Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Cancer genomes harbor a broad spectrum of structural variants (SV) driving tumorigenesis, a relevant subset of which are likely to escape discovery in short reads. We employed Oxford Nanopore Technologies (ONT) sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assemble complex rearrangements and such associated with telomeric sequences, including a 1.55 Megabasepair chromothripsis event. We uncover a complex SV pattern termed ‘templated insertion thread’, characterized by short (mostly <1kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50kbp in size. Templated insertion threads occur in 3% of cancers, with a prevalence ranging to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in seven cancer-driver genes. Our study shows the potential of long-read sequencing in cancer. Graphical abstract I) We investigate a single patient with chromothriptic sonic hedgehog medulloblastoma (Li-Fraumeni syndrome), with tissue samples taken from blood, the primary tumor at diagnosis, and a post-treatment (relapse) tumor. II) Data on the three samples has been collected from four sources, 1) Illumina whole-genome, 2) Illumina transcriptome sequencing, 3) Illumina Infinium HumanMethylation450k, as well as 4) long-read whole-genome sequencing using Oxford Nanopore Technologies (ONT) sequencing. III) An integrative analysis combines genomic, epigenomic as well as transcriptomic data to provide a comprehensive analysis of this heavily rearranged tumor sample. Long and short read sequencing data is used to inform the analysis of complex structural genomic variants and methylation called from haplotyped ONT reads and validated through the methylation array data allows for a haplotype-resolved study of genomic and epigenomic variation, which can then be examined for transcriptional effect. IV) This integrative analysis allows us to identify a large number of inter- and intra-chromosomal genomic rearrangements (A) including a complex rearrangement pattern we term templated insertion threads (B), as well as sample-specific and haplotype specific methylation patterns of known cancer genes (C).
Linear and superlinear spread for continuous-time frog model

Consider a stochastic growth model on $\mathbb{Z} ^d$. Start with some active particle at the origin and sleeping particles elsewhere. The initial number of particles at $x \in \mathbb{Z} ^d$ is $\eta(x)$, where $\eta (x)$ are independent random variables distributed according to $\mu$. Active particles perform a simple continuous-time random walk while sleeping particles stay put until the first arrival of an active particle to their location. Upon the arrival all sleeping particles at the site activate at once and start moving according to their own simple random walks. The aim of this paper is to give conditions on $\mu$ under which the spread of the process is linear or faster than linear. The proofs rely on comparison to various percolation models.
Uma ferramenta baseada em containers Docker para experimentação em Mobile Cloud Computing

Mobile Cloud Computing (MCC) is intended to improve the execution of applications on mobile devices through the processing power provided by cloud computing. Several MCC works analyze the inﬂuence of the network conditions onto the accomplishment of computation ofﬂoading; however, many of these works use single-device scenarios, which do not ﬁt into a classic cloud computing environment, where multiple users interact simultaneously with a service. This work presents a tool that uses Docker containers to create MCC experimentation environments with multiple mobile devices and cloudlets. By using the proposed tool, developers and researchers will be able to create more realistic experimentation scenarios to test their applications.
Hypercane

In the Dark and Stormy Archives (DSA) project, we focus on storytelling techniques to summarize collections of archived web pages. Since collections can have hundreds or even thousands of seeds (initial URLs) and each seed can be recrawled many times, with each version separately maintained, techniques that include information about all members of the collection can be overwhelming. The premise of storytelling is to focus on sampling exemplar pages from the collection, and present them in a social media interface familiar to users. We present Hypercane, the tool in the DSA suite responsible for selecting exemplar pages. Hypercane offers eight action statements that can be combined in various ways to customize the sample that is produced. Because of its modular design, Hypercane can also be used to analyze large web archive collections outside of the DSA suite.
Unraveling the Proteomic Landscape of Intestinal Epithelial Cell-Derived Exosomes in Mice

Purpose This study aimed to identify the biological functions of small intestine intestinal epithelial cell derived exosomes (IEC-Exos) and further distinguished the difference proteins in IEC-Exos between ileum and jejunum related to function of the digestive system and occurrence of several diseases. Materials and Methods IECs of Male C57BL/6J mice were isolated. IEC-Exos were extracted from jejunum and ileum epithelial cell culture fluid by ultracentrifugation. In addition, isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to detect IEC-Exo proteins and conduct biological information analysis. Results The results showed that compared with jejunum IEC-Exos from ileum IEC-Exos, there were 393 up-regulated proteins and 346 down-regulated proteins. IECs-Exos, especially derived from jejunum, were rich in angiotensin-converting enzyme 2 (ACE2). The highly expressed proteins from ileum IEC-Exos were mostly enriched in genetic information processing pathways, which mainly mediate the processes of bile acid transport, protein synthesis and processing modification. In contrast, the highly expressed proteins from jejunum IEC-Exos were mainly enriched in metabolic pathways involved in sugar, fatty acid, amino acid, drug, and bone metabolism, etc. The differentially expressed proteins between ileum and jejunum IEC-Exos were not only related to the function of the digestive system but also closely related to the occurrence of infectious diseases, endocrine diseases and osteoarthritis, etc. Conclusion IEC-Exos there were many differentially expressed proteins between ileum and jejunum, which played different roles in regulating intestinal biological functions. ACE2, the main host cell receptor of SARS-CoV-2, was highly expressed in IEC-Exos, which indicated that IEC-Exos may be a potential route of SARS-CoV-2 infection.
Clinical Applications and Anticancer Effects of Antimicrobial Peptides: From Bench to Bedside

Cancer is a multifaceted global health issue and one of the leading causes of death worldwide. In recent years, medical science has achieved great advances in the diagnosis and treatment of cancer. Despite the numerous advantages of conventional cancer therapies, there are major drawbacks including severe side effects, toxicities, and drug resistance. Therefore, the urgency of developing new drugs with low cytotoxicity and treatment resistance is increasing. Antimicrobial peptides (AMPs) have attracted attention as a novel therapeutic strategy for the treatment of various cancers, targeting tumor cells with less toxicity to normal tissues. In this review, we present the structure, biological function, and underlying mechanisms of AMPs. The recent experimental studies and clinical trials on anticancer peptides in different cancer types as well as the challenges of their clinical application have also been discussed.
Hybrid Swarming Algorithm With Van Der Waals Force

This paper proposes a hybrid swarming algorithm based on Ant Colony Optimization and Physarum Polycephalum Algorithm. And the Van Der Waals force is first applied to the pheromone update mechanism of the hybrid algorithm. The improved method can prevent premature convergence into the local optimal solution. Simulation results show the proposed approach has excellent in solving accuracy and convergence time. We also compare the improved algorithm with other advanced algorithms and the results show that our algorithm is more accurate than the literature algorithms. In addition, we use the capitals of 35 Asian countries as an example to verify the robustness and versatility of the hybrid algorithm.
Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins

The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
Benzalkonium Chloride Adaptation Increases Expression of the Agr System, Biofilm Formation, and Virulence in Listeria monocytogenes

Benzalkonium chloride (BC) is widely used for disinfection in food industry. However, prolonged exposure to BC may lead to the emergence of BC adapted strains of Listeria monocytogenes, an important foodborne pathogen. Until now, two communication systems, the LuxS/AI-2 system and the Agr system, have been identified in L. monocytogenes. This study aimed to investigate the role of communication systems in BC adaptation and the effect of BC adaptation on two communication systems and the communication-controlled behaviors in L. monocytogenes. Results demonstrated that the Agr system rather than the LuxS system plays an important role in BC adaptation of L. monocytogenes. Neither luxS expression nor AI-2 production was affected by BC adaptation. On the other hand, the expression of the agr operon and the activity of the agr promoter were significantly increased after BC adaptation. BC adaptation enhanced biofilm formation of L. monocytogenes. However, swarming motility was reduced by BC adaptation. Data from qRT-PCR showed that flagella-mediated motility-related genes (flaA, motA, and motB) were downregulated in BC adapted strains. BC adaptation increased the ability of L. monocytogenes to adhere to and invade Caco-2 cells but did not affect the hemolytic activity. Compared with the wild-type strains, the expression levels of virulence genes prfA, plcA, mpl, actA, and plcB increased more than 2-fold in BC adapted strains; however, lower than 2-fold changes in the expression of hemolysis-associated gene hly were observed. Our study suggests that BC adaptation could increase the expression of the Agr system and enhance biofilm formation, invasion, and virulence of L. monocytogenes, which brings about threats to food safety and public health. Therefore, effective measures should be taken to avoid the emergence of BC adapted strains of L. monocytogenes.
Shoot or Don’t Shoot? Tactical Gaze Control and Visual Attention Training Improves Police Cadets’ Decision-Making Performance in Live-Fire Scenarios

Police officers often encounter potentially dangerous situations in which they strongly rely on their ability to identify threats quickly and react accordingly. Previous studies have shown that practical experience and targeted training significantly improve threat detection time and decision-making performance in law enforcement situations. We applied 90-min traditional firearms training as a control condition (35 participants) and a specifically developed intervention training (25 participants) to police cadets. The intervention training contained theoretical and practical training on tactical gaze control, situational awareness, and visual attention, while the control training focused on precision and speed. In a pre- and posttest, we measured decision-making performance as well as (tactical) response preparation and execution to evaluate the training. Concerning cognitive performance training (i.e., decision-making), the number of correct decisions increased from pre- to posttest. In shoot scenarios, correct decisions improved significantly more in the intervention group than in the control group. In don’t-shoot scenarios, there were no considerable differences. Concerning the training of response preparation and execution in shoot scenarios, the intervention group’s response time (time until participants first shot at an armed attacker), but not hit time, decreased significantly from pre- to posttest. The control group was significantly faster than the intervention group, with their response and hit time remaining constant across pre- and posttest. Concerning the training of tactical action control, the intervention group performed significantly better than the control group. Moreover, the intervention group improved the tactical handling of muzzle position significantly. The results indicate that a single 90-min session of targeted gaze control and visual attention training improves decision-making performance, response time, and tactical handling of muzzle position in shoot scenarios. However, these faster response times do not necessarily translate to faster hit times – presumably due to the motor complexity of hitting an armed attacker with live ammunition. We conclude that theory-based training on tactical gaze control and visual attention has a higher impact on police officers’ decision-making performance than traditional firearms training. Therefore, we recommend law enforcement agencies include perception-based shoot/don’t-shoot exercises in training and regular tests for officers’ annual firearm requalification.
Screening of Common Retinal Diseases Using Six-Category Models Based on EfficientNet

Purpose A six-category model of common retinal diseases is proposed to help primary medical institutions in the preliminary screening of the five common retinal diseases. Methods A total of 2,400 fundus images of normal and five common retinal diseases were provided by a cooperative hospital. Two six-category deep learning models of common retinal diseases based on the EfficientNet-B4 and ResNet50 models were trained. The results from the six-category models in this study and the results from a five-category model in our previous study based on ResNet50 were compared. A total of 1,315 fundus images were used to test the models, the clinical diagnosis results and the diagnosis results of the two six-category models were compared. The main evaluation indicators were sensitivity, specificity, F1-score, area under the curve (AUC), 95% confidence interval, kappa and accuracy, and the receiver operator characteristic curves of the two six-category models were compared in the study. Results The diagnostic accuracy rate of EfficientNet-B4 model was 95.59%, the kappa value was 94.61%, and there was high diagnostic consistency. The AUC of the normal diagnosis and the five retinal diseases were all above 0.95. The sensitivity, specificity, and F1-score for the diagnosis of normal fundus images were 100, 99.9, and 99.83%, respectively. The specificity and F1-score for RVO diagnosis were 95.68, 98.61, and 93.09%, respectively. The sensitivity, specificity, and F1-score for high myopia diagnosis were 96.1, 99.6, and 97.37%, respectively. The sensitivity, specificity, and F1-score for glaucoma diagnosis were 97.62, 99.07, and 94.62%, respectively. The sensitivity, specificity, and F1-score for DR diagnosis were 90.76, 99.16, and 93.3%, respectively. The sensitivity, specificity, and F1-score for MD diagnosis were 92.27, 98.5, and 91.51%, respectively. Conclusion The EfficientNet-B4 model was used to design a six-category model of common retinal diseases. It can be used to diagnose the normal fundus and five common retinal diseases based on fundus images. It can help primary doctors in the screening for common retinal diseases, and give suitable suggestions and recommendations. Timely referral can improve the efficiency of diagnosis of eye diseases in rural areas and avoid delaying treatment.
Advances in the Understanding of Reactive Oxygen Species-Dependent Regulation on Seed Dormancy, Germination, and Deterioration in Crops

Reactive oxygen species (ROS) play an essential role in the regulation of seed dormancy, germination, and deterioration in plants. The low level of ROS as signaling particles promotes dormancy release and triggers seed germination. Excessive ROS accumulation causes seed deterioration during seed storage. Maintaining ROS homeostasis plays a central role in the regulation of seed dormancy, germination, and deterioration in crops. This study highlights the current advances in the regulation of ROS homeostasis in dry and hydrated seeds of crops. The research progress in the crosstalk between ROS and hormones involved in the regulation of seed dormancy and germination in crops is mainly summarized. The current understandings of ROS-induced seed deterioration are reviewed. These understandings of ROS-dependent regulation on seed dormancy, germination, and deterioration contribute to the improvement of seed quality of crops in the future.
Energy Epidemiology: an epidemiological approach to empirically-based population-level energy demand research

The shift to a low carbon economy and the need to address energy demand priorities will involve the retrofit of millions of buildings resulting in changes in energy demand services at the national and international scale. Studying energy demand in buildings at a population level is different than in individual or small samples because of population heterogeneity. Evaluating policies and determining the effect of technologies in situ in millions of buildings means using techniques that support that level of analysis and use empirically derived data that can represent complex real-world conditions. Health epidemiology, which studies the distribution and determinants of population health outcomes, offers a compelling framework for studying population level energy demand. The aim of this thesis is to determine whether the adaption of the conceptual and methodological framework of epidemiology can support the study of energy, people and buildings. This thesis tests this hypothesis by examining relevant epidemiological concepts and its methodological framework along with three studies that adapt and apply epidemiological methods to energy demand and energy efficiency retrofits in UK houses. The method studies use a database of over 13 million dwellings to study energy efficiency retrofit uptake and their impact on energy demand. The method study findings support the case that an epidemiological approach to energy demand provides an appropriate and plausible conceptual and methodological framework for determining population-level evidence to inform modelling and policy development and evaluation. Adapting the epidemiological approach is not a panacea to dealing with the challenges facing the field of research in energy demand in buildings. However, it does provide a set of concepts, methods and analysis tools that are capable of supporting an empirically-based population-level research approach, identified as a necessary step towards to developing a robust foundation of evidence.
Elevated SNRPA1, as a Promising Predictor Reflecting Severe Clinical Outcome via Effecting Tumor Immunity for ccRCC, Is Related to Cell Invasion, Metastasis, and Sunitinib Sensitivity

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and is associated with poor prognosis and notorious for its immune dysfunction characteristic. SNRPA1 is a spliceosome component responsible for processing pre-mRNA into mRNA, while the biological effect of SNRPA1 in ccRCC remains elusive. The aim of this study was to decipher the effect of SNRPA1 on clinical effect and tumor immunity for ccRCC patients. Multi-databases were collected to evaluate the different expression, prognostic value, DNA methylation, tumor immune microenvironment, and drug sensitivity of SNRPA1 on ccRCC. IHC was utilized to validate the expression and prognostic value of SNRPA1 in ccRCC patients from the SMMU cohort. The knockout expression of SNRPA by sgRNA plasmid inhibited the cell proliferation, migration, and metastasis ability and significantly increased the sensitivity of sunitinib treatment. In addition, we explored the role of SNRPA1 in pan-cancer level. The results indicated that SNRPA1 was differentially expressed in most cancer types. SNRPA1 may significantly influence the prognosis of multiple cancer types, especially in ccRCC patients. Notably, SNRPA1 was significantly correlated with immune cell infiltration and immune checkpoint inhibitory genes. In addition, the aggressive and immune inhibitory effects shown in SNRPA1 overexpression and the effect of SNRPA1 on ccRCC cell line invasion, metastasis, and drug sensitivity in vitro were observed. Moreover, SNRPA1 was related to Myc, MTORC, G2M, E2F, and DNA repair pathways in various cancer types. In all, SNRPA1 may prove to be a new biomarker for prognostic prediction, effect tumor immunity, and drug susceptibility in ccRCC.
Problematic Smartphone Use and Problematic Social Media Use: The Predictive Role of Self-Construal and the Mediating Effect of Fear Missing Out

Problematic smartphone use (PSU) and problematic social media use (PSMU) are two interrelated constructs which have received significant research attention over the past decade. The present study investigated the relationship between self-construal (distinguished as independent and interdependent), PSU and PSMU with Fear of Missing Out (FoMO) as a mediating variable. The sample comprised 405 Italian students who completed standardized psychometric scales assessing the variables of the study. Bivariate correlations analysis showed that FoMO and independent self-construal was significantly and negatively associated. On the contrary, interdependent self-construal was significantly and positively associated with FoMO, PSU, and PSMU. Mediation analysis showed that FoMO mediated the relationship between self-construal and both PSMU and PSU, but at different levels. The results demonstrated that FoMO full mediated the relationships between interdependent self and PSU, whereas only partial mediation was found between interdependent self and PSMU. Therefore, taking these personality characteristics into account may help reduce dysfunctional behaviour associated with problematic technology use and promote psychological well-being among students. However, it is recommended that further studies replicate the proposed model by including other psychological constructs.