Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented. 2. Importance In this study, TNT and DNT removal has been observed in field-scale experiments following periodic tilling of historically contaminated soils. The microbial community structures of uncontaminated pristine soils, untilled contaminated soils, and tilled contaminated soils were investigated using high-throughput sequencing platforms. In addition, shotgun metagenome libraries of samples from tilled contaminated soils were generated. The results indicated that a significant shift of the bacterial community at the family level between tilled and untilled contaminated soils, with tilled soils being dominated by Alcaligenaceae and untilled soils by Burkholderiacea. In-depth metagenomic analysis of samples from tilled contaminated soils, indicate the presence of genes that encode for enzymes that potentially could lead to mineralization of TNT and DNT under mixed aerobic and anaerobic periods.
On the Study of Microservices Antipatterns: a Catalog Proposal

Microservice architecture has become popular in the last few years as it allows the development of independent, highly reusable, and fine grained services. However, a lack of understanding of its core concepts and the absence of a ground-truth lead to design and implementation decisions, which might be applied often and introduce poorly designed solutions, called antipatterns. The definition of microservice antipatterns is essential for improving the design, maintenance, and evolution of microservice-based systems. Moreover, the few existing specifications and definitions of microservice antipatterns are scattered in the literature. Consequently, we conducted a systematic literature review of 27 papers related to microservices and analyzed 67 open-source microservice-based systems. Based on our analysis, we report in this paper 16 microservice antipatterns. We concisely describe these antipatterns, how they are implemented, and suggest refactoring solutions to remove them.
Græcissare: Ancient Greek Loanwords in the LiLa Knowledge Base of Linguistic Resources for Latin

English. This paper describes the addition of an index of 1, 763 Ancient Greek loanwords to the collection of Latin lemmas of the LiLa: Linking Latin Knowledge Base of interoperable linguistic resources. This lexical resource increases LiLa’s lemma count and tunes its underlying data model to etymological borrowing.
Adaptation of a fluoroquinolone-sensitive Shigella sonnei to norfloxacin exposure

Shigella causes shigellosis that requires antibiotic treatment in severe cases. Sub-lethal antibiotic concentrations can promote resistance, but their effect on antibiotic-sensitive bacteria before resistance development is unknown. This study investigated the effects of sublethal norfloxacin (NOR) challenges on a norfloxacin-sensitive strain, Shigella sonnei UKMCC1015. Firstly, the whole genome of S. sonnei UKMCC1015 was assembled, and 45 antimicrobial resistance (AMR) genes were identified. However, transcriptomic analysis showed that low NOR levels do not change the expression of AMR genes and norfloxacin targets. Instead, multiple ribosomal protein genes were downregulated, which could be attributed to decreased ribosomal protein promoter activity, modulated by elevated ppGpp levels. This alarmone is involved in the bacterial stringent response during environmental stress, and it is mainly produced from the ppGpp synthetase (relA). However, high levels of ppGpp (due to relA overexpression) are detrimental to the continued survival of S. sonnei during prolonged exposure to NOR. This study revealed that a norfloxacin-sensitive strain responds differently to sub-lethal NOR than commonly reported in resistant strains. Overexpression of relA (high ppGpp levels) may reduce the mutability of S. sonnei UKMCC1015 in response to NOR exposure and affect NOR tolerance.
A Diachronic Italian Corpus based on "L'Unità"

English. In this paper, we describe the creation of a diachronic corpus for Italian by exploiting the digital archive of the newspaper “L’Unit`a”. We automatically clean and annotate the corpus with PoS tags, lemmas, named entities and syntactic dependencies. Moreover, we compute frequency-based time series for tokens, lemmas and entities. We show some interesting corpus statistics taking into account the temporal dimension and describe some examples of usage of time series.
SSN NLP @ SardiStance : Stance Detection from Italian Tweets using RNN and Transformers (short paper)

Stance detection refers to the detection of one’s opinion about the target from their statements. The aim of sardistance task is to classify the Italian tweets into classes of favor, against or no feeling towards the target. The task has two sub-tasks : in Task A, the classification has to be done by considering only the textual meaning whereas in Task B the tweets must be classified by considering the contextual information along with the textual meaning. We have presented our solution to detect the stance utilizing only the textual meaning (Task A) using encoder-decoder model and transformers. Among these two approaches, simple transformers have performed better than the encoder-decoder model with an average F1-score of 0.4707.
LLAMA: a robust and scalable machine learning pipeline for analysis of cell surface projections in large scale 4D microscopy data

We present LLAMA, a pipeline for systematic analysis of terabyte scale 4D microscopy datasets. Analysis of individual biological structures in imaging at this scale requires efficient and robust methods which do not require human micromanagement or editing of outputs. To meet this challenge, we use a machine learning method for semantic segmentation, followed by a robust and configurable object separation and tracking algorithm, and the generation of detailed object level statistics. Advanced visualisation is a key element of LLAMA: we provide a specialised software tool which supports quality control and optimisation as well as visualisation of outputs. LLAMA was used in a quantitative analysis of macrophage surface membrane projections (filopodia, ruffles, tent-pole ruffles) examining the differential effects of two interventions: lipopolysaccharide (LPS) and macrophage colony stimulating factor (CSF-1). Distinct patterns of increased activity were identified. In addition, a continuity of behaviour was found between tent pole ruffling and wave-like ruffling, further defining the role of filopodia in ruffling.
ItaGLAM: A corpus of Cultural Communication on Twitter during the Pandemic

This paper describes the compilation and annotation of ItaGLAM, a corpus of tweets written by Italian Galleries, Li-breries, Archives and Museums (GLAMs) during the lockdown period in Italy due to the COVID-19 pandemic ItaGLAM has been annotated with a set of labels which may be useful to identify different types of communication Furthermore, the collected data have been used to train a set of classifiers The results are analyzed to evaluate the information flow between GLAM and users and to analyze cultural communication on the Web Copyright © 2020 for this paper by its authors
Identification of a Family of Vibrio Type III Secretion System Effectors That Contain a Conserved Serine/Threonine Kinase Domain

Vibrio parahaemolyticus is the leading bacterial cause of seafood-borne gastroenteritis worldwide. The pathogen relies on a type III secretion system to deliver a variety of effector proteins into the cytosol of infected cells to subvert cellular function. ABSTRACT Vibrio parahaemolyticus is a marine Gram-negative bacterium that is a leading cause of seafood-borne gastroenteritis. Pandemic strains of V. parahaemolyticus rely on a specialized protein secretion machinery known as the type III secretion system 2 (T3SS2) to cause disease. The T3SS2 mediates the delivery of effector proteins into the cytosol of infected cells, where they subvert multiple cellular pathways. Here, we identify a new T3SS2 effector protein encoded by VPA1328 (VP_RS21530) in V. parahaemolyticus RIMD2210633. Bioinformatic analysis revealed that VPA1328 is part of a larger family of uncharacterized T3SS effector proteins with homology to the VopG effector protein in Vibrio cholerae AM-19226. These VopG-like proteins are found in many but not all T3SS2 gene clusters and are distributed among diverse Vibrio species, including V. parahaemolyticus, V. cholerae, V. mimicus, and V. diabolicus and also in Shewanella baltica. Structure-based prediction analyses uncovered the presence of a conserved C-terminal kinase domain in VopG orthologs, similar to the serine/threonine kinase domain found in the NleH family of T3SS effector proteins. However, in contrast to NleH effector proteins, in tissue culture-based infections, VopG did not impede host cell death or suppress interleukin 8 (IL-8) secretion, suggesting a yet undefined role for VopG during V. parahaemolyticus infection. Collectively, our work reveals that VopG effector proteins, a new family of likely serine/threonine kinases, is widely distributed in the T3SS2 effector armamentarium among marine bacteria. IMPORTANCE Vibrio parahaemolyticus is the leading bacterial cause of seafood-borne gastroenteritis worldwide. The pathogen relies on a type III secretion system to deliver a variety of effector proteins into the cytosol of infected cells to subvert cellular function. In this study, we identified a novel Vibrio parahaemolyticus effector protein that is similar to the VopG effector of Vibrio cholerae. VopG-like effectors were found in diverse Vibrio species and contain a conserved serine/threonine kinase domain that bears similarity to the kinase domain in the enterohemorrhagic Escherichia coli (EHEC) and Shigella NleH effectors that manipulate host cell survival pathways and host immune responses. Together our findings identify a new family of Vibrio effector proteins and highlight the role of horizontal gene transfer events among marine bacteria in shaping T3SS gene clusters.
Evaluation of microbial diversification mechanisms in legume-based mixed cropping systems with different legume species and types of fertilizer management

Biodiversity loss is becoming a global concern due to its negative impact on services associated with the ecosystem. For agricultural soil to maintain these multi-services, the conservation of soil microbial diversity is of utmost importance. Mixed cropping systems involve the utilisation of multiple crop species on the field as well as the diversification of aboveground plants, although several contradicting results have been reported regarding their impacts on soil microbial diversity. Therefore, for the evaluation of the impact of different leguminous species used in mixed cropping systems as well as types of fertilizer on the diversity of soil microbes, a pot study was performed under maize/legume mixed cropping systems with one of three legumes, including cowpea (Vigna unguiculate (L.) Walp. ), velvet bean (Mucuna pruriens (L.) DC. ), and common bean (Phaseolus vulgaris L.) as well as one of three types of fertilizer treatments, namely chemical fertilizer (CF), carbonised chicken manure (CM), or the lack of fertilizer (Ctr). 16S rRNA analyses were conducted using the soils sampled from each pot for soil bacterial diversity assessment. Concerning the results, a decrease in the microbial diversity after CM application was shown by the soil with velvet bean + maize (MM) when compared to the Ctr treatment, while an increase in the microbial diversity was shown by the soil with common bean + maize (PM) under the same condition. In case of the CM application, the abundance of treatment-unique bacteria increased in the PM treatment, although their decrease was observed for the MM treatment. In contrast, the abundance of dominant microbes, including Thaumarchaeota was significantly lower in PM but higher in MM when the CM was applied. Legume species-dependent factors, including nutrient absorption and root exudate composition might be important concerning soil bacterial diversities. For the conservation of soil microbial diversity with mixed cropping, the interaction effect of legume species and fertilizer type should be considered in future studies.
Selective increase of functional network connectivity in Arc-positive neuronal engrams after long-term potentiation

New tools in optogenetics and molecular biology have culminated in recent studies which mark immediate-early gene (IEG)-expressing neurons as memory traces or engrams. Although the activity-dependent expression of IEGs has been successfully utilised to label memory traces, their roles in engram specification is incompletely understood. Outstanding questions remain as to whether expression of IEGs can interplay with network properties such as functional connectivity and also if neurons expressing different IEGs are functionally distinct. We investigated the expression of Arc and c-Fos, two commonly utilised IEGs in memory engram specification, in cultured hippocampal neurons. After pharmacological induction of long-term potentiation (LTP) in the network, we noted an emergent network property of refinement in functional connectivity between neurons, characterized by a global down-regulation of network connectivity, together with strengthening of specific connections. Subsequently, we show that Arc expression correlates with the effects of network refinement, with Arc-positive neurons being selectively strengthened. Arc positive neurons were also found to be located in closer physical proximity to each other in the network. While the expression pattern of IEGs c-Fos and Arc strongly overlaps, Arc was more selectively expressed than c-Fos. These IEGs also act together in coding information about connection strength pruning. These results demonstrate important links between IEG expression and network connectivity, which serve to bridge the gap between cellular correlates and network effects in learning and memory.
Dual Site-Specific Chemoenzymatic Antibody Fragment Conjugation Using CRISPR-Based Hybridoma Engineering

Functionalized antibodies and antibody fragments have found applications in the fields of biomedical imaging, theragnostics, and antibody-drug conjugates (ADC). Antibody functionalization is classically achieved by coupling payloads onto lysine or cysteine residues. However, such stochastic strategies typically lead to heterogenous products, bearing a varying number of payloads. This affects bioconjugate efficacy and stability, as well as its in vivo biodistribution, and therapeutic index, while potentially obstructing the binding sites and leading to off-target toxicity. In addition, therapeutic and theragnostic approaches benefit from the possibility to deliver more than one type of cargo to target cells, further challenging stochastic labelling strategies. Thus, bioconjugation methods to reproducibly obtain defined homogenous conjugates bearing multiple different cargo molecules, without compromising target affinity, are in demand. Here, we describe a straightforward CRISPR/Cas9-based strategy to rapidly engineer hybridoma cells to secrete Fab’ fragments bearing two distinct site-specific labelling motifs, which can be separately modified by two different sortase A mutants. We show that sequential genetic editing of the heavy chain (HC) and light chain (LC) loci enables the generation of a stable cell line that secretes a dual tagged Fab’ molecule (DTFab’), which can be easily isolated in high yields. To demonstrate feasibility, we functionalized the DTFab’ with two distinct cargos in a site-specific manner. This technology platform will be valuable in the development of multimodal imaging agents, theragnostics, and next-generation ADCs.
BRCA1-BARD1 regulates transcription through modulating topoisomerase IIβ

RNA polymerase II (Pol II)-dependent transcription in stimulus-inducible genes requires topoisomerase IIβ (TOP2B)-mediated DNA strand break and the activation of DNA damage response signaling in humans. Here, we report a novel function of the breast cancer 1 (BRCA1)-BRCA1 associated ring domain 1 (BARD1) complex, in this process. We found that BRCA1 is phosphorylated at S1524 by the kinases ATM and ATR during gene activation and that this event is essential for productive transcription. Our in vitro biochemical analyses showed TOP2B and BARD1 interaction and colocalization in the EGR1 transcription start site (TSS) and that the BRCA1-BARD1 complex ubiquitinates TOP2B, which appears to stabilize TOP2B protein in the cell and binding to DNA. Intriguingly, BRCA1 phosphorylation at S1524 controls this interaction. In addition, genomic analyses indicated colocalization between TOP2B and BRCA1 in a large number of protein-coding genes. Together, these findings reveal the novel function of the BRCA1-BARD1 complex in gene expression and in the regulation of TOP2B during Pol II transcription. Significance Statement Maintaining genomic integrity against cellular and extracellular genotoxic elements is essential for normal cell growth and function. Recent studies indicated that stimulus-induced transcription provokes topoisomerase IIβ-mediated DNA strand break and DNA damage response signaling, requiring DNA repair to be coupled with transcription. Here, we present a novel role for the BRCA1-BARD1 complex in regulating the transcription of serum-inducible genes and the stability of topoisomerase IIβ. The mechanism involving topoisomerase IIβ ubiquitination by the BRCA1-BARD1 complex and the phosphorylation of BRCA1 S1524 upon transcriptional activation appears to function as a switch to the reaction. Our findings provide the first evidence of functional interaction between the BRCA1-BARD1 complex and topoisomerase IIβ in transcription in humans.
Engineering clinically-approved drug gated CAR circuits

Chimeric antigen receptor (CAR) T cell immunotherapy has the potential to revolutionize cancer medicine. However, excessive CAR activation, lack of tumor-specific surface markers, and antigen escape have limited the safety and efficacy of CAR T cell therapy. A multi-antigen targeting CAR system that is regulated by safe, clinically-approved pharmaceutical agents is urgently needed, yet only a few simple systems have been developed, and even fewer have been evaluated for efficacy in vivo. Here, we present NASCAR (NS3 ASsociated CAR), a collection of induc-ible ON and OFF switch CAR circuits engineered with a NS3 protease domain deriving from the Hepatitis C Virus (HCV). We establish their ability to regulate CAR activity using multiple FDA-approved antiviral protease inhibitors, including grazoprevir (GZV), both in vitro and in a xenograft tumor model. In addition, we have engineered several dual-gated NASCAR circuits, consisting of an AND logic gate CAR, universal ON-OFF CAR, and a switchboard CAR. These engineered receptors enhance control over T cell activity and tumor-targeting specificity. Together, our com-prehensive set of multiplex drug-gated CAR circuits represent a dynamic, tunable, and clinically-ready set of modules for enhancing the safety of CAR T cell therapy.
Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine

Genetic analysis in zebrafish reveals conserved and novel aspects of nuclear receptor Fxr function and bile salt signaling. Bile salt synthesis, secretion into the intestinal lumen, and resorption in the ileum occur in all vertebrate classes. In mammals, bile salt composition is determined by host and microbial enzymes, affecting signaling through the bile salt–binding transcription factor farnesoid X receptor (Fxr). However, these processes in other vertebrate classes remain poorly understood. We show that key components of hepatic bile salt synthesis and ileal transport pathways are conserved and under control of Fxr in zebrafish. Zebrafish bile salts consist primarily of a C27 bile alcohol and a C24 bile acid that undergo multiple microbial modifications including bile acid deconjugation that augments Fxr activity. Using single-cell RNA sequencing, we provide a cellular atlas of the zebrafish intestinal epithelium and uncover roles for Fxr in transcriptional and differentiation programs in ileal and other cell types. These results establish zebrafish as a nonmammalian vertebrate model for studying bile salt metabolism and Fxr signaling.
Atypical mediofrontal theta oscillations underlying cognitive control in kindergarteners with autism spectrum disorder

Background Children with autism spectrum disorder (ASD) often exhibit deficits in cognitive control. Neuroimaging approaches have implicated disruptions to medio-frontal cortex (MFC) structure and function. However, prior work has not directly tested whether young children with ASD exhibit disruptions to task-related theta oscillations thought to arise from the MFC. Methods Forty-three children with ASD and 24 age- and gender-matched typically developing (TD) peers performed a child-friendly Go/No-go task while 64-channel electroencephalography (EEG) was recorded at kindergarten-entry. Time-frequency approaches were employed to assess the magnitude of mediofrontal theta oscillations immediately following error (vs. correct) responses (“early theta”), as well as later emerging theta oscillations (“late theta”). We tested whether error-related mediofrontal theta oscillations differed as a function of diagnosis (ASD/typical) and timing (early/late theta). Additionally, links to social and academic outcomes were tested. Results Overall, children showed increased theta power following error vs. correct responses. Compared to TD children, children with ASD exhibited a selective reduction in error-related mediofrontal theta power during the late theta time window. There were no significant group differences for early theta power. Moreover, reduced error-related theta power during the late, but not early, time window significantly predicted poorer academic and social skills. Conclusions Kindergarteners with ASD demonstrated a selective reduction in error-related mediofrontal theta power during a relatively late time window, which is consistent with impairments in specific cognitive processes that recruit top-down control. Targeting these particular cognitive control processes via intervention prior to school-entry may promote more successful functional outcomes for children with ASD.