Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of a Rhs effector clade domain identifies new mechanistic insights into type VI secretion system toxin delivery

The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins directly into adjacent bacteria, often providing a competitive advantage. Rearrangement hotspot (Rhs) effectors are known T6SS cargo effectors, but the precise delivery and activation of these toxins is poorly defined. We present the structure of a novel T6SS Rhs effector (Tse15) from the multidrug resistant nosocomial pathogen Acinetobacter baumannii. Tse15 forms a triple layered ý-cocoon Rhs domain with an N-terminal α-helical clade domain and an unfolded C-terminal toxin domain located entirely inside the Rhs cage. We identify that Tse15 is cleaved into three domains, through two independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for the cleavage of the N-terminal clade domain. Proteomic analyses showed that the N-terminal clade and toxin domains, but not the ý-strand rich Rhs cage, are delivered outside of the cell, suggesting a novel mechanism for Rhs toxin delivery and activation. Our findings suggest that this delivery mechanism requires an interaction between the N-terminal clade and toxin domains, with the clade domain acting as the internal chaperone to mediate tethering of the toxin to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggest this may be a common mechanism for T6SS toxin delivery.
Riboswitch and small RNA modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms

Small RNAs (sRNAs) and riboswitches represent distinct classes of RNA regulators that control gene expression upon sensing metabolic or environmental variations. While sRNAs and riboswitches regulate gene expression by affecting mRNA and protein levels, existing studies have been limited to the characterization of each regulatory system in isolation, suggesting that sRNAs and riboswitches target distinct mRNA populations. We report that the expression of btuB in Escherichia coli, which is regulated by an adenosylcobalamin (AdoCbl) riboswitch, is also controlled by the small RNAs OmrA and, to a lesser extent, OmrB. Strikingly, we find that the riboswitch and sRNAs reduce mRNA levels through distinct pathways. Our data show that while the riboswitch triggers Rho-dependent transcription termination, sRNAs rely on the degradosome to modulate mRNA levels. Importantly, OmrA pairs with the btuB mRNA through its central region, which is not conserved in OmrB, indicating that these two sRNAs may have specific targets in addition to their common regulon. In contrast to canonical sRNA regulation, we find that OmrA repression of btuB is lost using an mRNA binding-deficient Hfq variant. Together, our study demonstrates that riboswitch and sRNAs modulate btuB expression, providing an example of cis- and trans-acting RNA-based regulatory systems maintaining cellular homeostasis.
Long-distance communication can enable collective migration in a dynamic seascape

Social information is predicted to enhance migratory performance, but the relative benefits of social information in the long-range movements of marine megafauna are unknown. In particular, whether and how migrants use nonlocal information gained through social communication at the extreme spatial scale of oceanic ecosystems remains unclear. Here we combine long-term acoustic recordings of foraging and migratory blue whales, oceanographic and prey data, and individual-based modeling to discern the cues underlying timing of blue whales’ breeding migration in the Northeast Pacific. We find that individual whales rely on both personal and social sources of information about forage availability in deciding when to depart from their vast and dynamic foraging habitat and initiate breeding migration. Empirical patterns of migratory phenology can only be reproduced by models in which individuals use long-distance social information about conspecifics’ behavioral state, which is known to be encoded in the patterning of their widely-propagating songs. Further, social communication improves pre-migration seasonal foraging performance by over 60% relative to asocial movement mechanisms. Our results suggest that long-range communication enhances the perceptual ranges of migrating whales beyond that of any individual, resulting in increased foraging performance. These findings indicate the value of nonlocal social information in an oceanic migrant and highlight the importance of long-distance acoustic communication in the collective migration of wide-ranging marine megafauna.
The thiol methyltransferase activity of TMT1A (METTL7A) is conserved across species

Although few resistance mechanisms for histone deacetylase inhibitors (HDACis) have been described, we recently demonstrated that TMT1A (formerly METTL7A) and TMT1B (formerly METTL7B) can mediate resistance to HDACis with a thiol as the zinc-binding group by methylating and inactivating the drug. TMT1A and TMT1B are poorly characterized, and their normal physiological role has yet to be determined. As animal model systems are often used to determine the physiological function of proteins, we investigated whether the ability of these methyltransferases to methylate thiol-based HDACis is conserved across different species. We found that TMT1A was conserved across rats, mice, chickens, and zebrafish, displaying 85.7%, 84.8%, 60.7% and 51.0% amino acid sequence identity, respectively, with human TMT1A. Because TMT1B was not found in the chicken or zebrafish, we focused our studies on the TMT1A homologs. HEK-293 cells were transfected to express mouse, rat, chicken, or zebrafish homologs of TMT1A and all conferred resistance to the thiol-based HDACIs NCH-51, KD-5170 and romidepsin compared to empty vector-transfected cells. Additionally, all homologs blunted the downstream effects of HDACi treatment such as increased p21 expression, increased acetylated histone H3, and cell cycle arrest. Increased levels of dimethylated romidepsin were also found in the culture medium of cells transfected to express any of the TMT1A homologs after a 24 h incubation with romidepsin compared to empty-vector transfected cells. Our results indicate that the ability of TMT1A to methylate molecules is conserved across species. Animal models may therefore be useful in elucidating the role of these enzymes in humans.
Massively parallel mapping of substrate cleavage sites defines dipeptidyl peptidase four subsite cooperativity

Substrate specificity determines protease functions in physiology and in clinical and biotechnological application. However, affordable and unbiased assays for large-scale quantification of substrate cleavage have been lacking. Here, we develop hiMAPS (high-throughput mapping of protease cleavage sites), a cheap, mass spectrometry-based assay, to derive cleavage motifs for human Dipeptidyl Peptidase Four (DPP4), a key regulator of blood glucose levels. We recapitulate the known benefit of proline in the penultimate (P1) position from the substrate N-terminus, extend it to additional residues, and identify and quantify combinatorial interactions of P1 with its neighbors. These findings reveal extensive cooperativity among the enzyme’s active site subsites and allow us to derive a sequence motif that predicts substrate turnover. We show that this information provides new opportunities to engineer stabilized versions of a key substrate of DPP4, the small peptide hormone GLP-1, whose derivatives are used for clinical treatment of type 2 diabetes and obesity. Finally, structural and biochemical characterization of a DPP4 homologue, C. elegans DPF-3, reveal specific subsite differences and a distinct cleavage motif, providing insight into the mechanistic basis of the observed specificity. Collectively, our findings present a broadly applicable framework to high-throughput mapping of protease cleavage sites, extend our understanding of protease specificity, and provide a chemical space for substrate engineering of a clinically relevant family of exopeptidases.
Determinants of spring migration departure dates in a New World sparrow: Weather variables reign supreme

Numerous factors influence the timing of spring migration in birds, yet the relative importance of intrinsic and extrinsic variables on migration initiation remains unclear. To test for interactions among weather, migration distance, parasitism, and physiology in determining spring departure date, we used Dark-eyed Juncos (Junco hyemalis hyemalis) as a model migratory species known to harbor diverse and common haemosporidian parasites. Prior to spring migration departure from their wintering grounds in Indiana, USA, we quantified the intrinsic variables of fat, body condition (i.e., mass∼tarsus residuals), physiological stress (i.e., ratio of heterophils to lymphocytes), cellular immunity (i.e., leukocyte composition and total count), migration distance (i.e., distance to the breeding grounds) using stable isotopes of hydrogen from feathers, and haemosporidian parasite intensity. We then attached nanotags to determine the timing of spring migration departure date using the Motus Wildlife Tracking System. We used additive Cox proportional hazard mixed models to test how risk of spring migratory departure was predicted by the combined intrinsic measures, along with meteorological predictors on the evening of departure (i.e., average wind speed and direction, relative humidity, and temperature). Model comparisons found that the best predictor of spring departure date was average nightly wind direction and a principal component combining relative humidity and temperature. Juncos were more likely to depart for spring migration on nights with largely southwestern winds and on warmer and drier evenings (relative to cooler and more humid evenings). Our results indicate that weather conditions at take-off are more critical to departure decisions than the measured physiological and parasitism variables.
Measurements of black carbon properties during cloud, biomass burning, and free tropospheric conditions at a marine boundary layer site and high elevation mountain site

Black carbon is a subset of the total atmospheric aerosol population that is formed in the incomplete combustion of fossil fuels, biofuels, and biomass. This research focused on the properties of black carbon particles measured in the boundary layer and free troposphere, as well as the activation of black carbon particles by cloud droplets. The primary motivation for this research is to increase our understanding of the properties of black carbon under these different atmospheric conditions. A single particle soot photometer was used to study properties of black carbon particles incorporated into cloud droplets at two field locations: 1) a marine boundary layer site, and 2) a high elevation mountain site. At both sites, a size dependence on the fraction of black carbon incorporated into cloud droplets was observed; and for small (<100 nm) diameters, black carbon was efficiently incorporated into droplets. In addition, at the marine boundary layer site, thick coatings were observed on the small diameter black carbon particles that were incorporated into the droplets, which was consistent with theory. The single particle soot photometer was also used at a high elevation mountain site to investigate properties of black carbon from biomass burning and black car-
Anomaly Detection for Population Dynamics using Autoencoder Leveraging Periodic Residual Component in Disaster Situations

It is important for local governments to grasp the evacuation situation upon the occurrence of a large-scale disaster because administrative support can be provided, such as opening temporary accommodation facilities or distributing relief supplies. Early identification of locations where population transitions differ from normal conditions will help local governments to identify areas for disaster response. In this paper, we propose a simple yet effective anomaly detection method for population transition using an autoencoder that leverages periodic residual components using real-time population dynamics generated from operation data of cellular phone networks. We evaluated the effectiveness of our proposed method using data from three real earthquakes in Japan. The results demonstrated that our approach, which leverages periodic residual components, outperforms a baseline method that directly uses population transition. Moreover, the experimental results showed that the standard deviation of recall is smaller than that of the baseline method, indicating that utilizing the residual component has a stabilizing effect on accuracy.
Theoretical study of the sensitivity of the microwave backscattering coefficient to the soil surface parameters

Abstract The microwave backscattered signal from soil is sensitive to surface parameters and especially to roughness and moisture. The object of this work is to evaluate the optimum operating configuration for a spacecraft radar which would allow the extraction of one of these parameters, minimizing the effect of the other. A theoretical study, using a simulation model based on the scalar approximation, has permitted the estimation of the backscattering coefficient's sensitivity to a relative variation in soil parameters in terms of radar characteristics. The results show that, if a very low incidence angle is not acceptable, the best configuration for a soil moisture measurement requires the simultaneous use of two polarizations (HH and VV) and a large look-angle (>35°). For a roughness measurement, the coupling of two incidence angles (20° and 40°), a low frequency (S or C-band) and the HH polarization seem to give satisfactory results.
Team GPLSI at AuTexTification Shared Task: Determining the Authorship of a Text

AuTexTification is a shared task within the IberLEF workshop which aims to determine whether a text has been generated by an Artificial Intelligence (AI) or a human. The objective of this paper is to report the participation and results of the GPLSI team from the University of Alicante (Spain) in subtask 1: Human or Generated of the AuTexTification challenge for English and Spanish languages. We propose and experiment with different approaches based on Transfer Learning; Ensemble Learning; fine-tuning existing language models, such as RoBERTa or RemBERT; or relying on linguistic features. Our best models for both languages were trained through Transfer Learning techniques, obtaining the 6 th and 8 th position in the English and Spanish versions of this subtask, respectively. Results obtained in the Spanish-version were close to the top-performing team.
Petrophysical parameters of the Lower Triassic deposits in prospective location for Enhanced Geothermal System (central Poland)

In the years 2010-2013, analysis of rocks that build the sedimentary covers in Poland was carried out from the point of view of energy utilization accumulated in hot dry rocks – used in Enhanced Geothermal Systems (EGS). As a result of a number of analytical studies, the area situated in the central part of Poland was selected as one of prospective areas for location of EGS in sedimentary rocks. This area encompasses a major part of the Mogilno-Łodź Trough, a part of the Kujawy Swell and a small fragment of the Fore-Sudetic Monocline. The most favourable conditions for development of EGS occur in deposits of the Lower Triassic in the Krośniewice-Kutno vicinity where they are buried to depths greater than 5000 m b.s.l. , have thicknesses exceeding 1500 m and are characterized by porosity about 2.5% and permeability about 0.1 mD. In the selected area, thermal characterization of the formation was carried out for location of the EGS in sedimentary rocks. The temperature at the top of Lower Triassic reservoir is in the range 165-175°C. Characterization of petrophysical parameters constituted the basis for further modelling of EGS utilization in selected area. Normal 0 21 false false false PL X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:Standardowy; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi; mso-fareast-language:EN-US;}
UC3M at Da-Vincis-2023: using BETO for Detection of Aggressive and Violent Incidents on Social Networks

This article presents the contribution of the UC3M_PLN team to the DA-VINCIS competition organized at IberLEF-2023. The objective of the task is to identify accidents, murders, robberies, and other incidents on Twitter. The DA-VINCIS Corpus has been created using various messages recovered from tweets associated with violent acts. The competition includes subtasks for the identification and multi-categorization of violent events. We have successfully completed both subtasks by exploring different strategies to combine transformer language features and embeddings.
Univ. of Hildesheim at AuTexTification 2023: Detection of Automatically Generated Texts

Text generation models can pose a challenge for the legitimacy and authenticity of texts. Large pre-trained models have reached a high level of quality already. This paper presents experiments on classifying whether a text was written by a human or generated by a language model. The paper describes experiments within shared task AuTexTification: Automated Text Identification 2023. The approach is based on a pre-trained model. We selected the DeBERTaV2 model. Our run reached an Macro-F1 score of 67.2 and was ranked on position 15 out of 76 submissions for subtask 1. The paper also presents an analysis of both text classes based on text metrics. The observation of various readability metrics shows that the generated texts tend to show less diversity than human texts.
IIMAS-UNAM Team entry: Transformers Adapters for the Sentiment Analysis REST-MEX 2023

This work describes and presents the methodology of the IIMAS-UNAM team followed in the sentiment analysis task in the REST-MEX 2023 competition on tourist reviews. It shows the use of the Transformers architecture together with Adapters achieves a sufficiently good performance in this type of task. The submitted model was ranked third place, reaching a 75 . 00 Sentiment Track Score.
RMLANet: Random Multi-Level Attention Network for Shadow Detection and Removal

This paper addresses the problem of shadow detection and shadow removal from a single image. Despite awareness of utilizing both local and global contexts, previous works only aggregate features level by level in a coarse-to-fine manner. To overcome this problem, we present RMLANet, a novel Random Multi-Level Attention Network. To be specific, we first design a shuffled multi-level feature aggregation module to fuse the multi-level features and the guiding features using the self-attention mechanism. Nevertheless, the computational complexity of dense self-attention is unaffordable when processing high-resolution inputs. We argue that dense attention between any pixel pair is unnecessary due to the local consistency in images. Then we further propose a sparse attention mechanism to reduce the number of attention pairs, which greatly reduces the computational complexity. Through extensive experiments on four shadow detection and three shadow removal benchmark datasets, our proposed RMLANet achieves superior performance over current state-of-the-art approaches for both shadow detection and shadow removal. Codes are publicly available at https://github.com/LeipingJie/RMLANet.
Working conceptual model of citizen identification: the case of Mozambique

For a suitable participation of the citizen in the digital economic era, it is crucial to have an efficient, inclusive and embracing citizen identification system (CIDS). However, there are still many people worldwide without any legal identity. Strong action by governments and other stakeholders is therefore recommended to change this scenario. The Mozambican citizen identification system based on Information and Communications Technologies (ICT) is improving, for that reason, the purpose of this article is to describe the current situation, its problems and propose a model adjusted to the technological evolution, based on the fundamentals of Working Systems Theory (WST). Therefore, at the end of the article, we make recommendations focused on the rationalization of the identification system, aiming at proposing a Conceptual Model that maximizes the ICT potentials, interoperable and working system.
Monitoring Ransomware with Berkeley Packet Filter

The article delves comprehensively into employing the extended Berkeley Packet Filter (eBPF) for monitoring network traffic, filtering system calls, and overseeing processes for ransomware activity. The principles and architecture underlying this advanced technology are explored, laying a solid foundation for developing robust mechanisms for detecting and halting malware propagation across networks. The paper highlights potential strategies for tracking viruses within traffic and evaluates this approach, meticulously considering the security concerns and control mechanisms endowed by eBPF. A notable section of the article is dedicated to a comparative analysis. Traditional malware detection mechanisms are assessed alongside a program built on eBPF, offering a clear, unbiased insight into their respective efficiencies and potential pitfalls. This extensive comparison underscores the enhanced proficiency and security offered by eBPF-based monitoring mechanisms, solidifying their stance as a formidable tool against malware threats, including ransomware. The authors demonstrate the capability of an eBPF-based monitoring system in delivering potent network defense against various malware forms, including ransomware, presenting significant implications for antivirus protection developers. This comprehensive exploration and presented findings are pivotal for enhancing the overall security quotient of computer networks globally, emphasizing the critical role of eBPF in contemporary network security paradigms. The superior efficiency and security assurance offered by BPF reinforces its viability as a pivotal technology for monitoring network traffic and safeguarding against pervasive malware threats.
Using Vector Embeddings and Feature Vectors to Humor Identification

Expressing prejudice is the most common strategy to harm minority groups. Prejudice is defined as "the formation of a negative concept or judgment in advance about members of a race, religion, or any other significant social group, despite facts contradicting it. " This paper proposes two different approaches for the classification of tweets aiming to generate humor by expressing prejudice, detecting the target group to which the prejudice is being expressed, as well as the prejudice score, ranging from 1 to 5, contained in the tweet. The approaches to solve these tasks are from two perspectives: one focusing on if there are some lexical and morphological characteristics to discriminate tweets with humor and those who don’t, and the other utilizing word embeddings to tackle the same tasks.