Miracle-dz/UniFAR-FTUs huggingface dataset:
Sauropod dinosaur teeth from the lower Upper Cretaceous Winton Formation of Queensland, Australia and the global record of early titanosauriforms

The Upper Cretaceous Winton Formation of Queensland, Australia, has produced several partial sauropod skeletons, but cranial remains—including teeth—remain rare. Herein, we present the first description of sauropod teeth from this formation, based on specimens from three separate sites. An isolated tooth and a dentary fragment from the Diamantinasaurus matildae type locality are considered to be referable to that titanosaurian taxon. A single tooth from the D. matildae referred specimen site is similarly regarded as being part of that individual. Seventeen teeth from a new site that are morphologically uniform, and similar to the teeth from the two Diamantinasaurus sites, are assigned to Diamantinasauria. All sauropod teeth recovered from the Winton Formation to date are compressed-cone-chisel-shaped, have low slenderness index values (2.00–2.88), are lingually curved at their apices, mesiodistally convex on their lingual surfaces, and lack prominent carinae and denticles. They are markedly different from the chisel-like teeth of derived titanosaurs, more closely resembling the teeth of early branching members of the titanosauriform radiation. This provides further support for a ‘basal’ titanosaurian position for Diamantinasauria. Scanning electron microscope microwear analysis of the wear facets of several teeth reveals more scratches than pits, implying that diamantinasaurians were mid-height (1–10 m) feeders. With a view to assessing the spatio-temporal distribution of sauropod tooth morphotypes before and after deposition of the Winton Formation, we provide a comprehensive continent-by-continent review of the early titanosauriform global record (Early to early Late Cretaceous). This indicates that throughout the Early–early Late Cretaceous, sauropod faunas transitioned from being quite diverse at higher phylogenetic levels and encompassing a range of tooth morphologies at the start of the Berriasian, to faunas comprising solely titanosaurs with limited dental variability by the end-Turonian. Furthermore, this review highlights the different ways in which this transition unfolded on each continent, including the earliest records of titanosaurs with narrow-crowned teeth on each continent.
Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments

Transporter proteins are a vital interface between cells and their environment. In nutrient-limited environments, microbes with transporters that are effective at bringing substrates into their cells will gain a competitive advantage over variants with reduced transport function. Microbial ammonium transporters (Amt) bring ammonium into the cytoplasm from the surrounding periplasm space, but diagnosing Amt adaptations to low nutrient environments solely from sequence data has been elusive. Here, we report altered Amt sequence amino acid distribution from deep marine samples compared to variants sampled from shallow water in two important microbial lineages of the marine water column community—Marine Group I Archaea (Thermoproteota) and the uncultivated gammaproteobacterial lineage SAR86. This pattern indicates an evolutionary pressure towards an increasing dipole in Amt for these clades in deep ocean environments and is predicted to generate stronger electric fields facilitating ammonium acquisition. This pattern of increasing dipole charge with depth was not observed in lineages capable of accessing alternative nitrogen sources, including the abundant alphaproteobacterial clade SAR11. We speculate that competition for ammonium in the deep ocean drives transporter sequence evolution. The low concentration of ammonium in the deep ocean is therefore likely due to rapid uptake by Amts concurrent with decreasing nutrient flux.
The generalized Hashin–Shtrikman approach to Al/nano-TiC composite

The Hashin–Shtrikman approach is generalized and applied to a class of two-phase two-dimensional random macroscopically isotropic composites. The classic theory of the coated Hashin–Shtrikman assemblage (HSA) is extended to inhomogeneous complicated geometric structures. The first model is developed to the inhomogeneous core. The second model is constructed by introduction of the coating envelope considered as an HSA in another scale. The simulation explicitly demonstrates the dependence of the macroscopic properties of nanocomposites manufactured by Self-Propagating High-Temperature Synthesis in Bath on their geometrical structure. The models can be applied to optimal design problems to control the composite crystallization and solidification process by adding the moderator.
Experimental and modelling studies of collision avoidance strategy choices and behavioural characteristics in interweaving pedestrian flow

The mechanisms of collision avoidance (CA) behaviours in interweaving pedestrian flow movements are important for pedestrian space planning and emergency management but not well understood yet. In this paper, a series of controlled interweaving pedestrian flow experiments with different densities are carried out to investigate the CA behaviours, especially CA strategy choices. Four types of CA strategies are manually identified in these experiments. Nine characteristic parameters based on the trajectory data are defined to explore the characteristics of CA behaviours. The experimental results reveal that (i) the CA behaviours change with density levels; (ii) heterogeneities can be found for individual pedestrians; (iii) the defined characteristic parameters show different statistical features for different types of CA strategies, and correlations exist between most of the parameter pairs; (iv) it usually takes 0.5–2.5 s to complete a CA process with a trajectory length of 0.5–3.5 m. A multi-nomial logit (MNL) model and a long-short-term-memory (LSTM) model are established respectively for predicting pedestrians' choices of CA strategies using the selected characteristic parameters as inputs. The modelling results prove the importance of using time-series data for pedestrian behaviour modelling, and the LSTM models show advantages over the MNL model at this point.
THE CLINICAL MANIFESTATIONS IN PATIENTS WITH NASAL POLYPOSIS WHO UNDERWENT SURGERY IN DAMASCUS HOSPITAL

The objective of this retrospective study was to obtain epidemiological data from 110 patients with nasal polyposis who underwent surgery (FESS) in Damascus hospital. Moreover, this research aims to study the correlation between nasal polyposis with asthma and aspirin intolerance. The frequency of clinical manifestations, previous medical history, and recurrence rate were determined and then compared with other studies. Nasal polyposis is slightly more common in males compared to females. The most common affected age category was [31-40] years. The most common complaint was nasal obstruction 98.2% followed by rhinorrhea 80.9% then anosmia 80%. Recurrence rate (patients who underwent corrective surgery after initial surgery) constituted 23.6% of patients. Patients with asthma constituted 30% of patients. Aspirin intolerance was found in 24.5%, and Samter’s triad (nasal polyposis +asthma +aspirin intolerance) was found in 24.5%.
Flow field prediction on large variable sized 2D point clouds with graph convolution

Computational Fluid Dynamics (CFD) solvers are an important tool to predict the behaviour of fluid flows in many industrial sectors. Thereby, accelerating the solution process without compromising on geometric accuracy is a major goal in the development of numerical flow solvers and design optimization frameworks. For tackling the issue of complex geometries, this paper utilizes a graph-based machine learning approach for solving the regression problem of stationary fluid flow field prediction. Concretely, a graph convolutional network (GCN) architecture is applied and successfully predicts flow fields around geometrical different objects. As the GCN model operates on the numerical mesh directly, the exact geometry of the object as well as all other properties of the mesh are preserved. It turned out that a GCN is able to predict fluid flow fields of two-dimensional bluff-bodies and NACA airfoils, even considering predictions based on extrapolation. Furthermore, this approach is able to handle different sizes of point clouds up to 50k points. Finally, using the predicted flow field as an initial flow distribution for a CFD simulation, showed a decreased solver runtime in some cases.
Ja n 20 06 Black Rings , Boosted Strings and Gregory-Laflamme

We investigate the Gregory-Laflamme instability for black strings carrying KK-momentum along the internal direction. We demonstrate a simple kinematical relation between the thresholds of the classical instability for the boosted and static black strings. We also find that Sorkin’s critical dimension depends on the internal velocity and in fact disappears for sufficiently large boosts. Our analysis implies the existence of an analogous instability for the five-dimensional black ring of Emparan and Reall. We also use our results for boosted black strings to construct a simple model of the black ring and argue that such rings exist in any number of space-time dimensions. E-mail: jlhovdeb@sciborg.uwaterloo. ca E-mail: rmyers@perimeterinstitute.ca
This information is current as Expression Regulatory T Cells upon Loss of FOXP 3 Dominant Th 2 Differentiation of Human

CD4 + CD25 + FOXP3 + regulatory T cells (Treg) are pivotal for peripheral self-tolerance. They prevent immune responses to auto-and alloantigens and are thus under close scrutiny as cellular therapeutics for autoimmune diseases and the prevention or treatment of alloresponses after organ or stem cell transplantation. We previously showed that human Treg with a memory cell phenotype, but not those with a naive phenotype, rapidly downregulate expression of the lineage-deﬁning transcription factor FOXP3 upon in vitro expansion. We now compared the transcriptomes of stable FOXP3 + Treg and converted FOXP3 2 ex-Treg by applying a newly developed intranuclear staining protocol that permits the isolation of intact mRNA from ﬁxed, permeabilized, and FACS-puriﬁed cell populations. Whole-genome microarray analysis revealed strong and selective upregulation of Th2 signature genes, including GATA-3, IL-4, IL-5, and IL-13, upon downregulation of FOXP3. Th2 differentiation of converted FOXP3 2 ex-Treg occurred even under nonpolarizing conditions and could not be prevented by IL-4 signaling blockade. Thus, our studies identify Th2 differentiation as the default developmental program of human Treg after downregulation of FOXP3. The Journal of Immunology , 2012, 188: 000–000.
Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology

The number of unique transmembrane (TM) protein structures doubled in the last four years that can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
CXCR7 promotes foetal myoblast fusion at muscle fiber tips independently of Myomaker via a ß1integrin-EGFR-dependent mechanism

Muscle growth must be tightly regulated during development in order to obtain the final muscle shape. Myoblast fusion is a critical step of muscle growth, driving the formation of syncytial myofibers attaching at both ends to tendons. We investigated the role of the CXCR7 chemokine receptor in foetal muscle growth during chicken limb development. We show that CXCR7 displays a regionalized expression at the tips of myofibers close to tendons in foetal limb muscles, which is exclusive to the central location of the fusion gene MYOMAKER (TMEM8C in chicken) in foetal muscles. CXCR7 promotes myoblast fusion independently of TMEM8C in chicken limb muscles and in foetal myoblast cultures and requires EGF receptor signalling. The CXCR7 ligand, CXCL12, expressed in connective tissue, increases ß1integrin activation at the myotendinous junction and CXCR7 expression at muscle tips, resulting in a fusion promoting effect independent from a direct binding of CXCL12 to CXCR7 receptor. Our results evidence a CXCR7-dependent/TMEM8C-independent fusion mechanism at the myofiber tips that regulates muscle growth at the tendon/muscle interface during foetal myogenesis.
BayesTME: A unified statistical framework for spatial transcriptomics

Spatial variation in cellular phenotypes underlies heterogeneity in immune recognition and response to therapy in cancer and many other diseases. Spatial transcriptomics (ST) holds the potential to quantify such variation, but existing analysis methods address only a small part of the analysis challenge, such as spot deconvolution or spatial differential expression. We present BayesTME, an end-to-end Bayesian method for analyzing spatial transcriptomics data. BayesTME unifies several previously distinct analysis goals under a single, holistic generative model. This unified approach enables BayesTME to (i) be entirely reference-free without any need for paired scRNA-seq, (ii) outperform a large suite of methods in quantitative benchmarks, and (iii) uncover a new type of ST signal: spatial differential expression within individual cell types. To achieve the latter, BayesTME models each phenotype as spatially adaptive and discovers statistically significant spatial patterns amongst coordinated subsets of genes within phenotypes, which we term spatial transcriptional programs. On human and zebrafish melanoma tissues, BayesTME identifies spatial transcriptional programs that capture fundamental biological phenomena like bilateral symmetry, differential expression between interior and surface tumor cells, and tumor-associated fibroblast and macrophage reprogramming. Our results demonstrate BayesTME’s power in unlocking a new level of insight from spatial transcriptomics data and fostering a deeper understanding of the spatial architecture of the tumor microenvironment. BayesTME is open source and publicly available (https://github.com/tansey-lab/bayestme).
Neuromechanical Coupling is Reflected in the Spatial Organization of the Spinal Motoneuron Pools

The anatomy of muscles is complex, so that a given movement can result from the activity of multiple muscle combinations, a concept termed redundancy. The central nervous system must resolve this redundancy to produce coordinated and efficient motion. One proposed mechanism that simplifies motor control is through the neural embedding of musculoskeletal dynamics. We have shown previously that the musculoskeletal anatomy of the upper extremity is organized in functional agonistic and antagonistic groups through mechanical coupling. However, it remains unknown if the neural anatomy of the spinal motoneuron pools somatotopically embeds this musculoskeletal anatomy. Here, we develop a three-dimensional model of the macaque cervical spinal cord and a corresponding OpenSim model of the upper extremity to characterize the structure-function relationship of spinal motoneurons innervating upper limb musculature. We hypothesize that the motoneuron pools of agonistic muscles that perform a coordinated action are located closer together in the spinal cord compared to antagonistic muscles. We used the spinal cord model to quantify the spatial relationship between motoneuron pools, and we used the OpenSim model to quantify the functional relationship between muscles. We used a hierarchical clustering analysis compare the structural and functional relationships. We found that the spatial organization of motoneuron pools in the spinal cord broadly mimics the anatomical relationships between muscle lengths and moment arms. Furthermore, within the same segment, the motoneurons innervating synergistic muscles were located closer to each other than to the motoneurons innervating antagonistic muscles, while across segments the motoneurons innervating specific antagonistic groups of muscles were colocalized. These results suggest that the mechanical coupling of the musculoskeletal system is embedded in the spinal cord anatomy underlying the modular organization of the neural motor control system.
TPH2 knockout male rats are aggressive, show less anxiety, and exhibit an altered oxytocin system

The central serotoninergic system is critical for stress responsivity and social behavior, and its dysregulations has been centrally implicated in virtually all neuropsychiatric disorders. Genetic serotonin depletion animal models could provide a tool to elucidate the causes and mechanisms of diseases and to develop new treatment approaches. Previously mice lacking tryptophan hydroxylase 2 (Tph2) have been developed, showing altered behaviors and neurotransmission. However, the effect of congenital serotonin deficiency on emotional and social behavior in rats is still largely unknown, as are the underlying mechanisms. In this study, we used Tph2 knockout (Tph2-/-) male rat model to study how the lack of serotonin in the rat brain affects anxiety-like and social behaviors. Since oxytocin is centrally implicated in these behaviors, we furthermore explored whether effects of Tph2 knockout on behavior would relate to changes in the oxytocin system. We show that Tph2-/- rats display reduced anxiety-like behavior and a high level of aggression in social interactions. In addition, oxytocin receptor expression was increased in the infralimbic and prelimbic cortex, paraventricular nucleus, dorsal raphe nucleus and some subregions of hippocampus, which was paralleled by increased levels of oxytocin in the medial frontal cortex, paraventricular nucleus, but not the dorsal raphe nucleus, central amygdala and hippocampus. In conclusion, our study demonstrated reduced anxiety but exaggerated aggression in Tph2-/- male rats and reveals for the first time a potential involvement of altered oxytocin system function. SIGNIFICANCE STATEMENT We explored the changes in behavior and oxytocin system functioning in the tryptophan hydroxylase 2 (Tph2) knockout rat model, lacking serotonin in the brain. This rat model contributes to our understanding of the role of serotonin in psychiatric transdiagnostic features and underlying mechanisms. We found that Tph2 knockout male rats are aggressive, less anxious, and exhibit an altered oxytocin system. The observed changes in oxytocin signaling may lead to a new target for the treatment of diseases caused by genetic serotonin deficiency.
Nitrate-dependent salt tolerance mediated by OsNLP4-OsMADS27 module

Salt stress is a major constraint of plant growth and yield. Nitrogen (N) fertilizers are known to alleviate salt stress. However, the underlying molecular mechanisms remain unclear. Here we show that OsNLP4-OsMADS27 module controls nitrate-dependent salt tolerance in rice. The expression of OsMADS27 is specifically induced by nitrate. The OsMADS27 knockout mutants are more sensitive to salt stress than the wild type, whereas the OsMADS27 overexpression lines are more tolerant. Transcriptomic analyses revealed that OsMADS27 controls the expression of a number of known stress-responsive genes as well as those involved in ion homeostasis and antioxidation. We demonstrated that OsMADS27 directly binds to the promoter of OsHKT1.1 and OsSPL7 to regulate their expression. Notably, OsMADS27-mediated salt tolerance is nitrate-dependent and positively correlated with nitrate concentration. We further showed that OsNLP4, a nitrate-responsive key regulator in N metabolism and N use efficiency, positively regulates the expression of OsMADS27 by directly binding to the nitrate-responsive cis-element in its promoter, thereby transmitting the nitrate signal to OsMADS27 and conferring its nitrate dependence. Our results reveal the role of nitrate-responsive OsNLP4-OsMADS27 module and its downstream target genes in salt tolerance, filling the gap in the molecular mechanism of nitrate-dependent salt tolerance of rice. Moreover, OsMADS27 overexpression increased grain yield under salt stress in presence of sufficient nitrate, indicating that OsMADS27 is a promising candidate for the improvement of salt tolerance in rice.
A General Error Estimate For Parabolic Variational Inequalities

Abstract The gradient discretisation method (GDM) is a generic framework designed recently, as a discretisation in spatial space, to partial differential equations. This paper aims to use the GDM to establish a first general error estimate for numerical approximations of parabolic obstacle problems. This gives the convergence rates of several well-known conforming and non-conforming numerical methods. Numerical experiments based on the hybrid finite volume method are provided to verify the theoretical results.
Heteropolyoxometalate Catalyzed Selective Oxidation of Alcohols to Carbonyl Compounds by Hydrogen Peroxide under Mild Condition

Keggin-type heteropolyoxometalates have been used as catalysts for the oxidation of benzylic alcohols and secondary alcohols to the corresponding carbonyl compounds using environment-friendly H 2 O 2 as oxidant at room temperature. The catalysts used in this study exhibit high selectivity in the oxidation of alcohols with no over-oxidation and formation of carboxylic acids. For vanadium(V)-substituted heteropolyoxometalates [H x-2 PV x W 12-x O 40 ] 5- (x = 4 and 6), the catalytic activity decreased with the increase in number of vanadium atoms in the catalyst.