bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the boundaries of
Campylobacter
species through large-scale phylogenetic and nucleotide identity analyses
Authors: Wu Ruochen , Payne Michael , Zhang Li , Lan Ruiting 
Published: March 2024

ABSTRACT

Campylobacter
species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the
Campylobacter
genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the
Campylobacter
genus core genome (500 loci) using publicly available
Campylobacter
complete genomes (
n
= 498) and constructed a core genome phylogeny using 2,193 publicly available
Campylobacter
genomes to examine inter-species diversity and species boundaries. Utilizing 8,440
Campylobacter
genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated
Campylobacter
species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had
in silico
DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool
Campylobacter
Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the
Campylobacter
genus and will facilitate the detection of novel species in the future.

IMPORTANCE

In recent years,
Campylobacter
has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the
Campylobacter
genus in public databases. Currently, a standardized
Campylobacter
species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the
Campylobacter
genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the
Campylobacter
species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed
Campylobacter
Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to
Campylobacter
genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus
Campylobacter
.
Characterization of clumpy adhesion of
Escherichia coli
to human cells and associated factors influencing antibiotic sensitivity
Authors: Khan Muhammad Moman , Sidorczuk Katarzyna , Becker Juliane , Aleksandrowicz Adrianna , Baraniewicz Karolina , Ludwig Christina , Ali Aamir , Kingsley Robert A. , Schierack Peter , Kolenda Rafał 
Published: March 2024

ABSTRACT

Escherichia coli
intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of
E. coli
strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic
E. coli,
with the
pilV
and
spnT
genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes,
flgH
,
ffp
,
pilV
,
spnT,
and
yggT,
affected motility, adhesion, or antibiotic stress. Δ
flgH
exhibited 80% decrease and Δ
yggT
depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. Δ
flgH
lost motility and was regenerated when complemented, whereas Δ
ffp
had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by Δ
ffp
and Δ
spnT
were more resistant and protected the bacteria, with Δ
spnT
showing the best clump formation in terms of ampicillin stress protection. Δ
yggT
had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics.

IMPORTANCE

The study explores a biofilm-like clumpy adhesion phenotype in
Escherichia coli,
along with various factors and implications for antibiotic susceptibility. The phenotype permitted the bacteria to survive the onslaught of high antibiotic concentrations. Profiles of the transcriptome and proteome allowed the differentiation between adhered bacteria in clumps and planktonic bacteria in the supernatant. The deletion mutants of genes differentially expressed between adhered and planktonic bacteria, i.e.,
flgH
,
ffp
,
pilV
,
spnT
, and
yggT,
and respective complementations in
trans
cemented their roles in multiple capacities.
ffp
, an uncharacterized gene, is involved in motility and resistance to ampicillin in a clumpy state. The work also affirms for the first time the role of the
yggT
gene in adhesion and its involvement in susceptibility against another aminoglycoside antibiotic, i.e., gentamicin. Overall, the study contributes to the mechanisms of biofilm-like adhesion phenotype and understanding of the antimicrobial therapy failures and infections of
E. coli
.
How do clinicians use post-COVID syndrome diagnosis? Analysis of clinical features in a Swedish COVID-19 cohort with 18 months’ follow-up: a national observational cohort and matched cohort study
Authors: Ollila Hanna M , Fonseca-Rodríguez Osvaldo , Caspersen Ida Henriette , Kalucza Sebastian , Normark Johan , Trogstad Lill , Magnus Per Minor , Rod Naja Hulvej , Ganna Andrea , Eriksson Marie , Fors Connolly Anne-Marie 
Published: March 2024

IntroductionSARS-CoV-2 infection causes acute COVID-19 and may result in post-COVID syndrome (PCS). We aimed to investigate how clinicians diagnose PCS and identify associated clinical and demographic characteristics.MethodsWe analysed multiregistry data of all SARS-CoV-2 test-positive individuals in Sweden (n=1 057 174) between 1 February 2020 and 25 May 2021. We described clinical characteristics that prompt PCS diagnosis in outpatient and inpatient settings. In total, there were 6389 individuals with a hospital inpatient or outpatient diagnosis for PCS. To understand symptomatology, we examined individuals diagnosed with PCS at least 3 months after COVID-19 onset (n=6389) and assessed factors associated with PCS diagnosis.ResultsMechanical ventilation correlated with PCS (OR 114.7, 95% CI 105.1 to 125.3) compared with no outpatient/inpatient contact during initial COVID-19. Dyspnoea (13.4%), malaise/fatigue (8%) and abnormal pulmonary diagnostic imaging findings (4.3%) were the most common features linked to PCS. We compared clinical features of PCS with matched controls (COVID-19 negative, n=23 795) and COVID-19 severity-matched patients (COVID-19 positive, n=25 556). Hypertension associated with PCS cohort (26.61%) than in COVID-19-negative (OR 17.16, 95% CI 15.23 to 19.3) and COVID-19-positive (OR 9.25, 95% CI 8.41 to 10.16) controls, although most individuals received this diagnosis before COVID-19. Dyspnoea was the second most common feature in the PCS cohort (17.2%), and new to the majority compared with COVID-19-negative (OR 54.16, 95% CI 42.86 to 68.45) and COVID-19-positive (OR 18.7, 95% CI 16.21 to 21.57) controls.ConclusionsOur findings highlight factors Swedish physicians associate with PCS.
Coulomb effect in hybrid double quantum dot-metal nanoparticle systems considering the wetting layer
Authors: Nasser Nour A. , Al-Khursan Amin H. 
Published: March 2024

AbstractMany body effects in the wetting layer (WL)-double quantum dot (DQD)-metal nanoparticle (MNP) structure have been studied by modeling the Coulomb scattering rates in this structure. The strong coupling between WL-DQD-MNPs was considered. An orthogonalized plane wave (OPW) is assumed between WL-QD transitions. The transition momenta are calculated accordingly to specify the normalized Rabi frequency on this structure, considering the strong coupling between the WL-DQD-MNP structures. This approach is important for realizing scattering rates, including in-and-out capture and relaxation rates, which are essential for specifying the type of structure used depending on the optimum value of the scattering time required to fit the application. The QD hole capture rate is the highest, and the hole capture times are the shortest. The relaxation times are less than the electron capture times by one order, while they are half of the hole capture times. The capture rates increase with increasing distance R between the DQDs and the MNP. High tunneling increases hole-capture rates and changes the relaxation rates, showing the importance of tunneling in controlling the scattering rates.
PACMMOD Volume 2 Issue 1: Editorial
Authors: Agrawal Divy , Meliou Alexandra , Sudarshan S. 
Published: March 2024

Welcome to Issue 1 of Volume 2 of the Proceedings of the ACM on Management of Data, which has papers from the third round of submissions to the SIGMOD research track.
Out of 230 submissions in this round, whose submission deadline was July 15, 2023, a total of 71 articles were accepted and are presented in this issue.
MWP: Multi-Window Parallel Evaluation of Regular Path Queries on Streaming Graphs
Authors: Zhang Siyuan , He Zhenying , Jing Yinan , Zhang Kai , Wang X. Sean 
Published: March 2024

A persistent Regular Path Query (RPQ) on a streaming graph is to continuously find every pair of vertices that are connected by a path in the graph within a sliding window, such that the edge label sequence of this path matches a given regular expression. The existing RPQ evaluation algorithm in the literature incrementally maintains a set of spanning-tree-like data structures to quickly form query results and to avoid reprocessing edges that are shared by multiple sliding windows. This approach allows parallel processing of the graph edges within a sliding window but requires a blocking expiration phase between sliding windows to remove the old edges. This blocking phase can significantly degrade the query performance, especially when the edges arrive quickly and the sliding windows overlap significantly.
This paper presents a new RPQ evaluation strategy called Multi-Window Parallel (MWP) method leveraging a new data structure called Timestamped Rooted Digraph (TRD). The novel idea is to incrementally maintain TRDs for the quick formulation of query results, like the aforementioned spanning trees, but simultaneously contain needed information for multiple sliding windows. MWP eliminates the forced blocking expiration phase. Only when memory runs low, a quick "dirty garbage collection" (DGC) process is done to remove some unneeded edges and nodes on TRDs, without incurring large costs. Extensive experiments on real graph datasets show that MWP significantly outperforms the existing algorithm in terms of throughput, tail latency, and scalability, and that DGC provides an effective solution for releasing memory with minimum impact.
Parallel Algorithms for Hierarchical Nucleus Decomposition
Authors: Shi Jessica , Dhulipala Laxman , Shun Julian 
Published: March 2024

Nucleus decompositions have been shown to be a useful tool for finding dense subgraphs. The coreness value of a clique represents its density based on the number of other cliques it is adjacent to. One useful output of nucleus decomposition is to generate a hierarchy among dense subgraphs at different resolutions. However, existing parallel algorithms for nucleus decomposition do not generate this hierarchy, and only compute the coreness values. This paper presents a scalable parallel algorithm for hierarchy construction, with practical optimizations, such as interleaving the coreness computation with hierarchy construction and using a concurrent union-find data structure in an innovative way to generate the hierarchy. We also introduce a parallel approximation algorithm for nucleus decomposition, which achieves much lower span in theory and better performance in practice. We prove strong theoretical bounds on the work and span (parallel time) of our algorithms.
On a 30-core machine with two-way hyper-threading, our parallel hierarchy construction algorithm achieves up to a 58.84x speedup over the state-of-the-art sequential hierarchy construction algorithm by Sariyuce et al. and up to a 30.96x self-relative parallel speedup. On the same machine, our approximation algorithm achieves a 3.3x speedup over our exact algorithm, while generating coreness estimates with a multiplicative error of 1.33x on average.
On The Reasonable Effectiveness of Relational Diagrams: Explaining Relational Query Patterns and the Pattern Expressiveness of Relational Languages
Authors: Gatterbauer Wolfgang , Dunne Cody 
Published: March 2024

Comparing relational languages by their logical expressiveness is well understood. Less well understood is how to compare relational languages by their ability to represent relational query patterns. Indeed, what are query patterns other than "a certain way of writing a query"? And how can query patterns be defined across procedural and declarative languages, irrespective of their syntax? To the best of our knowledge, we provide the first semantic definition of relational query patterns by using a variant of structure-preserving mappings between the relational tables of queries. This formalism allows us to analyze the relative pattern expressiveness of relational language fragments and create a hierarchy of languages with equal logical expressiveness yet different pattern expressiveness. Notably, for the non-disjunctive language fragment, we show that relational calculus can express a larger class of patterns than the basic operators of relational algebra.
Our language-independent definition of query patterns opens novel paths for assisting database users. For example, these patterns could be leveraged to create visual query representations that faithfully represent query patterns, speed up interpretation, and provide visual feedback during query editing. As a concrete example, we propose Relational Diagrams, a complete and sound diagrammatic representation of safe relational calculus that is provably (i) unambiguous, (ii) relationally complete, and (iii) able to represent all query patterns for unions of non-disjunctive queries. Among all diagrammatic representations for relational queries that we are aware of, ours is the only one with these three properties. Furthermore, our anonymously preregistered user study shows that Relational Diagrams allow users to recognize patterns meaningfully faster and more accurately than SQL.
WeBridge: Synthesizing Stored Procedures for Large-Scale Real-World Web Applications
Authors: Hu Gansen , Wang Zhaoguo , Tang Chuzhe , Shen Jiahuan , Dong Zhiyuan , Yao Sheng , Chen Haibo 
Published: March 2024

Modern web applications use databases to store their data. When processing user requests, these applications retrieve and store data in the database server, which incurs network round trips. These round trips significantly increase the application's latency. Previous approaches have attempted to reduce these round trips by prefetching query results or batching database accesses. However, neither method can efficiently reduce the latency when some queries depend on previous queries' results. In real-world applications, nearly 50% of the queries depend on the result of other queries.
This paper presents WeBridge, the first system capable of synthesizing stored procedures for large-scale real-world web applications. First, WeBridge employs concolic execution technique to analyze the applications and generate stored procedures for hot program paths. Then, it seamlessly integrates the stored procedures into the application by extending the database access library. Finally, it improves the efficiency of the stored procedures with speculative execution. Evaluation using real-world web applications and workloads show that WeBridge achieves up to 79.8% median latency reduction and up to 2× peak throughput.
Syntax-aware Offensive Content Detection in Low-resourced Code-mixed Languages with Continual Pre-training
Authors: Bölücü Necva , Canbay Pelin 
Published: March 2024

Social media is a widely used platform that includes a vast amount of user-generated content, allowing the extraction of information about users’ thoughts from texts. Individuals freely express their thoughts on these platforms, often without constraints, even if the content is offensive or contains hate speech. The identification and removal of offensive content from social media are imperative to prevent individuals or groups from becoming targets of harmful language. Despite extensive research on offensive content detection, addressing this challenge in code-mixed languages remains unsolved, characterised by issues such as imbalanced datasets and limited data sources. Most previous studies on detecting offensive content in these languages focus on creating datasets and applying deep neural networks, such as Recurrent Neural Networks (RNNs), or pre-trained language models (PLMs) such as BERT and its variations. Given the low-resource nature and imbalanced dataset issues inherent in these languages, this study delves into the efficacy of the syntax-aware BERT model with continual pre-training for the accurate identification of offensive content and proposes a framework called Cont-Syntax-BERT by combining continual learning with continual pre-training. Comprehensive experimental results demonstrate that the proposed Cont-Syntax-BERT framework outperforms state-of-the-art approaches. Notably, this framework addresses the challenges posed by code-mixed languages, as evidenced by its proficiency on the DravidianCodeMix [10,19] and HASOC 2109 [37] datasets. These results demonstrate the adaptability of the proposed framework in effectively addressing the challenges of code-mixed languages.
Fenretinide in Young Women at Genetic or Familial Risk of Breast Cancer: A Placebo-Controlled Biomarker Trial
Authors: Aristarco Valentina , Serrano Davide , Maisonneuve Patrick , Guerrieri-Gonzaga Aliana , Lazzeroni Matteo , Feroce Irene , Macis Debora , Cavadini Elena , Albertazzi Elena , Jemos Costantino , Omodeo Salè Emanuela , Cortesi Laura , Massarut Samuele , Gulisano Marcella , Daidone Maria Grazia , Johansson Harriet , Bonanni Bernardo 
Published: March 2024

Abstract

Fenretinide, a retinoid with a low-toxicity profile that accumulates in the breast, has been shown to prevent second breast cancer in young women. Fenretinide exhibits apoptotic and antiinvasive properties and it improves insulin sensitivity in overweight premenopausal women with insulin resistance. This study aimed to further characterize its role in cancer prevention by measuring circulating biomarkers related to insulin sensitivity and breast cancer risk.
Sixty-two women, ages 20 to 46 years, healthy or who had already undergone breast cancer surgery, with a known BRCA1/2 mutation or a likelihood of mutation ≥20% according to the BRCAPRO model, were randomly assigned to receive fenretinide (200 mg/day) or placebo for 5 years (trial registration: EudraCT No. 2009–010260–41). Fasting blood samples were drawn at baseline, 12 and 36 months, and the following biomarkers were analyzed: retinol, leptin, adiponectin, retinol-binding protein 4 (RBP-4), total cholesterol, high-density lipoprotein (HDL) and low-density lipoprotein (LDL) cholesterol, triglycerides, glucose, insulin, insulin-like growth factor (IGF-1), IGF-binding protein 3, sex hormone binding globulin (SHBG), testosterone, and vascular endothelial growth factor (VEGF).
After 12 months of treatment, we observed a favorable effect of fenretinide on glucose (decrease; P = 0.005), insulin (decrease; P = 0.03), homeostatic model assessment index (decrease; P = 0.004), HDL cholesterol (increase; P = 0.002), even though these effects were less prominent after 36 months. Retinol and retinol-binding protein 4 markedly decreased (P &lt; 0.0001) throughout the study. None of the other measured biomarkers changed.

Prevention Relevance:
Fenretinide exhibits beneficial effects on the metabolic profile, supporting its clinical use in breast cancer prevention especially in premenopausal women with a positive family history and pathogenic variants in BRCA1/2 genes. This finding requires further investigations in larger trials to confirm its role in breast cancer prevention.
Species distribution modelling of Baya Weaver Ploceus philippinus in Nagaon District of Assam, India: a zoogeographical analysis
Authors: Kalita Nilotpal , Bora Neeraj , Choudhury Sandip , Sahariah Dhrubajyoti 
Published: March 2024

Identification and mapping of the spatial distribution of species is an important aspect of zoogeographical enquiry. The habitats of many species are facing the threat of depletion in increasingly human-influenced environments. This has already led to the extinction of many species in different localities, making understanding the linkages between anthropogenic threats and species distribution of utmost importance. A GIS-based model was applied to gain an overall picture of the potential distribution of Ploceus philippinus (Baya Weaver) in and around Nagaon District in Assam. The used maxent model in the GIS environment gives a highly significant Area Under Curve (AUC) validation statistic of 0.99. Out of the total area of 3,975 km2, 596.86 km2 (15%) is demarcated as a high-potential area. Such predictions are highly useful in assisting in the conservation of threatened species under current and future climatic conditions.