Miracle-dz/UniFAR-FTUs huggingface dataset:
The shared susceptibility epitope of HLA-DR4 binds citrullinated self-antigens and the TCR

Citrullination of a fibrinogen peptide influences HLA-DR4 binding and TCR usage by neoepitope-reactive T cells in rheumatoid arthritis. TCR detection of citrullinated epitopes The autoreactive T cell repertoire driving disease activity in rheumatoid arthritis (RA) includes CD4+ T cells that recognize MHC-bound peptides with arginine residues posttranslationally modified to citrulline. Some HLA-DRB1 alleles have a shared susceptibility epitope associated with increased RA incidence. Lim et al. analyzed the repertoire, binding properties, and structure of multiple T cell receptors (TCRs) derived from humanized mice reactive with citrullinated peptides presented by HLA-DR4. TCR repertoire analysis revealed a citrullinated antigen-specific motif, conserved in both mice and humans. Crystal structures revealed direct contact of the TCR with the shared epitope on HLA-DR4. Alleles of HLA-DRB1 with the shared epitope contribute to the development of RA through both binding of stimulatory peptide epitopes and direct contact with a biased set of TCRs. Individuals expressing HLA-DR4 bearing the shared susceptibility epitope (SE) have an increased risk of developing rheumatoid arthritis (RA). Posttranslational modification of self-proteins via citrullination leads to the formation of neoantigens that can be presented by HLA-DR4 SE allomorphs. However, in T cell–mediated autoimmunity, the interplay between the HLA molecule, posttranslationally modified epitope(s), and the responding T cell repertoire remains unclear. In HLA-DR4 transgenic mice, we show that immunization with a Fibβ-74cit69-81 peptide led to a population of HLA-DR4Fibβ-74cit69-81 tetramer+ T cells that exhibited biased T cell receptor (TCR) β chain usage, which was attributable to selective clonal expansion from the preimmune repertoire. Crystal structures of pre- and postimmune TCRs showed that the SE of HLA-DR4 represented a main TCR contact zone. Immunization with a double citrullinated epitope (Fibβ-72,74cit69-81) altered the responding HLA-DR4 tetramer+ T cell repertoire, which was due to the P2-citrulline residue interacting with the TCR itself. We show that the SE of HLA-DR4 has dual functionality, namely, presentation and a direct TCR recognition determinant. Analogous biased TCR β chain usage toward the Fibβ-74cit69-81 peptide was observed in healthy HLA-DR4+ individuals and patients with HLA-DR4+ RA, thereby suggesting a link to human RA.
Attribute-wise Explainable Fashion Compatibility Modeling

With the boom of the fashion market and people’s daily needs for beauty, clothing matching has gained increased research attention. In a sense, tackling this problem lies in modeling the human notions of the compatibility between fashion items, i.e., Fashion Compatibility Modeling (FCM), which plays an important role in a wide bunch of commercial applications, including clothing recommendation and dressing assistant. Recent advances in multimedia processing have shown remarkable effectiveness in accurate compatibility evaluation. However, these studies work like a black box and cannot provide appropriate explanations, which are indeed of importance for gaining users’ trust and improving their experience. In fact, fashion experts usually explain the compatibility evaluation through the matching patterns between fashion attributes (e.g., a silk tank top cannot go with a knit dress). Inspired by this, we devise an attribute-wise explainable FCM solution, named ExFCM, which can simultaneously generate the item-level compatibility evaluation for input fashion items and the attribute-level explanations for the evaluation result. In particular, ExFCM consists of two key components: attribute-wise representation learning and attribute interaction modeling. The former works on learning the region-aware attribute representation for each item with the threshold global average pooling. Besides, the latter is responsible for compiling the attribute-level matching signals into the overall compatibility evaluation adaptively with the attentive interaction mechanism. Note that ExFCM is trained without any attribute-level compatibility annotations, which facilitates its practical applications. Extensive experiments on two real-world datasets validate that ExFCM can generate more accurate compatibility evaluations than the existing methods, together with reasonable explanations.
Rolling spinners on the water surface

Fast-spinning discs on a liquid surface propagate along arbitrarily shaped boundaries, making a new type of surface vehicles. Angular momentum of spinning bodies leads to their remarkable interactions with fields, waves, fluids, and solids. Orbiting celestial bodies, balls in sports, liquid droplets above a hot plate, nanoparticles in optical fields, and spinning quantum particles exhibit nontrivial rotational dynamics. Here, we report self-guided propulsion of magnetic fast-spinning particles on a liquid surface in the presence of a solid boundary. Above some critical spinning frequency, such particles generate localized 3D vortices and form composite “spinner-vortex” quasiparticles with nontrivial, yet robust dynamics. Such spinner-vortices are attracted and dynamically trapped near the boundaries, propagating along the wall of any shape similarly to “liquid wheels. ” The propulsion velocity and the distance to the wall are controlled by the angular velocity of the spinner via the balance between the Magnus and wall repulsion forces. Our results offer a new type of surface vehicles and provide a powerful tool to manipulate spinning objects in fluids.
Netrin-1 receptor UNC5C cleavage by active δ-secretase enhances neurodegeneration, promoting Alzheimer’s disease pathologies

Netrin-1 reduction activates AEP that cleaves UNC5C receptor, contributing to AD pathogenesis. Netrin-1, a family member of laminin-related secreted proteins, mediates axon guidance and cell migration during neural development. T835M mutation in netrin receptor UNC5C predisposes to the late-onset Alzheimer’s disease (AD) and increases neuronal cell death. However, it remains unclear how this receptor is molecularly regulated in AD. Here, we show that δ-secretase selectively cleaves UNC5C and escalates its proapoptotic activity, facilitating neurodegeneration in AD. Netrin deficiency activates δ-secretase that specifically cuts UNC5C at N467 and N547 residues and enhances subsequent caspase-3 activation, additively augmenting neuronal cell death. Blockade of δ-secretase cleavage of UNC5C diminishes T835M mutant’s proapoptotic activity. Viral expression of δ-secretase–truncated UNC5C fragments into APP/PS1 mice strongly accelerates AD pathologies, impairing learning and memory. Conversely, deletion of UNC5C from netrin-1–depleted mice attenuates AD pathologies and rescues cognitive disorders. Hence, δ-secretase truncates UNC5C and elevates its neurotoxicity, contributing to AD pathogenesis.
Total Phenolics, Flavonoids, Condensed Tannins Content of Eight Centaurea Species and Their Broad Inhibitory Activities against Cholinesterase, Tyrosinase, Î±-Amylase and Î±-Glucosidase

Several bioactive compounds originate from natural sources and their uses are generally related with traditional or folk medicine. Synthetic drugs can have adverse side effects and, for this reason, the investigation of novel, safe, and natural-occurring products can account for the development of new drugs. The genus Centaurea L. is one of the most important genera of the Asteraceae family, containing more than 200 species in the Turkish i¬‚ora, about 140 of which are endemic. The aim of the present work was to determine enzyme inhibitory potentials of two extracts (chloroform and ethyl acetate) from eight Centaurea species against cholinesterase, tyrosinase, amylase, and glucosidase. The total phenolics, flavonoids and condensed tannin contents were also reported for each extract. These components in the extracts varied according to species and extraction solvents as well as enzyme inhibitory effects. The highest level of phenolics was found to be in the chloroform extract of C. pulchella (119.23 mg GAEs/g extract). Generally, chloroform extracts exhibited stronger enzyme inhibitory effects as compared to ethyl acetate. Additionally, possible correlations with total phenolics, flavonoids, and condensed tannins content were also highlighted. This paper is the first report of the inhibitory capacities of the eight Centaurea species on the selected enzymes. The present results may be a valuable starting point in the development of new bioactive formulations.
Non-Canonical Wnt Signaling Regulates Cochlear Outgrowth and Planar Cell Polarity via Gsk3β Inhibition

During development, sensory hair cells (HCs) in the cochlea assemble a stereociliary hair bundle on their apical surface with planar polarized structure and orientation. We have recently identified a non-canonical, Wnt/G-protein/PI3K signaling pathway that promotes cochlear outgrowth and coordinates planar polarization of the HC apical cytoskeleton and alignment of HC orientation across the cochlear epithelium. Here, we determined the involvement of the kinase Gsk3β and the small GTPase Rac1 in non-canonical Wnt signaling and its regulation of the planar cell polarity (PCP) pathway in the cochlea. We provided the first in vivo evidence for Wnt regulation of Gsk3β activity via inhibitory Ser9 phosphorylation. Furthermore, we carried out genetic rescue experiments of cochlear defects caused by blocking Wnt secretion. We showed that cochlear outgrowth was partially rescued by genetic ablation of Gsk3β but not by expression of stabilized β-catenin; while PCP defects, including hair bundle polarity and junctional localization of the core PCP proteins Fzd6 and Dvl2, were partially rescued by either Gsk3β ablation or constitutive activation of Rac1. Our results identify Gsk3β and likely Rac1 as downstream components of non-canonical Wnt signaling and mediators of cochlear outgrowth, HC planar polarity, and localization of a subset of core PCP proteins in the cochlea.
Do Aerial Nitrogen Depositions Affect Fungal and Bacterial Communities of Oak Leaves?

The amount of nitrogen (N) deposition onto forests has globally increased and is expected to double by 2050, mostly because of fertilizer production and fossil fuel burning. Several studies have already investigated the effects of N depositions in forest soils, highlighting negative consequences on plant biodiversity and the associated biota. Nevertheless, the impact of N aerial inputs deposited directly on the tree canopy is still unexplored. This study aimed to investigate the influence of increased N deposition on the leaf-associated fungal and bacterial communities in a temperate forest dominated by Sessile oak [Quercus petraea (Matt.) Liebl. ]. The study area was located in the Monticolo forest (South Tyrol, Italy), where an ecosystem experiment simulating an increased N deposition has been established. The results highlighted that N deposition affected the fungal beta-diversity and bacterial alpha-diversity without affecting leaf total N and C contents. We found several indicator genera of both fertilized and natural conditions within bacteria and fungi, suggesting a highly specific response to altered N inputs. Moreover, we found an increase of symbiotrophic fungi in N-treated, samples which are commonly represented by lichen-forming mycobionts. Overall, our results indicated that N-deposition, by increasing the level of bioavailable nutrients in leaves, could directly influence the bacterial and fungal community diversity.
Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Abstract Soybean (Glycine max (L.) Merr. ) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.
New arsenate minerals from the Arsenatnaya fumarole, Tolbachik volcano, Kamchatka, Russia. XV. Calciojohillerite, NaCaMgMg2(AsO4)3, a member of the alluaudite group

Abstract The new alluaudite-group mineral calciojohillerite is one of the major arsenates in sublimates of the Arsenatnaya fumarole at the Second scoria cone of the Northern Breakthrough of the Great Tolbachik Fissure Eruption, Tolbachik volcano, Kamchatka, Russia. In middle zones of the fumarole, calciojohillerite is associated with hematite, tenorite, johillerite, nickenichite, bradaczekite, badalovite, tilasite, lammerite, ericlaxmanite, aphthitalite-group sulfates, langbeinite, calciolangbeinite, anhydrite, sanidine, fluorophlogopite, fluoborite, cassiterite, pseudobrookite, rutile, sylvite and halite. In deep zones it occurs in association with anhydrite, diopside, hematite, svabite, berzeliite, schäferite, forsterite, magnesioferrite, ludwigite, rhabdoborite-group fluoroborates, powellite, baryte, fluorapatite, udinaite, arsenudinaite and paraberzeliite. Calciojohillerite forms prismatic crystals up to 1 cm long, their aggregates and crystal crusts up to 0.5 m2. It is transparent, colourless, pale green, pale yellow, light blue, pale lilac or pink, with vitreous lustre. The mineral is brittle, with imperfect cleavage. The Mohs hardness is 3½. Dcalc is 3.915 g cm–3. Calciojohillerite is optically biaxial (–), α = 1.719(3), β = γ = 1.732(3); 2Vmeas. = 15(10)°. Chemical composition (wt.%, electron-microprobe; holotype) is: Na2O 7.32, K2O 0.10, CaO 6.82, MgO 20.31, MnO 0.68, CuO 0.27, ZnO 0.02, Al2O3 0.56, Fe2O3 3.53, TiO2 0.01, SiO2 0.03, P2O5 1.25, V2O5 0.10, As2O5 58.77, SO3 0.13, total 99.90. The empirical formula based on 12 O atoms is (Na1.30K0.01Ca0.67Mg2.78Mn0.05Cu0.02Al0.06Fe3+0.24)Σ5. 13(As2.83P0.10S0.01V0.01)Σ2. 95O12. Calciojohillerite is monoclinic, C2/c, a = 11.8405(3), b = 12.7836(2), c = 6.69165(16) Å, β = 112.425(3)°, V = 936.29(4) Å3 and Z = 4. The crystal structure was solved from single-crystal X-ray diffraction data, R1 = 0.0227. Calciojohillerite is isostructural with other alluaudite-group minerals. Its simplified crystal chemical formula is A(1)CaA(1)′□A(2)□A(2)′NaM(1)MgM(2)Mg2(AsO4)3 (□ = vacancy). The idealised formula is NaCaMg3(AsO4)3, or, according to the nomenclature of alluaudite-group arsenates, NaCaMgMg2(AsO4)3. Calciojohillerite is named as an analogue of johillerite NaCu2+MgMg2(AsO4)3 with species-defining Ca instead of Cu in the ideal formula.
Evaluation of seed amino acid content and its correlation network analysis in wild soybean (Glycine soja) germplasm in Japan

Abstract Wild soybean (Glycine soja) is a valuable genetic resource for soybean improvement. Seed composition profiles provide beneficial information for the effective conservation and utilization of wild soybeans. Therefore, this study aimed to assess the variation in free amino acid abundance in the seeds of wild soybean germplasm collected in Japan. The free amino acid content in the seeds from 316 accessions of wild soybean ranged from 0.965 to 5.987 mg/g seed dry weight (DW), representing a 6.2-fold difference. Three amino acids had the highest coefficient of variation (CV): asparagine (1.15), histidine (0.95) and glutamine (0.94). Arginine (0.775 mg/g DW) was the predominant amino acid in wild soybean seeds, whereas the least abundant seed amino acid was glutamine (0.008 mg/g DW). A correlation network revealed significant positive relationships among most amino acids. Wild soybean seeds from different regions of origin had significantly different levels of several amino acids. In addition, a significant correlation between latitude and longitude of the collection sites and the total free amino acid content of seeds was observed. Our study reports diverse phenotypic data on the free amino acid content in seeds of wild soybean resources collected from throughout Japan. This information will be useful in conservation programmes for Japanese wild soybean and for the selection of accessions with favourable characteristics in future legume crop improvement efforts.
Kufahrite, PtPb, a new mineral from Ledyanoy Creek placer, Galmoenan ultramafic complex, Koryak Highlands, Russia

Abstract Kufahrite, PtPb, is a new mineral (IMA2020-045) from the Ledyanoy Creek placer, Koryak Highlands, Russia. The mineral was found in isoferroplatinum (Pt3Fe) grains extracted from a heavy-mineral concentrate, together with tetraferroplatinum (PtFe), tulameenite (Pt2FeCu), native iridium, hollingworthite (RhAsS) and Cr-rich spinel. Kufahrite occurs as part of alteration rims which are formed together with tetraferroplatinum after isoferroplatinum, or as grains up to 150 μm in size. According to powder X-ray diffraction analyses kufahrite is isotypic to its synthetic analogue, it is hexagonal and crystallises in space group P63/mmc adopting the nickeline structure type. Its unit-cell parameters are: a = 4.2492(6) Å; c = 5.486(6) Å; V = 85.78 Å3 and Z = 2. The calculated density is 14.80 g/cm–3. The strongest diffraction lines are [d, Å (I, %) (hkl)]: 3.052 (80) (101), 2.197 (100) (102), 2.125 (28) (110), 1.747 (18) (210), 1.528 (35) (202), 1.240 (18) (212) and 0.958 (22) (312). The Vickers hardness is 295 kg/mm2 (range 262–320, n = 5), corresponding to a Mohs hardness of 4. The empirical formula of kufahrite, calculated from a mean value of 23 electron-microprobe analyses is (Pt0.94Rh0.04)Σ0. 98(Pb0.83Sb0.19)Σ1. 02. The name (pronounced as [ku fa rait]) honours Fahrid Shakirovitch Kutyev (1943‒1993), a geologist from the Institute of Volcanology of USSR Academy of Sciences, who played a key role in the discovery of the Koryak–Kamchatka Platinum Belt, including the Ledyanoy Creek placer platinum deposit, where the new mineral has been discovered.
THIN LAYER CHROMATOGRAPHY AND HIGH PRESSURE LIQUID CHROMATOGRAPHY PROFILING OF PLANT EXTRACTS OF VIOLA ODORATA LINN

Medicinal plant contains matter that can be used for therapeutic reason or which are precursors for the production of useful drugs. Very few and periodic works are there in the literature regarding the phytochemistry and TLC of Viola odorata L. TLC profiling of plant extract gives an idea about the presence of various phytochemicals. Different Rf (Retention factor) value of various phytochemicals provide valuable clue regarding their polarity and selection of solvents for separation of phytochemicals. HPLC profile of petroleum ether extract of Viola odorata have characteristics peaks at retention time 2.885, 3.370, 3.487, 3.900, 4.067, 4.191, 5.207, 6.724 (Stigmasterol), 17.698 (Lupeol), 18.174 (β2Sitosterol), 23.118. These peaks showed that there are different compounds and characteristic fingerprints for each drug to judge in an herbal formulation.
D2D Assisted Cellular Networks in Licensed and Unlicensed Spectrum: Matching-Iteration-Based Joint User Access and Resource Allocation

Device-to-Device (D2D) communications, which enable direct communication between nearby user devices over the licensed spectrum, have been considered a key technique to improve spectral efficiency and system throughput in cellular networks (CNs). However, the limited spectrum resources cannot be sufficient to support more cellular users (CUs) and D2D users to meet the growth of the traffic data in future wireless networks. Therefore, Long-Term Evolution-Unlicensed (LTE-U) and D2D-Unlicensed (D2D-U) technologies have been proposed to further enhance system capacity by extending the CUs and D2D users on the unlicensed spectrum for communications. In this paper, we consider an LTE network where the CUs and D2D users are allowed to share the unlicensed spectrum with Wi-Fi users. To maximize the sum rate of all users while guaranteeing each user’s quality of service (QoS), we jointly consider user access and resource allocation. To tackle the formulated problem, we propose a matching-iteration-based joint user access and resource allocation algorithm. Simulation results show that the proposed algorithm can significantly improve system throughput compared to the other benchmark algorithms.
Data Wrangling for Fair Classification

Whenever decisions that affect people are informed by classifiers, there is a risk that the decisions can discriminate against certain groups as a result of bias in the training data. There has been significant work to address this, based on pre-processing the inputs to the classifier, changing the classifier itself, or post-processing the results of the classifier. However, upstream from these steps, there may be a variety of data wrangling processes that select and integrate the data that is used to train the classifier, and these steps could themselves lead to bias. In this paper, we propose an approach that generates schema mappings in ways that take into account bias observed in classifiers trained on the results of different mappings. The approach searches a space of candidate interventions in the mapping generation process, which change how these mappings are generated, informed by a bias-aware fitness function. The resulting approach is evaluated using Adult Census and German Credit data sets.
Electrochemical Immunosensors for Food Analysis: A Review of Recent Developments

ABSTRACT Electrochemical immunosensors have the potential to transform analytical procedures within the food industry by providing highly specific, rapid, and inexpensive determination of pathogens. In this paper, recent advances in this area are outlined. In particular, attention is paid to new methods that have been developed for the modification of working electrode surfaces. Many advances have been related to the use of novel nanomaterials such as carbon nanotubes, graphene, and metallic nanoparticles, often used in conjunction with each other or polymers. The use of these materials has generally provided superior sensor sensitivity. The application of immunosensors to the detection of a range of pathogens in real samples is then investigated to establish whether they provide solutions in practical applications.