High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition

Previous studies showed that high concentration of particulate matter (PM) 2.5 and PM10 carried a large number of bacterial and archaeal species, including pathogens and opportunistic pathogens. In this study, pharyngeal swabs from 83 subjects working in an open air farmer’s market were sampled before and after exposure to smog with PM2.5 and PM10 levels up to 200 and 300 μg/m3, respectively. Their microbiota were investigated using high-throughput sequencing targeting the V3–V4 regions of the 16S rRNA gene. The genus level phylotypes was increased from 649 to 767 in the post-smog pharyngeal microbiota, of which 142 were new and detected only in the post-smog microbiota. The 142 new genera were traced to sources such as soil, marine, feces, sewage sludge, freshwater, hot springs, and saline lakes. The abundance of the genera Streptococcus, Haemophilus, Moraxella, and Staphylococcus increased in the post-smog pharyngeal microbiota. All six alpha diversity indices and principal component analysis showed that the taxonomic composition of the post-smog pharyngeal microbiota was significantly different to that of the pre-smog pharyngeal microbiota. Redundancy analysis showed that the influences of PM2.5/PM10 exposure and smoking on the taxonomic composition of the pharyngeal microbiota were statistically significant (p < 0.001). Two days of exposure to high concentrations of PM2.5/PM10 changed the pharyngeal microbiota profiles, which may lead to an increase in respiratory diseases. Wearing masks could reduce the effect of high-level PM2.5/PM10 exposure on the pharyngeal microbiota

Jais and Jais-chat: Arabic-Centric Foundation and Instruction-Tuned Open Generative Large Language Models

We introduce Jais and Jais-chat, new state-of-the-art Arabic-centric foundation and instruction-tuned open generative large language models (LLMs). The models are based on the GPT-3 decoder-only architecture and are pretrained on a mixture of Arabic and English texts, including source code in various programming languages. With 13 billion parameters, they demonstrate better knowledge and reasoning capabilities in Arabic than any existing open Arabic and multilingual models by a sizable margin, based on extensive evaluation. Moreover, the models are competitive in English compared to English-centric open models of similar size, despite being trained on much less English data. We provide a detailed description of the training, the tuning, the safety alignment, and the evaluation of the models. We release two open versions of the model -- the foundation Jais model, and an instruction-tuned Jais-chat variant -- with the aim of promoting research on Arabic LLMs. Available at https://huggingface.co/inception-mbzuai/jais-13b-chatComment: Arabic-centric, foundation model, large-language model, LLM, generative model, instruction-tuned, Jais, Jais-cha

The molecular aspects of RecQ helicase family

Dans les cellules, le déroulement de l ADN double-brin est catalysé par une famille de protéines appelées hélicases. Ces protéines sont présentes chez tous les organismes des virus jusqu à l'homme. Parmi ces hélicases, celles de la famille RecQ jouent un rôle essentiel dans le métabolisme de l ADN en facilitant de nombreux processus cellulaires tels que la réplication, la réparation, la recombinaison, la transcription et la maintenance des télomères. Chez l'homme, il existe cinq membres de la famille RecQ identifiés comme RECQ1, BLM, WRN, RECQ4 et RECQ5. Les mutations dans BLM, WRN et RECQ4 sont associées à une prédisposition au cancer. En plus du domaine hélicase très conservé et contenant sept motifs bien distincts, la plupart des hélicases de la famille RecQ possèdent également un domaine RecQ C-terminal (RecQ-Ct) et un domaine hélicase RNase D (HRDC). Au cours de ce travail, nous nous concentrons sur les mécanismes intrafonctionnels de certains membres de la famille RecQ des hélicases. Tout d'abord, nous avons utilisé deux isoformes naturels de l hélicase RECQ5 humain comme modèle pour étudier la modulation fonctionnelle du domaine hélicase avec le doigt de zinc. Ici, nous montrons que la variante tronquée RECQ5a de l hélicase RECQ5b issue d un épissage alternatif et composée uniquement du domaine hélicase ne possède ni l activité ATPase ni l activité de déroulement de l ADN. A l inverse, et ce de matière étonnante, cette protéine est dotée d une forte activité de réhybridation du brin déroulé. Les mesures quantitatives indiquent que l amélioration de l affinité de la protéine pour l ADN que lui confère le doigt de zinc est à l origine de ses activités ATPase et hélicase. Le plus important est que l on constate que le doigt de zinc est capable d'agir comme un facteur moléculaire à même de supprimer l'activité de re-synthèse du brin déroulé par le domaine hélicase et de déclencher l activité de déroulement d'ADN à travers une modulation de la fixation à l ADN. Ensuite, nous avons analysé les propriétés biochimiques de deux isoformes de l hélicase RecQ de Bacillus subtilis : SubL et SubS. Parmi elles, SubS ne dispose pas du domaine HRDC. Nos études montrent que le domaine HRDC est crucial pour Bacillus subtilis RecQ hélicases dans la résolution des intermédiaires de réplication et / ou de réparation de l'ADN tels que les jonctions de Holliday et la jonction de kappa. Les activités ATPase, hélicase et l'activité de rehybridation du brin déroulé sont plus importantes en présence du domaine HRDC. Ces résultats nous permettent de spéculer sur l'importance du domaine HRDC des activités de la famille de RecQ hélicase. Nous avons découvert que dans la famille RecQ, le 12 domaine HRDC peut augmenter les activités ATPases et hélicases. De manière intéressante, le domaine HRDC de Bacillus subtilis joue un rôle critique dans la résolution des intermédiaires de réplication ou de réparation de l'ADN et des jonctions de Holliday. Nous suggérons l'hypothèse que le domaine HRDC des hélicases RecQ participe à exposer leurs fonctions dans le processus de réparation de l'ADN. Dans la dernière partie, nous nous sommes intéressés à l'existence et au rôle du doigt d'arginine dans la protéine BLM. Ces études ont été menées afin de démontrer son rôle dans l'hydrolyse d'ATP et dans la conversion en mouvement mécanique permettant à la protéine de progresser le long de l ADN. Nos études démontrent que le résidu R982, situé à proximité du g-phosphate de l'ATP, fonctionne comme un doigt d arginine dans la protéine BLM. Nos conclusions indiquent en outre que ce doigt d arginine interagit avec d'autres motifs conservés situés autour du g-phosphate des nucléotides et qu ils effectuent ensemble les fonctions enzymatiques au sein d un réseau complexe.In the cells, the unwinding of double-stranded polynucleotides is catalyzed by helicases that exist in all kingdoms of life from virus to human. RecQ family helicases play essential roles in nucleic acid metabolism by facilitating cellular processes including genome replication, DNA repair, recombination, transcription and telomere maintenance. In human, five RecQ family members named RECQ1, BLM, WRN, RECQ4 and RECQ5, have been identified. Defects in BLM, WRN and RECQ4 will give rise to autosomal recessive disorders and predisposition to cancer. In addition to the highly conserved helicase core domain containing seven helicase motifs, most RecQ family helicases have a unique RecQ C-terminal domain (RecQ-Ct) and the Helicase RNase D conserved domain (HRDC). In the present studies, we focus on the intra-functional mechanisms of some important members of RecQ family helicases. Firstly, we have chosen two natural isoforms of human RECQ5 helicase as models to study the functional modulation of the helicase core domain by the zinc-binding domain. Here we show that a truncated variant of the human RECQ5b helicase comprised of the conserved helicase domain only, a splice variant named RECQ5a, possesses neither ATPase nor DNA unwinding activities, but surprisingly displays a strong strand annealing activity. Quantitative measurements indicate that the regulatory role of the zinc-binding motif of RECQ5b is achieved by enhancing the DNA binding affinity of the helicase. More important, the zinc-binding motif of RECQ5b is found to act as a molecular switch that suppresses the strand-annealing activity of the helicase domain and triggers DNAunwinding activity of the enzyme through enhancing DNA binding. Subsequently, we analyzed the biochemical properties of two isoforms of Bacillus subtilis RecQ helicases: SubL and SubS. Between them, SubS naturally lacks the HRDC domain. Our studies demonstrate that the HRDC domain is crucial in Bacillus subtilis RecQ helicases in unwinding of DNA replication/repair intermediates such as Holliday junction and kappa junction. The enzyme with HRDC domain shows stronger ATPase activity and DNA unwinding and annealing activities than the other one. These results allow us to speculate on the importance of HRDC domain in the basic activities of RecQ family helicases. In the last part, we investigated the existence and role of the arginine finger in the Bloom syndrome protein (BLM) in ATP hydrolysis and energy coupling. Our studies demonstrate that R982 is the residue located near the g-phosphate of ATP which functions as a BLM 14 arginine finger. Our finding further indicates that the arginine finger interacts with other conserved motifs around g-phosphate of the nucleotide to carry out the functions as a complex network.CACHAN-ENS (940162301) / SudocSudocFranceF

Precomputing architecture for flexible and efficient big data analytics

Abstract The rising of big data brings revolutionary changes to many aspects of our lives. Huge volume of data, along with its complexity poses big challenges to data analytic applications. Techniques proposed in data warehousing and online analytical processing, such as precomputed multidimensional cubes, dramatically improve the response time of analytic queries based on relational databases. There are some recent works extending similar concepts into NoSQL such as constructing cubes from NoSQL stores and converting existing cubes into NoSQL stores. However, only limited attention in literature have been devoted to precomputing structure within the NoSQL databases. In this paper, we present an architecture for answering temporal analytic queries over big data by precomputing the results of granulated chunks of collections which are decomposed from the original large collection. In extensive experimental evaluations on drill-down and roll-up temporal queries over large amount of data we demonstrated the effectiveness and efficiency under different settings

Dependency graph for short text extraction and summarization

A sheer amount of text generated from microblogs and social media brings huge opportunities to the text mining applications. Many techniques such as sentiment analysis and opinion mining are proven effective to deliver insights from documents. However, most of these textual data are in the form of short and fragmented texts which are difficult to visually extract due to the sparsity issue and the context in the content is often unknown. Naive while widely used models, term frequency and the bag-of-words never considered the semantic relationship between the words, making the results relatively difficult to interpret. A well-known technique in text mining like topic model may provide a general ‘at glance’ understanding but can be difficult to interpret or to understand. One alternative is to aggregate words in a semantical order and generates an output of human-understandable sentences. In this paper, we address this direction by proposing the belief graph data model that joins short texts by inducing the part-of-speech tagging to maintain the order and to preserve the context of the content. Extensive experiments showed that our approach improves the overall qualitative evaluation of text understanding compared to the previous state of the art text mining techniques

Design and implementation of multi-grooved simultaneous separation and screening equipment

The separating and screening of cylindrical parts are always difficult in the assembly industry, and the previous devices have the weakness of low working efficiency, low accuracy, and low automaticity. Based on the theoretical analysis, modelling and simulation, a theory of simultaneous separation and equidistant screening is proposed, and the corresponding equipment is established with the core modules of the multi-grooved cylindrical cam mechanism, pneumatic system, sensing, and controlling system. Solidworks software is used for three-dimensional modelling and kinematic simulation, which verify the correctness of the equipment design

Fast and Robust Distributed Subgraph Enumeration

We study the subgraph enumeration problem under distributed settings. Existing solutions either suffer from severe memory crisis or rely on large indexes, which makes them impractical for very large graphs. Most of them follow a synchronous model where the performance is often bottlenecked by the machine with the worst performance. Motivated by this, in this paper, we propose RADS, a Robust Asynchronous Distributed Subgraph enumeration system. RADS first identifies results that can be found using singlemachine algorithms. This strategy not only improves the overall performance but also reduces network communication and memory cost. Moreover, RADS employs a novel region-grouped multi-round expand verify & filter framework which does not need to shuffle and exchange the intermediate results, nor does it need to replicate a large part of the data graph in each machine. This feature not only reduces network communication cost and memory usage, but also allows us to adopt simple strategies for memory control and load balancing, making it more robust. Several optimization strategies are also used in RADS to further improve the performance. Our experiments verified the superiority of RADS to state-of-the-art subgraph enumeration approaches.1

Ferromagnetic Property and Synthesis of Onion-Like Fullerenes by Chemical Vapor Deposition Using Fe and Co Catalysts Supported on NaCl

Metal-encapsulating onion-like fullerenes (M@OLFs) were synthesized by CVD at relatively low temperature (420C∘) using Fe and Co nanoparticles impregnated into NaCl as catalyst. The morphology and structure of the products were characterized by field emission scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, and Raman spectroscopy. The results show that Fe@OLFs and Co@OLFs with stacked graphitic fragments were prepared using Fe/NaCl or Co/NaCl as catalysts; after Co@OLFs were immersed in concentrated HCl for 48 hours, Co nanoparticles encapsulated by carbon shells were not removed, meaning that carbon shells can protect the encapsulated Co cores against environmental degradation. The coercivity value (750.23 Oe) of Co@OLFs showed an obvious magnetic property

Orthogonal Regression Based Multihop Localization Algorithm for Large-Scale Underwater Wireless Sensor Networks

For large-scale underwater wireless sensor networks (UWSNs) with a minority of anchor nodes, multihop localization is a popular scheme for determining the geographical positions of normal nodes. However, existing multihop localization studies have considered the anchor positions to be free of errors, which is not a valid assumption in practice. In this paper, the problems existing in nonlinear least square-based node self-localization schemes are analyzed, and the biased distribution characteristic of multihop distance estimation errors is pointed out. Then, the orthogonal regression method is employed for the localization of normal nodes in the presence of anchor position errors. In particular, the influences of errors in independent variables and biases in dependent variables on node coordinate estimation are taken into account simultaneously. Extensive simulation results illustrate the robustness and effectiveness of our method

Study on the Water Quality Characteristics of the Baoan Lake Basin in China under Different Land Use and Landscape Pattern Distributions

Land use and landscape pattern highly affect water quality. Their relationship can assist in land-use management and improve land-use efficiency. In this study, a water quality survey of rivers and lakes was performed in 2020 to analyze the effects of land use and the landscape pattern on the water quality of the rivers and lakes in the Baoan Lake basin and is expected to provide a reference for land use planning. The results demonstrated that the effects of land use on water quality were generally higher during the dry season than during the wet season; however, the opposite was demonstrated for the landscape pattern index. Cropland and urban land were closely correlated with deteriorating water quality, with contributions to total nitrogen, total phosphorous, and ammonia nitrogen in the basin. The impact of the landscape pattern of the basin on water quality was controlled by the original land-use type. In addition, the landscape configuration formed different land-use types to produce different effects on water quality. The basin scale better explained the changes in water quality, especially for construction land, followed by the 250 m and 500 m scales in the buffer zone