Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum autoantibody profiling of oral squamous cell carcinoma patients reveals NUBP2 as a potential diagnostic marker

Introduction Oral Squamous Cell Carcinoma (OSCC), a common malignancy of the head and neck region, is frequently diagnosed at advanced stages, necessitating the development of efficient diagnostic methods. Profiling autoantibodies generated against tumor-associated antigens have lately demonstrated a promising role in diagnosis, predicting disease course, and response to therapeutics and relapse. Methods In the current study, we, for the first time, aimed to identify and evaluate the diagnostic value of autoantibodies in serum samples of patients with OSCC using autoantibody profiling by an immunome protein array. The utility of anti-NUBP2 antibody and tissue positivity in OSCC was further evaluated. Results and discussion We identified a total of 53 autoantibodies with significant differential levels between OSCC and control groups, including 25 that were increased in OSCC and 28 that were decreased. These included autoantibodies against Thymidine kinase 1 (TK1), nucleotide-binding protein 2 (NUBP2), and protein pyrroline-5-carboxylate reductase 1 (PYCR1), among others. Immunohistochemical validation indicated positive staining of NUBP2 in a large majority of cases (72%). Further, analysis of OSCC data available in TCGA revealed higher NUBP2 expression correlated with better disease-free patient survival. In conclusion, the differential serum autoantibodies identified in the current study, including those for NUBP2, could be used as potential biomarkers for early diagnosis or as screening biomarkers for OSCC pending investigation in a larger cohort.
Exploring the mechanisms of endophytic bacteria for suppressing early blight disease in tomato (Solanum lycopersicum L.)

Controlling early blight of tomatoes using endophytic bacteria is an eco-friendly and sustainable approach to manage this common fungal disease caused by Alternaria solani, Alternaria alternata, and Curvularia lunata. Endophytic bacteria are microorganisms that live inside plant tissues without causing harm and can help protect the host plant from pathogens. In this work, twenty endophytic bacterial isolates from tomato healthy plants were tested against pathogenic fungal isolates that caused early blight disease in vitro. Out of the 20 tested isolates, three (B4, B7, and B17) were considered effective isolates against the growth of fungal pathogens. The three isolates were recognized as Enterobacter cloacae HS-6 (B4), Pseudomonas gessardii HS-5 (B 7), and Pseudomonas mediterranea HS-4 (B17) using 16s-rDNA sequencing. Different concentrations of bacterial cultural diltrates at 20, 40, and 60% were tested for their antagonistic effects on the development of pathogenic fungi in vitro. The lowest dry weights of pathogenic isolates in all bacterial culture filtrates were discovered at 60%. In all culture filtrates, phenolic compounds showed the largest peak area. Under greenhouse conditions, the least disease severity of tomato early blight was found for E. cloacae and its culture filtrate compared to other treatments. Real-time PCR was used to examine the expression pattern of the defense response gene β-1.3 glucanase gene in infected tomato plants with pathogenic fungi (control) as well as its relations with efficient biocontrol agent (E. cloacae). The expression of the gene increased substantially and significantly after three days from the inoculation-infected plants with C. lunata and E. cloacae while it reached the maximum after five days from the inoculation with A. alternata, A. solani and E. cloacae. Our study concluded that the endophytic bacterial isolate E. cloacae can be considered a promising biocontrol agent for preventing tomato early blight.
Robust 3D Semantic Segmentation Based on Multi-Phase Multi-Modal Fusion for Intelligent Vehicles

3D semantic segmentation is a key technology for intelligent vehicles. Recently, great efforts have been made to achieve accurate and robust 3D semantic segmentation results through LiDAR-camera fusion, due to the complementary information of images like color and texture. However, current LiDAR-camera fusion methods still lag behind LiDAR-only methods in complex and varied scenarios containing sparse and similar geometric features. Three main factors limit their performance: sparse mappings between two modalities, the contribution of different modality features, and the gap between results of two modalities. Addressing that, we present a multi-phase LiDAR-camera fusion method, which comprehensively fuses information of two modalities in three phases: first, a context sampler block is proposed to fuse low-level image contextual features into LiDAR points; second, a cross dimensional fusion block is designed to implement the interaction of shared features for hierarchical supervision while retaining private features for jointly refining their predictions; third, a modality perceptual conformance loss is induced to make them learn from each other in an explicit manner by minimizing the gap between two modality predictions. Quantitative and qualitative evaluations with state-of-the-art (SOTA) methods are performed on urban dataset SemanticKITTI, off-road dataset RELLIS-3D and our unstructured test set. The experimental results validate the competitiveness of our method in improving accuracy and scene-adaptivity.
Accretion in the Early Kuiper Belt

A speed regulator and control system for controlling a motor from a polyphase AC source includes a data processor and a regulator and rectifier control interfacing the data processor with a controllable rectifier driving the motor is disclosed. The regulator and rectifier control, under control of the data processor, selectively transfers system parameters to the data processor, receives a calculated value proportional to firing angle from the data processor and supplies firing pulses to the rectifier to selectively connect each phase of the AC source to the motor as calculated by the data processor.
Epidemiology and Transmission of Theileria orientalis in Australasia

Oriental theileriosis, a disease primarily impacting cattle is caused by an apicomplexan hemoprotozoan parasite, Theileria orientalis. It has now become established in the Australasia region. The organism was long considered a benign cause of persistent infections; however, an increase in clinical outbreaks since 2006 in the eastern Australian states and New Zealand was associated with the identification of the pathogenic Ikeda (Type 2) and Chitose (Type 1) genotypes. Unlike the pathogenic T. parva and T. annulate, which target leucocytes, clinical manifestation with T. orientalis is due to its effects on erythrocytes, with the infection sometimes designated as Theileria associated bovine anemia (TABA). In Australia and New Zealand, the tick Haemaphysalis longicornis is the principal vector, though other Haemaphysalis species are also likely vectors. The endemic status of infection with pathogenic genotypes in areas with low or absent tick populations is an apparent paradox that may be attributable to alternative modes of transmission, such as mechanical transmission by hematophagous insects (lice, mosquitoes, and biting flies), vertical transmission, and transmission via iatrogenic means. This review addresses the evidence for the different modes of transmission of T. orientalis with particular focus on the reported and potential vectors in Australasia.
Advances in the design, generation, and application of tissue-engineered myocardial equivalents

Due to the limited regenerative ability of cardiomyocytes, the disabling irreversible condition of myocardial failure can only be treated with conservative and temporary therapeutic approaches, not able to repair the damage directly, or with organ transplantation. Among the regenerative strategies, intramyocardial cell injection or intravascular cell infusion should attenuate damage to the myocardium and reduce the risk of heart failure. However, these cell delivery-based therapies suffer from significant drawbacks and have a low success rate. Indeed, cardiac tissue engineering efforts are directed to repair, replace, and regenerate native myocardial tissue function. In a regenerative strategy, biomaterials and biomimetic stimuli play a key role in promoting cell adhesion, proliferation, differentiation, and neo-tissue formation. Thus, appropriate biochemical and biophysical cues should be combined with scaffolds emulating extracellular matrix in order to support cell growth and prompt favorable cardiac microenvironment and tissue regeneration. In this review, we provide an overview of recent developments that occurred in the biomimetic design and fabrication of cardiac scaffolds and patches. Furthermore, we sift in vitro and in situ strategies in several preclinical and clinical applications. Finally, we evaluate the possible use of bioengineered cardiac tissue equivalents as in vitro models for disease studies and drug tests.
Impaired cAMP processivity by phosphodiesterase-protein kinase A complexes in acrodysostosis

Acrodysostosis represents a group of rare genetic disorders characterized by defective skeletal development and is often accompanied by intellectual disabilities. Mutations in the 3′5′cyclic AMP (cAMP)-dependent protein kinase (PKA) type I regulatory subunit isoform α (RIα) and phosphodiesterase (PDE) PDE4D have both been implicated in impaired PKA regulation in acrodysostosis. How mutations on PDEs and RIα interfere with the regulation of cAMP-PKA signaling is not understood. cAMP-PKA signaling can be described in two phases. In the activation phase, cAMP binding to RIα dissociates the free C-subunit (Catalytic subunit). PDEs hydrolyze cAMP bound to RIα, priming the cAMP-free RIα for reassociation with the C-subunit, thereby completing one PKA activation cycle. Signal termination is thus critical for resetting PKA to its basal state and promoting adaptation to hormonal hyperstimulation. This proceeds through formation of a transient signal termination RIα: PDE complex that facilitates cAMP channeling from the cAMP-binding domain of RIα to the catalytic site of PDE. Signal termination of cAMP-PKA proceeds in three steps: Step 1) Channeling: translocation of cAMP from the CNB of RIα to the PDE catalytic site for hydrolysis. Step 2) Processivity: binding of free cAMP from the cytosol at both CNBs of RIα. Step 3) Product (5′AMP) release from the PDE hydrolysis site through competitive displacement by a new molecule of cAMP that triggers subsequent activation cycles of PKA. We have identified the molecular basis for two acrodysostosis mutants, PDE (PDE8 T690P) and RIα (T207A), that both allosterically impair cAMP-PKA signal termination. A combination of amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and fluorescence polarization (FP) reveals that PDE8 T690P and RIα T207A both blocked processive hydrolysis of cAMP by interfering with competitive displacement of product 5′AMP release from the nucleotide channel at the end of each round of cAMP hydrolysis. While T690P blocked product 5′AMP release from the PDE, T207A greatly slowed the release of the substrate from RIα. These results highlight the role of processivity in cAMP hydrolysis by RIα: PDE termination complexes for adaptation to cAMP from GPCR hyperstimulation. Impairment of the signal termination process provides an alternate molecular basis for acrodysostosis.
Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium

The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response.
Iron-Enhanced Sand Filtration for Stormwater Phosphorus Removal

Most treatment practices for urban runoff utilize either settling or filtration to remove compounds associated with particulates (e.g., phosphorus) while dissolved substances are typically not captured. Dissolved phosphorus, for example, represents an average of 35-45% of total phosphorus in stormwater but can be more than 95% at some locations. Previous research has shown that a combination of sand filtration with 0.3 to 5% by weight steel wool can capture 34% to 81% dissolved phosphorus (1). In this study, iron filings were tested as an enhancement to sand filtration for removing dissolved phosphorus for synthetic stormwater. Iron filings sand columns capture on average between 35% and 93% dissolved phosphorus, depending on the fraction of iron filings used, which is significantly more than C 33 sand alone. A field application of an iron-enhanced sand filter was installed in Maplewood, Minnesota using approximately 5% iron filings by weight with the purpose of removing both total and dissolved phosphorus from stormwater runoff. A model developed from the column studies is used to predict the phosphorus removal in the field application.
Analysis of the Role of Negative T Cell Costimulatory Pathways in CD4 and CD8 T Cell-Mediated Alloimmune Responses In Vivo1

Negative costimulatory signals mediated via cell surface molecules such as CTLA-4 and programmed death 1 (PD-1) play a critical role in down-modulating immune responses and maintaining peripheral tolerance. However, their role in alloimmune responses remains unclear. This study examined the role of these inhibitory pathways in regulating CD28-dependent and CD28-independent CD4 and CD8 alloreactive T cells in vivo. CTLA-4 blockade accelerated graft rejection in C57BL/6 wild-type recipients and in a proportion of CD4−/− but not CD8−/− recipients of BALB/c hearts. The same treatment led to prompt rejection in CD28−/− and a smaller proportion of CD4−/−CD28−/− mice with no effect in CD8−/−CD28−/− recipients. These results indicate that the CTLA-4:B7 pathway provides a negative signal to alloreactive CD8+ T cells, particularly in the presence of CD28 costimulation. In contrast, PD-1 blockade led to accelerated rejection of heart allografts only in CD28−/− and CD8−/−CD28−/− recipients. Interestingly, PD-1 ligand (PD-L1) blockade led to accelerated rejection in wild-type mice and in all recipients lacking CD28 costimulation. This effect was accompanied by expansion of IFN-γ-producing alloreactive T cells and enhanced generation of effector T cells in rejecting allograft recipients. Thus, the PD-1:PD-L1 pathway down-regulates alloreactive CD4 T cells, particularly in the absence of CD28 costimulation. The differential effects of PD-1 vs PD-L1 blockade support the possible existence of a new receptor other than PD-1 for negative signaling through PD-L1. Furthermore, PD-1:PD-L1 pathway can regulate alloimmune responses independent of an intact CD28/CTLA-4:B7 pathway. Harnessing physiological mechanisms that regulate alloimmunity should lead to development of novel strategies to induce durable and reproducible transplantation tolerance.
Soil Parameter Inversion – Potential and Limits Hydrology and Earth System Sciences Discussions Inverse Modeling of Soil Characteristics from Surface Soil Moisture Observations: Potential and Limitations Hessd Soil Parameter Inversion – Potential and Limits

Introduction Conclusions References Tables Figures ◭ ◮ ◭ ◮ Back Close Full Screen / Esc Papers published in Hydrology and Earth System Sciences Discussions are under open-access review for the journal Hydrology and Earth System Sciences Abstract Introduction Conclusions References Tables Figures ◭ ◮ ◭ ◮ Back Close Full Screen / Esc Printer-friendly Version Interactive Discussion EGU Abstract Land surface models (LSM) are widely used as scientific and operational tools to simulate mass and energy fluxes within the soil vegetation atmosphere continuum for numerous applications in meteorology, hydrology or for geobiochemistry studies. A reliable parameterization of these models is important to improve the simulation skills. 5 Soil moisture is a key variable, linking the water and energy fluxes at the land surface. An appropriate parameterisation of soil hydraulic properties is crucial to obtain reliable simulation of soil water content from a LSM scheme. Parameter inversion techniques have been developed for that purpose to infer model parameters from soil moisture measurements at the local scale. On the other hand, remote sensing methods provide 10 a unique opportunity to estimate surface soil moisture content at different spatial scales and with different temporal frequencies and accuracies. The present paper investigates the potential to use surface soil moisture information to infer soil hydraulic characteristics using uncertain observations. Different approaches to retrieve soil characteristics from surface soil moisture observations is evaluated and the impact on the accuracy of 15 the model predictions is quantified. The results indicate that there is in general potential to improve land surface model parameterisations by assimilating surface soil moisture observations. However, a high accuracy in surface soil moisture estimates is required to obtain reliable estimates of soil characteristics.
EVALUATING THE POTENTIAL FOR USING SPECIES PRESENCE DATA COLLECTED BY COMMERCIAL FISHERMEN FOR SPECIES DISTRIBUTION MODELING IN THE GULF OF MAINE

2015 ii Executive Summary Fishermen and scientists have noted that fish species distributions are changing along the Northeast Continental Shelf. The Northeast Shelf Large Marine Ecosystem has undergone changes in temperature, stratification, and circulation patterns due to local climate variability and large scale warming trends. In response to physical changes, there have been adjustments to phytoplankton dynamics, and changes in the abundance and distribution of economically important marine fish and invertebrates, including groundfish and lobsters. Northeast Fisheries Science Center (NEFSC) semiannual trawl survey data have been modeled to demonstrate these distributional and poleward shifts in species assemblages. Many New England groundfishermen argue that management structures are slow to reflect these changes and that species distribution modeling of trawl survey data has failed to accurately characterize them, as the NEFSC trawl survey may not be frequent enough or sensitive enough to pick up on distributional changes as they occur. Since commercial fishermen are on the water more frequently, they have requested an outlet to submit information to scientists regarding where they are encountering shifting species while fishing. Data collected by fishermen themselves may be suitable for gaining a deeper understanding of moving fish populations. In response, the Gulf of Maine Research Institute and Island Institute have proposed to create a phone application that would allow fishermen to take photographs of species they encounter, logging geographic coordinate information at the time of the photograph. The purpose of this study is to evaluate whether data submitted though such an application would be useful to scientists in modeling distributional shifts of commercially important species. In order to determine the fitness of potential citizen science data, I created a proxy for data submitted by commercial fishermen and used it as input data in maximum entropy models to determine whether such data would be comprehensive enough or spatially distributed in a manner that would make it suitable for species distribution modeling. The following steps were carried out to evaluate proxy data quality for a single species known to be currently on the move, red hake:  A baseline maximum entropy model was carried out using only presence data from the NEFSC trawl survey. Models were evaluated via the AUC (area under the curve) of the Receiver Operator Characteristic (ROC).  Complete NEFSC trawl data were used to produce a general additive model (GAMs), of the probability of encountering red hake. The GAM outputs were used to …
Environmental geotechnics: Challenges and opportunities in the post-Covid-19 world

Environmental geotechnics: Challenges and opportunities in the post-Covid-19 world — Source link Chao-Sheng Tang, Evan K. Paleologos, Claudia Vitone, Yan-Jun Du . +22 more authors Institutions: Nanjing University, Abu Dhabi University, Instituto Politécnico Nacional, Southeast University . +14 more institutions Published on: 01 May 2021 Environmental geotechnics (Thomas Telford Ltd) Topics: Pandemic and Outbreak
Identification of Thyroid Hormone Transporters in Humans: Different Molecules Are Involved in a Tissue-Specific Manner*,†.

We have recently identified that rat organic anion transporters, polypeptide2 (oatp2) and oatp3, both of which transport thyroid hormones. However, in humans the molecular organization of the organic anion transporters has diverged, and the responsible molecule for thyroid hormone transport has not been clarified, except for human liver-specific transporter (LST-1) identified by us. In this study we isolated and characterized a novel human organic anion transporter, OATP-E from human brain. The isolated complementary DNA encodes a polypeptide of 722 amino acids with 12 transmembrane domains. A rat counterpart, oatp-E, was also identified. Homology analysis and the phylogenetic tree analysis revealed that OATP-E/oatp-E is a subfamily of the organic anion transporter. Human OATP-E transported 3,3′,5-triiodo-l-thyronine (Km, 0.9μ m), thyronine, and rT3 in a Na+-independent manner. Although the clone was isolated from the brain, OATP-E messenger RNA was abundantly expressed in various peripheral tissues. The .