and dictionary learning methods have been utilized in ECG biometric recognition. However, to produce better classification results, lP -norm is used to regularize the representation coefficients, which undoubtedly brings time cost problem. To overcome this limitation, our method, namely label-guided dictionary pair learning, aims to learn a projective dictionary and reconstructed dictionary jointly, which achieves signal representation and reconstruction simultaneously. Introduction of label information with each dictionary item and Fisher-like regularization on projective dictionary enforce discriminability during the dictionary learning process. Alternating direction method of multipliers is then exploited to optimize the corresponding objective function. Extensive experiments on two databases demonstrate that our method can achieve better performance compared with state-of-the-art ECG biometric recognition methods.