Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide association mapping of Pyrenophora teres f. maculata and Pyrenophora teres f. teres resistance loci utilizing natural Turkish wild and landrace barley populations

Unimproved landraces and wild relatives of crops are sources of genetic diversity that were lost post domestication in modern breeding programs. To tap into this rich resource, genome wide association studies in large plant genomes have enabled the rapid genetic characterization of desired traits from natural landrace and wild populations. Wild barley (Hordeum spontaneum), the progenitor of domesticated barley (H. vulgare), is dispersed across Asia and North Africa, and has co-evolved with the ascomycetous fungal pathogens Pyrenophora teres f. teres and P. teres f. maculata, the casual agents of the diseases net form of net blotch and spot form of net blotch, respectively. Thus, these wild and local adapted barley landraces from the region of origin of both the host and pathogen represent a diverse gene pool to identify new sources of resistance, due to millions of years of co-evolution. The barley - P. teres pathosystem is governed by complex genetic interactions with dominant, recessive, and incomplete resistances and susceptibilities, with many isolate-specific interactions. Here we provide the first genome wide association study of wild and landrace barley from the Fertile Crescent for resistance to both forms of P. teres. A total of 14 loci, four against P. teres f. maculata and ten against Pyrenophora teres f. teres, were identified in both wild and landrace populations, showing that both are genetic reservoirs for novel sources of resistance. We also highlight the importance of using multiple algorithms to both identify and validate additional loci.
A screen of covalent inhibitors in Mycobacterium tuberculosis identifies serine hydrolases involved in lipid metabolism as potential therapeutic targets

The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat necessitating the development of new antibiotics. Serine hydrolases (SHs) are a promising class of targets because of their importance for the synthesis of the mycobacterial cell envelope. We screened a library of small molecules containing serine-reactive electrophiles and identified narrow spectrum inhibitors of M. tuberculous growth. Using these lead molecules, we performed competitive activity-based protein profiling and identified multiple SH targets, including enzymes with uncharacterized functions. Lipidomic analyses of compound-treated cultures revealed an accumulation of free lipids and a substantial decrease in lipooligosaccharides, linking SH inhibition to defects in cell envelope biogenesis. Mutant analysis revealed a path to resistance via the synthesis of mycocerates, but not through mutations to target enzymes. Our results suggest that simultaneous inhibition of multiple SH enzymes is likely to be an effective therapeutic strategy for the treatment of M. tuberculosis infections.
Studies on Adjuvants for Anaphylactic Response to Hen Egg-White Proteins by MAHT

Previously, we proposed a standard approach for quantification of the intensities of mouse anaphylactic responses using the fall in blood pressure (mouse anaphylactic hypotension test; MAHT) after treatment with food allergens. In the present study, we examined the effects of several adjuvants in an attempt to shorten the period required for the test.We compared Freund's incomplete adjuvant (FIA) and aluminum hydroxide gel (Alum) as adjuvants. Ovalbumin was easily adsorbed on Alum, but hen egg-white lysozyme was poorly adsorbed. The adsorption of proteins on Alum was dependent on molecular weight and isoelectric point. The protein's molecular form and surface electric charge might also influence adsorption on Alum. Accordingly, Alum appeared to be unsuitable as an adjuvant for this method. Therefore we mixed 20mg/mL Alum and FIA (1:1) (Alum+FIA), and found that allergic reaction intensities with Alum+FIA were stronger than those with either Alum or FIA alone. Moreover, Alum could also be utilized for evaluating allergenicity of egg-white, and allergic reaction intensity with Alum+FIA was stronger than that with FIA alone. The allergenicity of boiled egg-white was weaker than that of raw egg-white. Boiling may convert water-soluble into water-insoluble substances in egg-white, or antigenic determinants may be partly denatured.
Privacy Enhancement on Unilateral Bluetooth Authentication Protocol for Mobile Crowdsensing

As an open standard for the short-range radio frequency communications, Bluetooth is suitable for Mobile Crowdsensing Systems (MCS). However, the massive deployment of personal Bluetooth-enabled devices also raises privacy concerns on their wielders. Hence, we investigate the privacy of the unilateral authentication protocol according to the recent Bluetooth standard v5.2. ,e contributions of the paper are twofold. (1) We demonstrate that the unilateral authentication protocol suffers from privacy weakness. ,at is, the attacker is able to identify the target Bluetooth-enabled device once he observed the device’s previous transmitted messages during the protocol run. More importantly, we analyze the privacy threat of the Bluetooth MCS, when the attacker exploits the proposed privacy weakness under the typical Internet of ,ings (IoT) scenarios. (2) An improved unilateral authentication protocol is therefore devised to repair the weakness. Under our formal privacy model, the improved protocol provably solves the traceability problem of the original protocol in the Bluetooth standard. Additionally, the improved protocol can be easily adapted to the Bluetooth standards because it merely employs the basic cryptographic components available in the standard specifications. In addition, we also suggest and evaluate two countermeasures, which do not need to modify the original protocol.
Name Disambiguation Based on Graph Convolutional Network

Recently, massive online academic resources have provided convenience for scientific study and research. However, the author name ambiguity degrades the user experience in retrieving the literature bases. Extracting the features of papers and calculating the similarity for clustering constitute the mainstream of present name disambiguation approaches, which can be divided into two branches: clustering based on attribute features and clustering based on linkage information. They cannot however get high performance. In order to improve the efficiency of literature retrieval and provide technical support for the accurate construction of literature bases, a name disambiguation method based on Graph Convolutional Network (GCN) is proposed. The disambiguation model based on GCN designed in this paper combines both attribute features and linkage information. We first build paper-to-paper graphs, coauthor graphs, and paper-to-author graphs for each reference item of a name. The nodes in the graphs contain attribute features and the edges contain linkage features. The graphs are then fed to a specialized GCN and output a hybrid representation. Finally, we use the hierarchical clustering algorithm to divide the papers into disjoint clusters. Finally, we cluster the papers using a hierarchical algorithm. The experimental results show that the proposed model achieves average F1 value of 77.10% on three name disambiguation datasets. In order to let the model automatically select the appropriate number of convolution layers and adapt to the structure of different local graphs, we improve upon the prior GCN model by utilizing attention mechanism. Compared with the original GCN model, it increases the average precision and F1 value by 2.05% and 0.63%, respectively. What is more, we build a bilingual dataset, BAT, which contains various forms of academic achievements and will be an alternative in future research of name disambiguation.
User Identification Based on Integrating Multiple User Information across Online Social Networks

User identification can help us build more comprehensive user information. It has been attracting much attention from academia. Most of the existing works are profile-based user identification and relationship-based user identification. Due to user privacy settings and social network restrictions on user data crawl, user data may be missing or incomplete in real social networks. User data include profiles, user-generated contents (UGCs), and relationships. The features extracted in previous research may be sparse. In order to reduce the impact of the above problems on user identification, we propose a multiple user information user identification framework (MUIUI). Firstly, we develop multiprocess crawlers to obtain the user data from two popular social networks, Twitter and Facebook. Secondly, we use named entity recognition and entity linking to obtain and integrate locations and organizations from profiles and UGCs. We also extract URLs from profiles and UGCs. We apply the locations jointly with the relationships and develop several algorithms to measure the similarity of the display name, all locations, all organizations, location in profile, all URLs, following organizations, and user ID, respectively. Afterward, we propose a fusion classifier machine learning-based user identification method. The results show that the F1 score of MUIUI reaches 86.46% on the dataset. It proves that MUIUI can reduce the impact of user data that are missing or incomplete.
NOMA Application to Satellite Communication Networks for 5G: A Comprehensive Survey of Existing Studies

The 4 generation of communication networks (4G) seems limited and unable to satisfy the growing networks’ performances demands of new intended communication services such as the internet-of-things (IoTs). The 5 generation of communication networks (5G) has therefore been envisaged to fill the gap. The non-orthogonal multiple access (NOMA) technology and the satellite communication have been identified as key enabling technologies for the achievement of 5G networks. There are many ongoing NOMA related works for 5G; however, the few existing reviews mostly discuss works that apply NOMA to terrestrial networks. This paper therefore, gives a comprehensive and up-to-date review of existing works applying NOMA to satellite communication networks. More precisely, it presents studies that have either designed or do performance analysis of NOMA-based multibeam satellitesystems (MBSSs) or integrated satellite-terrestrial networks (ISTNs). The surveys presented showed that the application of NOMA to satellite communications for 5G is starting to gain considerable interest. Most of the current PD-NOMA design works attempt to maximize the system capacity (sum-rate), and most of the current PD-NOMA performance analysis works demonstrate the superiority of NOMA over OMA through Ergodic Capacity and Outage probability estimations. The surveys also showed that this field is still quite opened for research, with issues such as user-fairness maximization, satellite capacity improvement, ground-surface moving beams (for LEOs and MEOs satellites) and multiple gateways combination . etc. remaining prospective research areas to be explored. 
Augmenting the Transplant Team With Artificial Intelligence: Toward Meaningful AI Use in Solid Organ Transplant

Advances in systems immunology, such as new biomarkers, offer the potential for highly personalized immunosuppression regimens that could improve patient outcomes. In the future, integrating all of this information with other patient history data will likely have to rely on artificial intelligence (AI). AI agents can help augment transplant decision making by discovering patterns and making predictions for specific patients that are not covered in the literature or in ways that are impossible for humans to anticipate by integrating vast amounts of data (e.g. trending across numerous biomarkers). Similar to other clinical decision support systems, AI may help overcome human biases or judgment errors. However, AI is not widely utilized in transplant to date. In this rapid review, we survey the methods employed in recent research in transplant-related AI applications and identify concerns related to implementing these tools. We identify three key challenges (bias/accuracy, clinical decision process/AI explainability, AI acceptability criteria) holding back AI in transplant. We also identify steps that can be taken in the near term to help advance meaningful use of AI in transplant (forming a Transplant AI Team at each center, establishing clinical and ethical acceptability criteria, and incorporating AI into the Shared Decision Making Model).
Rhizospheric Bacillus spp. Rescues Plant Growth Under Salinity Stress via Regulating Gene Expression, Endogenous Hormones, and Antioxidant System of Oryza sativa L

Salinity has drastically reduced crop yields and harmed the global agricultural industry. We isolated 55 bacterial strains from plants inhabiting the coastal sand dunes of Pohang, Korea. A screening bioassay showed that 14 of the bacterial isolates secreted indole-3-acetic acid (IAA), 12 isolates were capable of exopolysaccharide (EPS) production and phosphate solubilization, and 10 isolates secreted siderophores. Based on our preliminary screening, 11 bacterial isolates were tested for salinity tolerance on Luria–Bertani (LB) media supplemented with 0, 50, 100, and 150 mM of NaCl. Three bacterial isolates, ALT11, ALT12, and ALT30, had the best tolerance against elevated NaCl levels and were selected for further study. Inoculation of the selected bacterial isolates significantly enhanced rice growth attributes, viz., shoot length (22.8–42.2%), root length (28.18–59%), fresh biomass (44.7–66.41%), dry biomass (85–90%), chlorophyll content (18.30–36.15%), Chl a (29.02–60.87%), Chl b (30.86–64.51%), and carotenoid content (26.86–70%), under elevated salt stress of 70 and 140 mM. Furthermore, a decrease in the endogenous abscisic acid (ABA) content (27.9–23%) and endogenous salicylic acid (SA) levels (11.70–69.19%) was observed in inoculated plants. Antioxidant analysis revealed an increase in total protein (TP) levels (42.57–68.26%), whereas it revealed a decrease in polyphenol peroxidase (PPO) (24.63–34.57%), glutathione (GSH) (25.53–24.91%), SOA (13.88–18.67%), and LPO levels (15.96–26.06%) of bacterial-inoculated plants. Moreover, an increase in catalase (CAT) (26–33.04%), peroxidase (POD) (59.55–78%), superoxide dismutase (SOD) (13.58–27.77%), and ascorbic peroxidase (APX) (5.76–22.74%) activity was observed. Additionally, inductively coupled plasma mass spectrometry (ICP-MS) analysis showed a decline in Na+ content (24.11 and 30.60%) and an increase in K+ (23.14 and 15.45%) and Mg+ (2.82 and 18.74%) under elevated salt stress. OsNHX1 gene expression was downregulated (0.3 and 4.1-folds), whereas the gene expression of OsPIN1A, OsCATA, and OsAPX1 was upregulated by a 7–17-fold in bacterial-inoculated rice plants. It was concluded that the selected bacterial isolates, ALT11, ALT12, and ALT30, mitigated the adverse effects of salt stress on rice growth and can be used as climate smart agricultural tools in ecofriendly agricultural practices.
Remote, but Not Isolated—Microplastics in the Sub-surface Waters of the Canadian Arctic Archipelago

As the remote Canadian Arctic Archipelago (CAA) becomes increasingly connected to the rest of the world, there is an impetus to monitor the possible impact of this connectivity. The potential for increases in localised sources of plastic pollution resulting from the increasing navigability of the remote north has yet to be explored. Here we investigate microplastic samples which were collected aboard the Canadian Coast Guard Ship (CCGS) Amundsen in the summer of 2018 using the underway pump and a filtration system with Fourier transform infrared analysis. We investigate the character, abundance, and distribution of microplastic particles and fibres in the sub-surface waters across the Canadian Arctic and add to the limited dataset on plastic pollution in this region. We find that there are low concentrations of microplastics ranging from 0 to 0.282 n L–1 (average 0.031 ± 0.017 n L–1), comprising 71% polyester and acrylics. We investigate the size distribution of retained particles and fibres on three different filter mesh sizes connected to the underway pump (300, 100, and 50 μm) and find that a 300 μm mesh and a 100 μm mesh retain only 6 and 56%, respectively, of the total particles and fibres. We explore the role of shipping as a potential source of textile fibres and we suggest that future monitoring of plastics in the Canadian Arctic should use the current shipping fleet to monitor its own plastic footprint, utilising the underway pump and mesh sizes < 100 μm.
Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat

Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.
δ60Ni and δ13C Composition of Serpentinites and Carbonates of the Tekirova Ophiolite, Turkey, and Meatiq Ophiolite, Egypt

Nickel isotope fractionation patterns in continental ultramafic environments generally show a depletion of δ60Ni in weathered rocks and an enrichment in bedrock samples. The present study focuses on stable Ni isotope fractionation patterns in carbonate-rich, ultramafic ophiolite samples with concomitant fluids at an active serpentinization site in southwestern Turkey, with a comparison to results from an inactive serpentinization site in the Eastern Desert of Egypt with carbonate-rich samples. All solid phase data from the inactive serpentinization area are consistent with previously reported values from serpentinites, whereas the solid precipitates in the active area (SW Turkey) give values slightly heavier than previously reported data. However, the Ni isotopic signatures in the active serpentinization system likely reflect the scavenging of light Ni by iron oxide and carbonate precipitation, as has been previously demonstrated in laboratory coprecipitation experiments. It is also possible that the active system results resemble previous laboratory experimental results that show a relatively strong initial fractionation between fluids and solids, which then diminishes with time due to aging of the precipitates.
Coping With Human-Cat Interactions Beyond the Limits of Domesticity: Moral Pluralism in the Management of Cats and Wildlife

Although human interactions with cats are often even typically analyzed in the context of domesticity, with a focus on what sorts of interactions might make both people and cats “happy at home,” a large number of cats in the world live, for one reason or another, beyond the bounds of domesticity. Human interactions with these more or less free-living cats raise deeply controversial questions about how both the cats and the people they interact with should be sensibly managed, and about the moral imperatives that ought to guide the management of their interactions through the laws and public policies regulating both human interactions with pets and with wildlife. We review the geography of human interactions with cats living beyond the bounds of domesticity. We acknowledge the contributions made to ideas about how to manage cats by the animal protection movement. We review the tensions that have emerged over time between advocates for the eradication of free-living cats, because of the impacts they have on native wildlife species, and those who have imagined alternatives to eradication, most notably one or another variant of trap-neuter-return (TNR). The conflict over how best to deal with cats living beyond the bounds of domesticity and their wildlife impacts raises the prospect of stalemate, and we canvass and critique possibilities for moving beyond that stalemate.
Gestational Folic Acid Administration Alleviated Maternal Postpartum Emotional and Cognitive Dysfunction in Mice

Gestational folic acid (FA) supplementation has been widely recognized for its benefits in preventing offspring defects, but its effect on postpartum females has not yet been adequately assessed. The occurrence of emotional and cognitive dysfunction is common in postpartum women, and its treatment remains limited. Considering the promising results of FA in various psychiatric disorders both in human and redents, we tested the effect of gestational FA administration on postpartum psychiatric behavioral phenotypes and the implicated brain-related mechanisms in a murine model. FA was administered orally in both the hormone-stimulated-pregnancy (HSP) model and pregnant mice at doses of 1 and 5 mg/kg. Postpartum behavioral results showed that the disorders of cognitive performance, depressive, and anxiety-related behaviors were all alleviated in the 5 mg/kg FA group. However, the general development of their offspring remained unaffected. Immunofluorescence and immunoblot results revealed that FA pretreatment significantly activated the maternal hippocampal BDNF-related pathway. Morphological studies have confirmed that FA promotes hippocampal neurogenesis. Moreover, synaptic plasticity and synaptic transmission are enhanced. All of these hippocampal changes play critical roles in rescuing neuronal function and behaviors. Thus, our data suggest that gestational FA administration has a therapeutic effect that improves cognition and reduces depression and anxiety in a murine postpartum model. This may be developed as a preventive and adjuvant therapeutic option for pregnant women.