Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription complexes as RNA chaperones

ABSTRACT To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
SepA Enhances Shigella Invasion of Epithelial Cells by Degrading Alpha-1 Antitrypsin and Producing a Neutrophil Chemoattractant

Shigella is the second leading cause of diarrheal death globally. In this study, we identified the host protein targets of SepA, Shigella’s major protein secreted in culture. ABSTRACT Shigella spp. are highly adapted pathogens that cause bacillary dysentery in human and nonhuman primates. An unusual feature of Shigella pathogenesis is that this organism invades the colonic epithelia from the basolateral pole. Therefore, it has evolved the ability to disrupt the intestinal epithelial barrier to reach the basolateral surface. We have shown previously that the secreted serine protease A (SepA), which belongs to the family of serine protease autotransporters of Enterobacteriaceae, is responsible for the initial destabilization of the intestinal epithelial barrier that facilitates Shigella invasion. However, the mechanisms used by SepA to regulate this process remain unknown. To investigate the protein targets cleaved by SepA in the intestinal epithelium, we incubated a sample of homogenized human colon with purified SepA or with a catalytically inactive mutant of this protease. We discovered that SepA targets an array of 18 different proteins, including alpha-1 antitrypsin (AAT), a major circulating serine proteinase inhibitor in humans. In contrast to other serine proteases, SepA cleaved AAT without forming an inhibiting complex, which resulted in the generation of a neutrophil chemoattractant. We demonstrated that the products of the AAT-SepA reaction induce a mild but significant increase in neutrophil transepithelial migration in vitro. Moreover, the presence of AAT during Shigella infection stimulated neutrophil migration and dramatically enhanced the number of bacteria invading the intestinal epithelium in a SepA-dependent manner. We conclude that by cleaving AAT, SepA releases a chemoattractant that promotes neutrophil migration, which in turn disrupts the intestinal epithelial barrier to enable Shigella invasion. IMPORTANCE Shigella is the second leading cause of diarrheal death globally. In this study, we identified the host protein targets of SepA, Shigella’s major protein secreted in culture. We demonstrated that by cleaving AAT, a serine protease inhibitor important to protect surrounding tissue at inflammatory sites, SepA releases a neutrophil chemoattractant that enhances Shigella invasion. Moreover, SepA degraded AAT without becoming inhibited by the cleaved product, and SepA catalytic activity was enhanced at higher concentrations of AAT. Activation of SepA by an excess of AAT may be physiologically relevant at the early stages of Shigella infection, when the amount of synthesized SepA is very low compared to the concentration of AAT in the intestinal lumen. This observation may also help to explain the adeptness of Shigella infectivity at low dose, despite the requirement of reaching the basolateral side to invade and colonize the colonic epithelium.
High-Throughput Mutagenesis and Cross-Complementation Experiments Reveal Substrate Preference and Critical Residues of the Capsule Transporters in Streptococcus pneumoniae

All licensed pneumococcal vaccines target the capsular polysaccharide (CPS). This layer is highly variable and is important for virulence in many bacterial pathogens. ABSTRACT MOP (Multidrug/Oligosaccharidyl-lipid/Polysaccharide) family transporters are found in almost all life forms. They are responsible for transporting lipid-linked precursors across the cell membrane to support the synthesis of various glycoconjugates. While significant progress has been made in elucidating their transport mechanism, how these transporters select their substrates remains unclear. Here, we systematically tested the MOP transporters in the Streptococcus pneumoniae capsule pathway for their ability to translocate noncognate capsule precursors. Sequence similarity cannot predict whether these transporters are interchangeable. We showed that subtle changes in the central aqueous cavity of the transporter are sufficient to accommodate a different cargo. These changes can occur naturally, suggesting a potential mechanism of expanding substrate selectivity. A directed evolution experiment was performed to identify gain-of-function variants that translocate a noncognate cargo. Coupled with a high-throughput mutagenesis and sequencing (Mut-seq) experiment, residues that are functionally important for the capsule transporter were revealed. Lastly, we showed that the expression of a flippase that can transport unfinished precursors resulted in an increased susceptibility to bacitracin and mild cell shape defects, which may be a driving force to maintain transporter specificity. IMPORTANCE All licensed pneumococcal vaccines target the capsular polysaccharide (CPS). This layer is highly variable and is important for virulence in many bacterial pathogens. Most of the CPSs are produced by the Wzx/Wzy mechanism. In this pathway, CPS repeating units are synthesized in the cytoplasm, which must be flipped across the cytoplasmic membrane before polymerization. This step is mediated by the widely conserved MOP (Multidrug/Oligosaccharidyl-lipid/Polysaccharide) family transporters. Here, we systematically evaluated the interchangeability of these transporters and identified the residues important for substrate specificity and function. Understanding how CPS is synthesized will inform glycoengineering, vaccine development, and antimicrobial discovery.
Image quality assessment based on the image contents visual perception

Abstract. Image quality assessment (IQA) is widely used in image transmission, processing, and storage, which has important application value. To obtain an IQA model with the excellent performance, combining with the image content features and human visual system characteristics, based on the contrast definition in visual psychology, an IQA method and its mathematical model are proposed. In this method, first based on the contrast definition, combining with the visual characteristics, the contrast between the distorted image and the reference image is used to describe the difference between them; further, based on the difference, a definition method for image quality is proposed. Second, based on the gray and gradient co-occurrence matrix, a concept, which is called as the image gray-gradient expectation (GGE), is proposed, and its calculation method is also illustrated. And based on the GGE values and local contrast of image, a method for describing the image content and its visual perception is proposed. Finally, based on the image content features and the proposed definition method of image quality, an IQA method and its mathematical model are proposed. Further, they were tested using the 142 reference images and 7220 distorted images in the LIVE, CSIQ, TID2008, TID2013, CIDIQ, and IVC databases. And the results were compared with those of seven existing typical IQA models in terms of accuracy, complexity, and generalization performance. These experimental results show that, in the six databases, the IQA accuracy Pearson linear correlation coefficient of the proposed model can all be more than 0.7892 and reach 0.9638 highest, whose comprehensive efficiency is better than ones of the seven existing IQA models. These analysis and comparison show that the proposed model is an excellent IQA model on performance.
SAR image super-resolution reconstruction based on cross-resolution discrimination

Abstract. High-resolution (HR) synthetic aperture radar (SAR) images play an important role in people’s daily life and military applications. However, due to the interference of speckle noise, the texture details of the SAR images become relatively blurred. The fine texture details can be reconstructed by increasing the resolution of the SAR images. Generative adversarial networks achieve high performance in image super-resolution (SR) reconstruction, but the existing generative adversarial networks only pay attention to the discrimination of HR images without that of the low-resolution (LR) images. If the reconstructed HR image is sufficiently realistic, the LR image obtained from downsampled super-resolved images should also be the same as the original LR image. To take advantage of the LR image, an SAR image SR reconstruction algorithm based on cross-resolution discrimination (CRD) using teacher–student network is proposed. First, the teacher discriminator network (TD-Net) discriminates the HR images, which enriches the reconstructed HR images with more high-frequency texture details. Second, the student discriminator network (SD-Net) discriminates the LR images, which enables the reconstructed HR images to be accurately downsampled to the original LR image. Finally, the TD-Net guides the training of the SD-Net by transmitting distillation knowledge to the SD-Net, which further improves the discriminative performance of the SD-Net. Experiments on the SAR image dataset demonstrate that the performance of the proposed CRD algorithm is better than other algorithms when both the objective evaluations and subjective effects are considered.
FT-IR spectroscopy of carbonized acenes: a possible key for the UIBs/AIBs origins

Abstract The complete acene series from naphthalene to anthracene, tetracene and pentacene were carbonized directly in a differential scanning calorimeter (DSC) special crucible heating up to 700 °C under autogenous pressure. In these conditions the carbonization of all the acenes was detected as an endothermal process occurring above 550 °C. The resulting carbonized acenes were studied by FT-IR spectroscopy showing a band pattern matching the spectrum of a mature coal and the unidentified infrared bands (UIBs) as well as the aromatic infrared bands (AIBs) detected in the interstellar and in certain circumstellar media. It is speculated that carbonized organic matter could be a valid model to explain the carriers of the UIBs/AIBs bands in space. Carbonized PAHs can be conceived as carbon dust grains formed under the action of shock waves, which are quite common in certain circumstellar and interstellar media.
Sustainability disclosure and its impact on firm's value for Energy and Healthcare industry

Abstract This paper investigates the relationship between sustainability disclosure measured through the combined and individual environmental, social, and governance (ESG) scores and the value of European companies from energy and health care industries. The reasons for this research are the increased awareness of sustainability disclosure, the inclusion of nonfinancial information in corporate reporting and possible added value to the company, the ongoing COVID-19 pandemic, and its impact on the global economy. The sample consists of 305 observations for 61 European companies from different categories in the energy industry and 225 observations for 45 European companies in the health care industry. To apply the research model to the samples of companies set as panel data, two linear regressions were designed, each using a different dependent variable to increase the reliability of the outputs. The results indicate a negative and significant correlation between the environmental factor and firms’ value for the energy sector and no influence of the sustainability disclosure on the value of companies in the health care industry. The research contributes to the literature by addressing the impact of sustainability disclosure on the value of the European companies from sensitive industries, using both the combined and individual ESG scores to measure sustainability disclosure. Furthermore, the study encourages other academic research on this subject.
It's over 9000: analyzing early QUIC deployments with the standardization on the horizon

After nearly five years and 34 draft versions, standardization of the new connection oriented transport protocol QUIC was finalized in May 2021. Designed as a fundamental network protocol with increased complexity due to the combination of functionality from multiple network stack layers, it has the potential to drastically influence the Internet ecosystem. Nevertheless, even in its early stages, the protocol attracted a variety of parties including large providers. Our study shows, that more than 2.3 M IPv4 and 300k IPv6 addresses support QUIC hosting more than 30 M domains. Using our newly implemented stateful QUIC scanner (QScanner) we are able to successfully scan 26 M targets. We show that TLS as an integral part is similarly configured between QUIC and TLS over TCP stacks for the same target. In comparison, we identify 45 widely varying transport parameter configurations, e.g., with differences in the order of magnitudes for performance relevant parameters. Combining these configurations with HTTP Server header values and associated domains reveals two large edge deployments from Facebook and Google. Thus, while found QUIC deployments are located in 4667 autonomous systems, numerous of these are again operated by large providers. In our experience, IETF QUIC already sees an advanced deployment status mainly driven by large providers. We argue that the current deployment state and diversity of existing implementations and seen configurations solidifies the importance of QUIC as a future research topic. In this work, we provide and evaluate a versatile tool set, to identify QUIC capable hosts and their properties. Besides the stateful QScanner we present and analyze a newly implemented IPv4 and IPv6 ZMap module. We compare it to additional detection methods based on HTTP Alternative Service Header values from HTTP handshakes and DNS scans of the newly drafted HTTPS DNS resource record. While each method reveals unique deployments the latter would allow lightweight scans to detect QUIC capable targets but is drastically biased towards Cloudflare.
Cruise passengers’ risk reduction strategies in the wake of COVID-19

ABSTRACT The COVID-19 pandemic devastated the cruise sector with an initial global shutdown and ongoing patchy resumption, widespread reporting of virus transmission onboard and billions of dollars in economic losses. This study explores how COVID-19 has impacted Australian and UK consumers’ risk perceptions, revealing cruises are no longer considered “safe”. Consumers are more negative about, and less willing to, cruise. Cluster and Leximancer analyses identified five distinct market segments differentiated by the extent of travel risk they perceived. Specific risk reduction strategies are identified and include risk mitigation, use of risk relievers, and risk avoidance.
Solubility analysis of nano particles, cellulose crystalline region and cellulose molecule, and the impact study of crystalline region on properties of cellulose insulating paper

ABSTRACT For the first time, molecular dynamics simulation was used to analyse the solubility of five kinds of nanoparticles (SiO2, ZnO, Al2O3, Fe2O3, TiO2), cellulose crystalline region and cellulose molecules in this paper. The results show that the solubility of cellulose nanoparticles is positively related to the number of –OH groups on the surface of nanoparticles. The solubility between nano particles and cellulose molecules is smaller than that between cellulose crystalline region and cellulose molecules, which leads to the direct introduction of nano particles for physical modification reducing the solubility parameters of insulating paper. Through the analysis of mechanical properties, thermal stability and insulation properties, it is concluded that the comprehensive performance of the model with 70% crystalline region ratio is the best. The proportion of crystalline region further increased, the improvement of thermal stability is not obvious; the relative permittivity and the content of crystalline region are in line with the binomial fitting curve, and the constant term in the fitting curve is the relative permittivity of the amorphous region model; increasing the proportion of crystalline region is beneficial to improve the insulation performance of cellulose insulation paper.
Differences in the biological properties of mesenchymal stromal cells from traumatic temporomandibular joint fibrous and bony ankylosis: a comparative study

ABSTRACT The aim of this study was to compare the functional characteristics of mesenchymal stromal cells (MSCs) from a sheep model of traumatic temporomandibular joint (TMJ) fibrous and bony ankylosis. A sheep model of bilateral TMJ trauma-induced fibrous ankylosis on one side and bony ankylosis on the contralateral side was used. MSCs from fibrous ankylosed callus (FA-MSCs) or bony ankylosed callus (BA-MSCs) at weeks 1, 2, 4, and 8 after surgery were isolated and cultured. MSCs derived from the bone marrow of the mandibular condyle (BM-MSCs) were used as controls. The MSCs from the different sources were characterized morphologically, phenotypically, and functionally. Adherence and trilineage differentiation potential were presented in the ovine MSCs. These cell populations highly positively expressed MSC-associated specific markers, namely CD29, CD44, and CD166, but lacked CD31 and CD45 expressions. The BA-MSCs had higher clonogenic and proliferative potentials than the FA-MSCs. The BA-MSCs also showed higher osteogenic and chondrogenic potentials, but lower adipogenic capacity than the FA-MSCs. In addition, the BA-MSCs demonstrated higher chondrogenic, but lower osteogenic capacity than the BM-MSCs. Our study suggests that inhibition of the osteogenic and chondrogenic differentiations of MSCs might be a promising strategy for preventing bony ankylosis in the future.
Fabrication and characterization of PCL/Gel nanofibrous scaffolds incorporated with graphene oxide applicable in cardiac tissue engineering

ABSTRACT Herein, we fabricated poly (caprolactone)/Gelatin (PCL/Gel) nanofibrous scaffolds and graphene oxide (GO 0.3, 0.6 and 1% w/w) was incorporated into scaffolds. Morphological, structural, mechanical and in vitro analyses of the samples were performed. The diameter of PCL nanofibers was increased by adding Gel and GO, especially by adding 1%w/w of GO (210 ± 20 nm versus 482 ± 104 nm). Mechanical properties and hydrophilicity were improved. All scaffolds were nontoxic and the most biocompatibility values obtained were 91.71 ± 0.1% and 94.29 ± 1.1%, which were related to PCL/Gel and PCL/Gel/GO0.3, respectively. Among all samples, PCL/Gel/GO0.3 showed the highest cell area (0.973 ± 0.041). Graphical abstract
Taming the Merge Operator

Abstract Calculi with disjoint intersection types support a symmetric merge operator with subtyping. The merge operator generalizes record concatenation to any type, enabling expressive forms of object composition, and simple solutions to hard modularity problems. Unfortunately, recent calculi with disjoint intersection types and the merge operator lack a (direct) operational semantics with expected properties such as determinism and subject reduction, and only account for terminating programs. This paper proposes a type-directed operational semantics (TDOS) for calculi with intersection types and a merge operator. We study two variants of calculi in the literature. The first calculus, called λi, is a variant of a calculus presented by Oliveira et al. (2016) and closely related to another calculus by Dunfield (2014). Although Dunfield proposes a direct small-step semantics for her calculus, her semantics lacks both determinism and subject reduction. Using our TDOS, we obtain a direct semantics for λi that has both properties. The second calculus, called λi+, employs the well-known subtyping relation of Barendregt, Coppo and Dezani-Ciancaglini (BCD). Therefore, λi+ extends the more basic subtyping relation of λi, and also adds support for record types and nested composition (which enables recursive composition of merged components). To fully obtain determinism, both λi and λi+ employ a disjointness restriction proposed in the original λi calculus. As an added benefit the TDOS approach deals with recursion in a straightforward way, unlike previous calculi with disjoint intersection types where recursion is problematic. We relate the static and dynamic semantics of λi to the original version of the calculus and the calculus by Dunfield. Furthermore, for λi+, we show a novel formulation of BCD subtyping, which is algorithmic, has a very simple proof of transitivity and allows for the modular addition of distributivity rules (i.e. without affecting other rules of subtyping). All results have been fully formalized in the Coq theorem prover.
Exploring CBT therapists’ experience of feeling of safety within self-practice/self-reflection: an interpretative phenomenological analysis

Abstract Self-practice/self-reflection (SP/SR) is an experiential training strategy implemented to develop the skills of CBT therapists through the self-application of CBT techniques and subsequent reflection on the experience in relation to clinical practice. Outcome studies report significant personal and professional benefits from SP/SR but engagement studies suggest that CBT therapists’ experience is mixed. In order to inform the design and implementation of SP/SR within CBT, this study aims to explore CBT therapists’ experience of feeling of safety (FOS) within SP/SR. FOS has been identified as an important engagement factor. Three CBT therapists were interviewed using semi-structured interviews. The data, which took the form of verbatim transcripts, were subjected to interpretative phenomenological analysis. Four superordinate themes relating to participants’ experience of FOS within SP/SR emerged: FOS and its absence as embodied and non-verbal, role of the instructor, awareness of others and venturing beyond safety. Ensuing recommendations for instructors include proactive use of interventions within SP/SR which directly impact embodied FOS, monitoring the wellbeing and engagement of participants through awareness of physical cues and employment of measures designed to promote a sense of equality among group members. Areas of future research include exploration of factors which influence FOS, investigation of the effect on FOS of pre-existing relationships within the SP/SR group and review of interventions which are currently used by SP/SR instructors to promote FOS. Key learning aims (1) To explore the lived experience of FOS within SP/SR as experienced by CBT therapists. (2) To identify factors which influence CBT therapists’ experience of FOS within SP/SR. (3) To identify practical recommendations for use in SP/SR instruction which will promote participants’ FOS.