Miracle-dz/UniFAR-FTUs huggingface dataset:
Marchantia polymorpha, a New Model Plant for Autophagy Studies

Autophagy is a catabolic process for bulk and selective degradation of cytoplasmic components in the vacuole/lysosome. In Saccharomyces cerevisiae, ATG genes were identified as essential genes for autophagy, and most ATG genes are highly conserved among eukaryotes, including plants. Although reverse genetic analyses have revealed that autophagy is involved in responses to abiotic and biotic stresses in land plants, our knowledge of its molecular mechanism remains limited. This limitation is partly because of the multiplication of some ATG genes, including ATG8, in widely used model plants such as Arabidopsis thaliana, which adds complexity to functional studies. Furthermore, due to limited information on the composition and functions of the ATG genes in basal land plants and charophytes, it remains unclear whether multiplication of ATG genes is associated with neofunctionalization of these genes. To gain insight into the diversification of ATG genes during plant evolution, we compared the composition of ATG genes in plants with a special focus on a liverwort and two charophytes, which have not previously been analyzed. Our results showed that the liverwort Marchantia polymorpha and the charophytes Klebsormidium nitens and Chara braunii harbor fundamental sets of ATG genes with low redundancy compared with those of A. thaliana and the moss Physcomitrella patens, suggesting that multiplication of ATG genes occurred during land plant evolution. We also attempted to establish an experimental system for analyzing autophagy in M. polymorpha. We generated transgenic plants expressing fluorescently tagged MpATG8 to observe its dynamics in M. polymorpha and produced autophagy-defective mutants by genome editing using the CRISPR/Cas9 system. These tools allowed us to demonstrate that MpATG8 is transported into the vacuole in an MpATG2-, MpATG5-, and MpATG7-dependent manner, suggesting that fluorescently tagged MpATG8 can be used as an autophagosome marker in M. polymorpha. M. polymorpha can provide a powerful system for studying the mechanisms and evolution of autophagy in plants.
Gender Differences in Throwing Revisited: Sensorimotor Coordination in a Virtual Ball Aiming Task

Numerous studies have demonstrated that boys throw balls faster, farther and more accurately than girls. This may be largely due to well-known anatomical and muscle-physiological differences that play a central role in overarm throwing. With the objective to understand the potential contribution of the equally essential coordinative aspects in throwing for this gender difference, this large cross-sectional study examined a simplified forearm throw that eliminated the requirements that give males an advantage.While the overall performance error indeed became similar in the age groups younger than 20 years and older than 50 years, it was attenuated for middle-aged individuals. The gender differences remained in individuals who reported no throwing experience, but females with throwing experience reached similar performance as males. Two fine-grained spatiotemporal metrics displayed similar age-dependent gender disparities: while overall, males showed better spatiotemporal coordination of the ball release, age group comparisons specified that it was particularly middle-aged females that made more timing errors and did not develop a noise-tolerant strategy as males did. As throwing experience did not explain this age-dependency, the results are discussed in the context of spatial abilities and video game experience, both more pronounced in males. In contrast, a measure of rhythmicity developed over successive throws only revealed weak gender differences, speaking to the fundamental tendency in humans to fall into rhythmic patterns. Only the youngest individuals between 5 and 9 years of age showed significantly less rhythmicity in their performance. This computational study was performed in a large cohort in the context of an outreach activity, demonstrating that robust quantitative measures can also be obtained in less controlled environments. The findings also alert that motor neuroscience may need to pay more attention to gender differences.
Usutu virus: A new threat?

Abstract Usutu virus (USUV) is an emerging arbovirus that was first isolated in South Africa in 1959. This Flavivirus is maintained in the environment through a typical enzootic cycle involving mosquitoes and birds. USUV has spread to a large part of the European continent over the two decades mainly leading to substantial avian mortalities with a significant recrudescence of bird infections recorded throughout Europe within the few last years. USUV infection in humans is considered to be most often asymptomatic or to cause mild clinical signs. Nonetheless, a few cases of neurological complications such as encephalitis or meningoencephalitis have been reported. USUV and West Nile virus (WNV) share many features, like a close phylogenetic relatedness and a similar ecology, with co-circulation frequently observed in nature. However, USUV has been much less studied and in-depth comparisons of the biology of these viruses are yet rare. In this review, we discuss the main body of knowledge regarding USUV and compare it with the literature on WNV, addressing in particular virological and clinical aspects, and pointing data gaps.
Global Increase in Circular RNA Levels in Myotonic Dystrophy

Splicing aberrations induced as a consequence of the sequestration of muscleblind-like splicing factors on the dystrophia myotonica protein kinase transcript, which contains expanded CUG repeats, present a major pathomechanism of myotonic dystrophy type 1 (DM1). As muscleblind-like factors may also be important factors involved in the biogenesis of circular RNAs (circRNAs), we hypothesized that the level of circRNAs would be decreased in DM1. To test this hypothesis, we selected 20 well-validated circRNAs and analyzed their levels in several experimental systems (e.g., cell lines, DM muscle tissues, and a mouse model of DM1) using droplet digital PCR assays. We also explored the global level of circRNAs using two RNA-Seq datasets of DM1 muscle samples. Contrary to our original hypothesis, our results consistently showed a global increase in circRNA levels in DM1, and we identified numerous circRNAs that were increased in DM1. We also identified many genes (including muscle-specific genes) giving rise to numerous (>10) circRNAs. Thus, this study is the first to show an increase in global circRNA levels in DM1. We also provided preliminary results showing the association of circRNA level with muscle weakness and alternative splicing changes that are biomarkers of DM1 severity.
Body Composition and Cognitive Functioning in a Sample of Active Elders

The purpose of this paper was to analyze the relationship between body composition and cognitive functioning in an elderly people’s sample. A total of 106 older adults between the ages of 60 and 79 were involved in physical activity (M = 67.57; SD = 4.96). About 31.10% were men (n = 33) and 68.90% were women (n = 73). The instruments used to assess cognitive capacity were the Trail Making Test (forms A and B), the Stroop Test, and the Attention Test d2. The body composition of the participants was evaluated by electrical bioimpedance. Correlation analysis, linear regression (successive steps), and cluster analysis were carried out to analyze the relationships between the different measures. The results showed significant relationships between the analyzed variables. In addition, muscle mass predicted the cognitive functioning values. These results suggest that healthy lifestyles, including physical activity, are essential for well-being and quality of life in older people. In addition, it appears from the results found that it would be necessary for these lifestyles to contribute to preserving their level of physical condition, because of the possible impact it would have on their health.
Ferroptosis Induction in Pentylenetetrazole Kindling and Pilocarpine-Induced Epileptic Seizures in Mice

Epilepsy is a serious neurological disorder and is characterized by recurrent and unprovoked seizures. A critical pathological factor in the seizure genesis is neuronal loss. Until now, apart from the known regulatory cell death pathways, ferroptosis is a newly discovered type of cell death with the features of iron accumulation and the excessive production of lipid reactive oxygen species (ROS). In our present work, it was illustrated that ferroptosis occurs in murine models of pentylenetetrazole (PTZ) kindling and pilocarpine (Pilo)-induced seizures. In both of these seizure models, treatment with ferroptosis inhibitor ferrostatin-1 (Fer-1) efficiently alleviates seizures. This was achieved through elevated levels of glutathione peroxidase 4 (GPX4) and glutathione (GSH) as well as inhibitions of lipid degradation products including 4-hydroxynonenal (4-HNE) and malonaldehyde (MDA), iron accumulation, and PTGS2 mRNA in the hippocampus. It was concluded that ferroptosis is involved in seizure genesis in PTZ- and Pilo-treated mice, while the suppression of ferroptosis mitigates PTZ kindling, and Pilo-induced seizures in mice.
A SpoIID Homolog Cleaves Glycan Strands at the Chlamydial Division Septum

Chlamydiales species are obligate intracellular bacteria and important human pathogens that have a minimal division machinery lacking the proteins that are essential for bacterial division in other species, such as FtsZ. Chlamydial division requires synthesis of peptidoglycan, which forms a ring at the division septum and is rapidly turned over. However, little is known of peptidoglycan degradation, because many peptidoglycan-degrading enzymes are not encoded by chlamydial genomes. Here we show that an homologue of SpoIID, a peptidoglycan-degrading enzyme involved in sporulation of bacteria such as Bacillus subtilis, is expressed in Chlamydiales, localizes at the division septum, and degrades peptidoglycan in vitro, indicating that SpoIID is not only involved in sporulation but also likely implicated in division of some bacteria. ABSTRACT Chlamydiales species are obligate intracellular bacteria lacking a classical peptidoglycan sacculus but relying on peptidoglycan synthesis for cytokinesis. While septal peptidoglycan biosynthesis seems to be regulated by MreB actin and its membrane anchor RodZ rather than FtsZ tubulin in Chlamydiales, the mechanism of peptidoglycan remodeling is poorly understood. An amidase conserved in Chlamydiales is able to cleave peptide stems in peptidoglycan, but it is not clear how peptidoglycan glycan strands are cleaved since no classical lytic transglycosylase is encoded in chlamydial genomes. However, a protein containing a SpoIID domain, known to possess transglycosylase activity in Bacillus subtilis, is conserved in Chlamydiales. We show here that the SpoIID homologue of the Chlamydia-related pathogen Waddlia chondrophila is a septal peptidoglycan-binding protein. Moreover, we demonstrate that SpoIID acts as a lytic transglycosylase on peptidoglycan and as a muramidase on denuded glycan strands in vitro. As SpoIID-like proteins are widespread in nonsporulating bacteria, SpoIID might commonly be a septal peptidoglycan remodeling protein in bacteria, including obligate intracellular pathogens, and thus might represent a promising drug target. IMPORTANCE Chlamydiales species are obligate intracellular bacteria and important human pathogens that have a minimal division machinery lacking the proteins that are essential for bacterial division in other species, such as FtsZ. Chlamydial division requires synthesis of peptidoglycan, which forms a ring at the division septum and is rapidly turned over. However, little is known of peptidoglycan degradation, because many peptidoglycan-degrading enzymes are not encoded by chlamydial genomes. Here we show that an homologue of SpoIID, a peptidoglycan-degrading enzyme involved in sporulation of bacteria such as Bacillus subtilis, is expressed in Chlamydiales, localizes at the division septum, and degrades peptidoglycan in vitro, indicating that SpoIID is not only involved in sporulation but also likely implicated in division of some bacteria.
Incidence and Mortality of Sarcomas in Shanghai, China, During 2002–2014

Background: Sarcomas are a heterogeneous group of rare but deadly malignant tumors. The aim of this study was to comprehensively describe the incidence and mortality of sarcomas in Shanghai during 2002–2014. Method: Data were from Shanghai Cancer Registry. All new cases diagnosed with sarcomas and all death records where the cause of death listed as sarcomas were included. The characteristics of sarcomas incidence and mortality were analyzed. Age-standardized rates (ASRs) were adjusted by the world standard population. The trends were assessed by Joinpoint analysis. Results: A total of 9,440 incident cases were identified. The ASR was 3.4/105 for all sarcomas combined. Incidence of sarcomas overall was similar in females (3.5/105) as in males (3.4/105). Except for sarcomas “Not Otherwise Specified” (NOS), the most common histological subtype was gastrointestinal stromal sarcoma (GISS) (14.8%), which was followed by fibrosarcoma (7.2%), lipoblastoma (6.7%), leiomyosarcomas (6.5%), and osteosarcoma (5.3%). Among those incident cases, 87.9% were located in soft tissue sarcomas (STS) and 12.1% in bone and joint (bone sarcomas). The ASRs for STS and bone sarcomas were 2.8/105 and 0.6/105, respectively. Incidence rates for all STS combined rose exponentially with age, while bone sarcomas had the highest incidence at age 0–19. There were 4,279 deaths during 2002–2014 with the ASR of 1.3/105. Age-adjusted mortality due to sarcomas was slightly higher in males (1.5/105) than females (1.2/105). Except for sarcomas NOS, leiomyosarcomas was the most common subtype, comprising 9.9% of deaths due to sarcomas, followed by lipoblastoma (6.4%) and osteosarcoma (6.3%). The ASRs of mortality for STS and bone sarcomas were 1.0/105 and 0.2/105, respectively. For both males and females, the age-standardized incidence for STS and bone sarcomas did not change meaningfully over the study period. In contrast, age-standardized STS mortality in females increased by 2.3% per year (95% CI: 0.3, 4.4%), but was unchanged in males. No meaningful trends in bone sarcomas mortality were observed for either males or females. Conclusion: This population-based study was the first report of epidemiology of sarcomas in Shanghai according to anatomic site and histologic type. The diversity and rarity of sarcomas suggested more detailed data are warranted.
Encountering relatable information in experiential learning spaces

PurposeThe purpose of this paper is to provide an emerging framework for university libraries’ research and reference services, which aims to strengthen partnerships between research information specialists and early career researchers (ECRs). Design/methodology/approachThe conceptual model used in this paper was originally developed from a constructivist grounded theory study, analyzing data from a sample of ECRs across multiple disciplines at two universities and contextualized by a review of recent research into ECRs’ information experiences, and researcher–librarian partnerships in experiential learning spaces within and beyond libraries.FindingsThis paper provides a review of the literature on one aspect of the knowledge ecosystem model relevant to research information specialists: tangible forms of information such as texts, tools, humans, cultures and environments encountered during informal learning experiences in six spaces: professional development programs, formal coursework, events, community, home and social media.Research limitations/implicationsThis paper is a catalyst for discussions and research into how research information specialists can facilitate access to the forms of information and learning experienced by ECRs, and what research information specialists can do with tangible information to respond to ECRs needs for experiential learning.Practical implicationsAs the previous study found that ECRs perceived their knowledge as vital resources toward their research career progression, it would be useful for research information specialists to understand and design services paying attention to the importance of ECRs’ initial encounters with tangible information to create the knowledge they need.Social implicationsWorking toward improved engagement and partnership through increased awareness and understanding of informed learning experiences between ECRs, their mentors and other developers and research librarians/information specialists can result in higher quality development and communication of new research, which can impact on society’s innovation and advancement.Originality/valueThe new integrative framework presented in this paper can assist in terms of identifying what informs ECRs professional development toward strengthening ECR and librarian/information specialist partnerships.
FC2N: Fully Channel-Concatenated Network for Single Image Super-Resolution

Most current image super-resolution (SR) methods based on deep convolutional neural networks (CNNs) use residual learning in network structural design, which contributes to effective back propagation, thus improving SR performance by increasing model scale. However, deep residual network suffers some redundancy in model representational capacity by introducing short paths, thus hindering the full mining of model capacity. In addition, blindly enlarging the model scale will cause more problems in model training, even with residual learning. In this work, a novel network architecture is introduced to fully exploit the representational capacity of the model, where all skip connections are implemented by weighted channel concatenation, followed by a 1$\times$1 conv layer. Based on this weighted skip connection, we construct the building modules of our model, and improve the global feature fusion (GFF). Unlike most previous models, all skip connections in our network are channel-concatenated and no residual connection is adopted. It is therefore termed as fully channel-concatenated network (FC$^2$N). Due to the full exploitation of model capacity, the proposed FC$^2$N achieves better performance than other advanced models with fewer model parameters. Extensive experiments demonstrate the superiority of our method to other methods, in terms of both quantitative metrics and visual quality.
Parametric protein shape recognition.

Declaration I declare that this thesis has been composed by myself, that it describes my own work, that it has not been accepted in any previous application for a degree, that all verbatim extracts are distinguished by quotation marks, and that all sources of information have been speciically acknowledged. i Acknowledgements I would like to thank my supervisors Dr. They made this project possible. They also made it a pleasure to work on. Graham in particular has been an unfailing source of encouragement. Without his interest, and many stimulating lunchtime discussions, this thesis would have been a very lonely endeavour indeed. I am also grateful to the BBSRC for funding this work (and for awarding further funding to continue this research). I would also like to acknowledge Professors Peter Gray and Derek Sleeman for their support. In a Department that is mostly dominated by database and machine learning experts, they seemed to sense that my tinkerings with spherical harmonics and the like might just lead to something useful. I'd like to think that they were right. Probably the most important person during this period has been my girlfriend Terry. She tolerated long hours and even days of isolation; and yet still she seemed interested when all I wanted to talk about was proteins. We get married this October. Apart from everything else, I would like to thank Terry and my parents for proofreading this manuscript so thoroughly. They have an uncanny ability, amongst many other qualities, to instantly detect split innnitives and spelling mistakes (they didn't see this part! ). Any errors that remain are entirely my own later additions. Finally, I must acknowledge several greater men than I: Fourier, Laguerre, Legendre, Schrr odinger and Wigner. If they had had computers, little of what follows would have been necessary; without Knuth's beautiful typesetting system, T E X, nothing of what follows would have been legible. ii Summary The salient points of this thesis are as follows: A two-dimensional parametric representation of protein surface shape may be used to superpose pairs of similar protein surfaces rapidly and accurately. A three-dimensional parametric surface shape representation provides an eecient and accurate way to nd complementary arrangements of a pair of surfaces, hence allowing two proteins to be \docked". Both the two-dimensional and the three-dimensional shape parameterisations are based on expansions of real spherical harmonic functions. In the 3D case, the spherical harmonic functions are …
Supervised word sense disambiguation using new features based on word embeddings

Supervised Word Sense Disambiguation (WSD) systems use features of the target word and its context to learn about all possible samples in an annotated dataset. Recently, word embeddings have emerged as a powerful feature in many NLP tasks. In supervised WSD, word embeddings can be used as a high-quality feature representing the context of an ambiguous word. In this paper, four improvements to existing state-of-the-art WSD methods are proposed. First, we propose a new model for assigning vector coefﬁcients for a more precise context representation. Second, we apply a PCA dimensionality reduction process to ﬁnd a better transformation of feature matrices and train a more informative model. Third, a new weighting scheme is suggested to tackle the problem of unbalanced data in standard WSD datasets and ﬁnally, a novel idea is presented to combine word embedding features extracted from different independent corpora, which uses a voting aggregator among available trained models. All of these proposals individually improve disambiguation performance on Standard English lexical sample tasks, and using the combination of all proposed ideas makes a signiﬁcant improvement in the accuracy score.
Measuring User Satisfaction and Perceived Usefulness in the ERP Context

Initially, Enterprise Resource Planning (ERP) systems held the promise of easily integrating all processes within and around the organization. Many reported ERP failures have led us to conduct, within the context of ERP implementation, an empirical examination of two success indicators: user satisfaction and perceived usefulness. The results reveal high levels of user satisfaction and perceived usefulness, both in nominal values and in comparison to other systems. They also show a strong correlation between perceived usefulness and user satisfaction, suggesting that perceived usefulness is one of the factors affecting user satisfaction with ERP systems. On the other hand, hypotheses testing revealed no supporting evidence for possible relationships between user satisfaction or perceived usefulness and organizational characteristics such as the department to which the respondent belonged or user characteristics such as organizational level, education, age, computing experience, and gender.