Miracle-dz/UniFAR-FTUs huggingface dataset:
A modified relief of unilateral ureteral obstruction model

Abstract Objectives: To improve the mouse model of relief for unilateral ureteral obstruction (RUUO) and explore the pathological process of renal fibrosis after the obstruction was relieved. Methods: C57BL/6 mice in model group were randomly divided into RUUO group, improved RUUO group, and UUO group. After leaving Unilateral Ureteral Obstruction (UUO) for 3 days, the obstruction was released by reimplantation way in RUUO group and in reimplantation + catheter way in improved RUUO group. C57BL/6 mice in observation group were randomly divided into 1d RUUO group, 3d RUUO group, 7d RUUO group, and 14d RUUO group. Three days after UUO, the obstruction was released by reimplantation + catheter in four groups. We detected the renal volume, H&E, Masson staining, and immunohistochemistry of kidney pathology on the seventh day after RUUO in model group and on the 1st, 3rd, 7th, and 14th day after RUUO in observation group. Results: Comparing with mice in RUUO group, mice in improved RUUO group had lower renal volume, tubular damage score, and collagen area percentage. After the obstruction was relieved, the renal volume decreased gradually within 2 weeks. The tubular damage score in 7d RUUO group was lower than that in 1d RUUO and 3d RUUO group. However, the tubular damage score in 14d RUUO group was higher than that in 7d RUUO group. The tendency of collagen area percentage and α-SMA IOD value were consistent with the tubular damage score. Conclusions: Using the method of reimplantation + catheter, a reliable mice model of RUUO can be got. After RUUO, the de-obstructed kidneys are still in damage and fibrosis state.
XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence

Abstract XAB2 is a multi-functional protein participating processes including transcription, splicing, DNA repair and mRNA export. Here, we report POLR2A, the largest catalytic subunit of RNA polymerase II, as a major target gene down-regulated after XAB2 depletion. XAB2 depletion led to severe splicing defects of POLR2A with significant intron retention. Such defects resulted in substantial loss of POLR2A at RNA and protein levels, which further impaired global transcription. Treatment of splicing inhibitor madrasin induced similar reduction of POLR2A. Screen using TMT-based quantitative proteomics identified several proteins involved in mRNA surveillance including Dom34 with elevated expression. Inhibition of translation or depletion of Dom34 rescued the expression of POLR2A by stabilizing its mRNA. Immuno-precipitation further confirmed that XAB2 associated with spliceosome components important to POLR2A expression. Domain mapping revealed that TPR motifs 2–4 and 11 of XAB2 were critical for POLR2A expression by interacting with SNW1. Finally, we showed POLR2A mediated cell senescence caused by XAB2 deficiency. Depletion of XAB2 or POLR2A induced cell senescence by up-regulation of p53 and p21, re-expression of POLR2A after XAB2 depletion alleviated cellular senescence. These data together support that XAB2 serves as a guardian of POLR2A expression to ensure global gene expression and antagonize cell senescence.
Experimental results of a pulse position modulation infrared transceiver

Infrared technology is a suitable alternative for the support of indoor wireless local area networks (WLANs). When compared to radio technologies, infrared offers the potential for lower cost, higher security and better resilience to interference provoked by users from adjacent cells. This paper presents experimental results of an infrared transceiver for diffuse systems based on pulse position modulation. The implementation followed the upcoming IEEE 802.11 specification. This transceiver was developed within the ESPRIT.6892 POWER (Portable Workstation for Education in Europe) project.
Abnormal behavior, striatal dopamine turnover and opioid peptide gene expression in histamine‐deficient mice

Hypothalamic histaminergic neurons regulate a variety of homeostatic, metabolic and cognitive functions. Recent data have suggested a modulatory role of histamine and histamine receptors in shaping striatal activity and connected the histaminergic system to neuropsychiatric disorders. We characterized exploratory behavior and striatal neurotransmission in mice lacking the histamine producing enzyme histidine decarboxylase (Hdc). The mutant mice showed a distinct behavioral pattern during exploration of novel environment, specifically, increased frequency of rearing seated against the wall, jumping and head/body shakes. This behavioral phenotype was associated with decreased levels of striatal dopamine and serotonin and increased level of dopamine metabolite DOPAC. Gene expression levels of dynorphin and enkephalin, opioids released by medium spiny neurons of striatal direct and indirect pathways respectively, were lower in Hdc mutant mice than in control animals. A low dose of amphetamine led to similar behavioral and biochemical outcomes in both genotypes. Increased striatal dopamine turnover was observed in Hdc KO mice after treatment with dopamine precursor l‐Dopa. Overall, our study suggests a role for striatal dopamine and opioid peptides in formation of distinct behavioral phenotype of Hdc KO mice.
Dynamic Measurements Using FDM 3D-Printed Embedded Strain Sensors

3D-printing technology is opening up new possibilities for the co-printing of sensory elements. While quasi-static research has shown promise, the dynamic performance has yet to be researched. This study researched smart 3D structures with embedded and printed sensory elements. The embedded strain sensor was based on the conductive PLA (Polylactic Acid) material. The research was focused on dynamic measurements of the strain and considered the theoretical background of the piezoresistivity of conductive PLA materials, the temperature effects, the nonlinearities, the dynamic range, the electromagnetic sensitivity and the frequency range. A quasi-static calibration used in the dynamic measurements was proposed. It was shown that the temperature effects were negligible, the sensory element was linear as long as the structure had a linear response, the dynamic range started at ∼ 30 μϵ and broadband performance was in the range of few kHz (depending on the size of the printed sensor). The promising results support future applications of smart 3D-printed systems with embedded sensory elements being used for dynamic measurements in areas where currently piezo-crystal-based sensors are used.
Evaluation of ESA Active, Passive and Combined Soil Moisture Products Using Upscaled Ground Measurements

The European Space Agency (ESA) Climate Change Initiative (CCI) project combines multi-sensors at different microwave frequencies to derive three harmonized soil moisture products using active, passive and combined approaches. These long-term soil moisture products assist in understanding the global water and carbon cycles. However, extensive validations are a prerequisite before applying the retrieved soil moisture into climatic or hydrological models. To fulfill this objective, we assess the performances of three CCI soil moisture products (active, passive and combined) with respect to in-situ soil moisture networks located in China, Spain and Canada. In order to compensate the scale differences between ground stations and the CCI product’s coarse resolution, we adopted two upscaling approaches of Inverse Distance Weighting (IDW) interpolation and simple Arithmetic Mean (AM). The temporal agreements between the satellite retrieved and ground-measured soil moisture were quantified using the unbiased root mean square error (ubRMSE), RMSE, correlation coefficients (R) and bias. Furthermore, the temporal variability of the CCI soil moisture is interpreted and verified with respect to the Tropical Rainfall Measuring Mission (TRMM) precipitation observations. The results show that the temporal variations of CCI soil moisture agreed with the in-situ ground measurements and the precipitation observations over the China and Spain test sites. In contrast, a significant overestimation was observed over the Canada test sites, which may be due to the strong heterogeneity in soil and vegetation characteristics in accordance with the reported poor performance of soil moisture retrieval there. However, despite a retrieval bias, the relatively temporal variation of the CCI soil moisture also followed the ground measurements. For all the three test sites, the soil moisture retrieved from the combined approach outperformed the active-only and passive-only methods, with ubRMSE of 0.034, 0.050, and 0.050–0.054 m3/m3 over the test sites in China, Spain and Canada, respectively. Thus, the CCI combined soil moisture product is suggested to drive the climatic and hydrological studies.
Microcapsule-Based Signal Amplification Method for Biomolecules

The direct signal amplification of target molecules could be an effective means of increasing the sensitivity and reducing the size of biosensors. The purpose of this study was to propose a novel signal amplification method suitable for the detection of biomolecules using microcapsules that can quickly respond to concentration variation. This microcapsule-based amplification method consists of two elements—microcapsules and a well-array. The microcapsules consist of (i) an inner shell fabricated through layer-by-layer assembly, (ii) a lipid bilayer, and (iii) loaded target molecules. In this method, the inner surface of the well-array was modified using TiO2 as a photocatalyst. The diameter and thickness of the fabricated micro-capsules for biomarker loading were shown to be 2.7 μm and 78 nm, respectively. An ultraviolet (UV) irradiation time of 5 min was needed when the change in optical density reached 90% saturation of the optical density change. Dye molecules were incorporated into the microcapsules and were subsequently released, and the concentration of the released solution changed in proportion with the encapsulated dye concentration. This demonstrates the proof of concept for this novel signal amplification method based on microcapsules.
Triptonide acts as a novel antiprostate cancer agent mainly through inhibition of mTOR signaling pathway

The increasing incidence of prostate cancer (PCa) indicates an urgent need for the development of new effective drugs in PCa therapy. Triptonide has been reported to have a strong inhibition activity in cancers through screening of Chinese herbal medicine. This study aims to investigate the effects of triptonide on anti‐PCa activity and its mechanisms.
Increased Immunogenicity of Full-Length Protein Antigens through Sortase-Mediated Coupling on the PapMV Vaccine Platform

Background: Flexuous rod-shape nanoparticles—made of the coat protein of papaya mosaic virus (PapMV)—provide a promising vaccine platform for the presentation of viral antigens to immune cells. The PapMV nanoparticles can be combined with viral antigens or covalently linked to them. The coupling to PapMV was shown to improve the immune response triggered against peptide antigens (<39 amino acids) but it remains to be tested if large proteins can be coupled to this platform and if the coupling will lead to an immune response improvement. Methods: Two full-length recombinant viral proteins, the influenza nucleoprotein (NP) and the simian immunodeficiency virus group-specific protein antigen (GAG) were coupled to PapMV nanoparticles using sortase A. Mice were immunized with the nanoparticles coupled to the antigens and the immune response directed to the antigens were analyzed by ELISA and ELISPOT. Results: We showed the feasibility of coupling two different full-length proteins (GAG and NP) to the nanoparticle. We also showed that the coupling to PapMV nanoparticles improved significantly the humoral and the cytotoxic T lymphocyte (CTL) immune response to the antigens. Conclusion: This proof of concept demonstrates the versatility and the efficacy of the PapMV vaccine platform in the design of vaccines against viral diseases.
The Lipid A 1-Phosphatase, LpxE, Functionally Connects Multiple Layers of Bacterial Envelope Biogenesis

Dephosphorylation of the lipid A 1-phosphate by LpxE in Gram-negative bacteria plays important roles in antibiotic resistance, bacterial virulence, and modulation of the host immune system. Our results demonstrate that in addition to removing the 1-phosphate from lipid A, LpxEs also dephosphorylate undecaprenyl pyrophosphate, an important metabolite for the synthesis of the essential envelope components, peptidoglycan and O-antigen. Therefore, LpxEs participate in multiple layers of biogenesis of the Gram-negative bacterial envelope and increase antibiotic resistance. This discovery marks an important step toward understanding the regulation and biogenesis of the Gram-negative bacterial envelope. ABSTRACT Although distinct lipid phosphatases are thought to be required for processing lipid A (component of the outer leaflet of the outer membrane), glycerophospholipid (component of the inner membrane and the inner leaflet of the outer membrane), and undecaprenyl pyrophosphate (C55-PP; precursors of peptidoglycan and O antigens of lipopolysaccharide) in Gram-negative bacteria, we report that the lipid A 1-phosphatases, LpxEs, functionally connect multiple layers of cell envelope biogenesis in Gram-negative bacteria. We found that Aquifex aeolicus LpxE structurally resembles YodM in Bacillus subtilis, a phosphatase for phosphatidylglycerol phosphate (PGP) with a weak in vitro activity on C55-PP, and rescues Escherichia coli deficient in PGP and C55-PP phosphatase activities; deletion of lpxE in Francisella novicida reduces the MIC value of bacitracin, indicating a significant contribution of LpxE to the native bacterial C55-PP phosphatase activity. Suppression of plasmid-borne lpxE in F. novicida deficient in chromosomally encoded C55-PP phosphatase activities results in cell enlargement, loss of O-antigen repeats of lipopolysaccharide, and ultimately cell death. These discoveries implicate LpxE as the first example of a multifunctional regulatory enzyme that orchestrates lipid A modification, O-antigen production, and peptidoglycan biogenesis to remodel multiple layers of the Gram-negative bacterial envelope. IMPORTANCE Dephosphorylation of the lipid A 1-phosphate by LpxE in Gram-negative bacteria plays important roles in antibiotic resistance, bacterial virulence, and modulation of the host immune system. Our results demonstrate that in addition to removing the 1-phosphate from lipid A, LpxEs also dephosphorylate undecaprenyl pyrophosphate, an important metabolite for the synthesis of the essential envelope components, peptidoglycan and O-antigen. Therefore, LpxEs participate in multiple layers of biogenesis of the Gram-negative bacterial envelope and increase antibiotic resistance. This discovery marks an important step toward understanding the regulation and biogenesis of the Gram-negative bacterial envelope.
Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets

Trans-splicing mechanisms have been documented in many lineages that are widely distributed phylogenetically, including dinoflagellates. The spliced leader (SL) sequence itself is conserved in dinoflagellates, although its gene sequences and arrangements have diversified within or across different species. In this study, we present 18 Fugacium kawagutii SL genes identified from stranded RNA-seq reads. These genes typically have a single SL but can contain several partial SLs with lengths ranging from 103 to 292 bp. Unexpectedly, we find the SL gene transcripts contain sequences upstream of the canonical SL, suggesting that generation of mature transcripts will require additional modifications following trans-splicing. We have also identified 13 SL-like genes whose expression levels and length are comparable to Dino-SL genes. Lastly, introns in these genes were identified and a new site for Sm-protein binding was proposed. Overall, this study provides a strategy for fast identification of SL genes and identifies new sequences of F. kawagutii SL genes to supplement our understanding of trans-splicing.
Spectra–Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study

The effect of isotopic substitution on near-infrared (NIR) spectra has not been studied in detail. With an exception of few major bands, it is difficult to follow the spectral changes due to complexity of NIR spectra. Recent progress in anharmonic quantum mechanical calculations allows for accurate reconstruction of NIR spectra. Taking this opportunity, we carried out a systematic study of NIR spectra of six isotopomers of ethanol (CX3CX2OX; X = H, D). Besides, we calculated the theoretical spectra of two other isotopomers (CH3CD2OD and CD3CH2OD) for which the experimental spectra are not available. The anharmonic calculations were based on generalized vibrational second-order perturbation theory (GVPT2) at DFT and MP2 levels with several basis sets. We compared the accuracy and efficiency of various computational methods. It appears that the best results were obtained with B2PLYP-GD3BJ/def2-TZVP//CPCM approach. Our simulations included the first and second overtones, as well as binary and ternary combinations bands. This way, we reliably reproduced even minor bands in the spectra of diluted samples (0.1 M in CCl4). On this basis, the effect of isotopic substitution on NIR spectra of ethanol was accurately reproduced and comprehensively explained.
A Taste for Corpora. In Honour of Sylviane Granger

The eleven contributions to this volume, written by expert corpus linguists, tackle corpora from a wide range of perspectives and aim to shed light on the numerous linguistic and pedagogical uses to which corpora can be put. They present cutting-edge research in the authors’ respective domain of expertise and suggest directions for future research. The main focus of the book is on learner corpora, but it also includes reflections on the role of other types of corpora, such as native corpora, expert users corpora, parallel corpora or corpora of New Englishes. For readers who are already familiar with corpora, this volume offers an informed account of the key role that corpus data play in applied linguistics today. As for readers who are new to corpus linguistics, the overview of approaches, methods and domains of applications presented will undoubtedly help them develop their own taste for corpora. This volume has been edited in honour of Sylviane Granger, who has been one of the pioneers of learner corpus research.
Mechanisms of immunogenicity in colorectal cancer

The immune response in cancer is increasingly understood to be important in determining clinical outcomes, including responses to cancer therapies. New insights into the mechanisms underpinning the immune microenvironment in colorectal cancer are helping to develop the role of immunotherapy and suggest targeted approaches to the management of colorectal cancer at all disease stages.
High‐Performance Polymeric Materials through Hydrogen‐Bond Cross‐Linking

It has always been critical to develop high‐performance polymeric materials with exceptional mechanical strength and toughness, thermal stability, and even healable properties for meeting performance requirements in industry. Conventional chemical cross‐linking leads to enhanced mechanical strength and thermostability at the expense of extensibility due to mutually exclusive mechanisms. Such major challenges have recently been addressed by using noncovalent cross‐linking of reversible multiple hydrogen‐bonds (H‐bonds) that widely exist in biological materials, such as silk and muscle. Recent decades have witnessed the development of many tailor‐made high‐performance H‐bond cross‐linked polymeric materials. Here, recent advances in H‐bond cross‐linking strategies are reviewed for creating high‐performance polymeric materials. H‐bond cross‐linking of polymers can be realized via i) self‐association of interchain multiple H‐bonding interactions or specific H‐bond cross‐linking motifs, such as 2‐ureido‐4‐pyrimidone units with self‐complementary quadruple H‐bonds and ii) addition of external cross‐linkers, including small molecules, nanoparticles, and polymer aggregates. The resultant cross‐linked polymers normally exhibit tunable high strength, large extensibility, improved thermostability, and healable capability. Such performance portfolios enable these advanced polymers to find many significant cutting‐edge applications. Major challenges facing existing H‐bond cross‐linking strategies are discussed, and some promising approaches for designing H‐bond cross‐linked polymeric materials in the future are also proposed.
Systematic Analysis of a Military Wearable Device Based on a Multi-Level Fusion Framework: Research Directions

With the development of the Internet of Battlefield Things (IoBT), soldiers have become key nodes of information collection and resource control on the battlefield. It has become a trend to develop wearable devices with diverse functions for the military. However, although densely deployed wearable sensors provide a platform for comprehensively monitoring the status of soldiers, wearable technology based on multi-source fusion lacks a generalized research system to highlight the advantages of heterogeneous sensor networks and information fusion. Therefore, this paper proposes a multi-level fusion framework (MLFF) based on Body Sensor Networks (BSNs) of soldiers, and describes a model of the deployment of heterogeneous sensor networks. The proposed framework covers multiple types of information at a single node, including behaviors, physiology, emotions, fatigue, environments, and locations, so as to enable Soldier-BSNs to obtain sufficient evidence, decision-making ability, and information resilience under resource constraints. In addition, we systematically discuss the problems and solutions of each unit according to the frame structure to identify research directions for the development of wearable devices for the military.
Identification of the Molecular Events Involved in the Development of Prefrontal Cortex Through the Analysis of RNA-Seq Data From BrainSpan

Human brain development is a complex process that follows sequential orchestration of gene expression, begins at conceptual stages, and continues into adulthood. Altered profile of gene expression drives many cellular and molecular events required for development. Here, the molecular events during development of human prefrontal cortex (PFC) (as an important executive part of the brain) were investigated. First, the RNA-sequencing data of BrainSpan were used to obtain differentially expressed genes between each two developmental stages and then, the relevant biological processes and signaling pathways were deduced by gene set enrichment analysis. In addition, the changes in transcriptome landscape of PFC during development were analyzed and the potential biological processes underlie the changes were found. Comparison of the four regions of PFC based on their biological processes showed that additional to common biological processes and signaling pathways, each PFC region had its own molecular characteristics, conforming their previously reported functional roles in brain physiology. The most heterogeneity in transcriptome between the PFC regions was observed at the time of birth which was concurrent with the activity of some region-specific regulatory systems such as DNA methylation, transcription regulation, RNA splicing, and presence of different transcription factors and microRNAs. In conclusion, this study used bioinformatics to present a comprehensive molecular overview on PFC development which may explain the etiology of brain neuropsychiatric disorders originated from malfunctioning of PFC.