bluuebunny/crossref_metadata_2025 huggingface dataset:
Global assembly of microbial communities
Authors: Wang Jianing , Pan Zhuo , Yu Jianshui , Zhang Zheng , Li Yue-zhong
Published: May 2023

Different habitats harbor different microbial communities with elusive assembly mechanisms. This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. We found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, and, specifically, deterministic processes generally play a major role in free-living and plant-associated (but not plant corpus) environments, while stochastic processes are the major contributor in animal-associated environments. In contrast with the assembly of microorganisms, the assembly of functional genes, predicted from PICRUSt, is mainly attributed to deterministic processes in all microbial communities. The sink and source microbial communities are normally assembled using similar mechanisms, and the core microorganisms are specific to different environment types. On a global scale, deterministic processes are positively related to the community alpha diversity, microbial interaction degree and bacterial predatory-specific gene abundance. Our analysis provides a panoramic picture and regularities of global and environment-typical microbial community assemblies.

IMPORTANCE

With the development of sequencing technologies, the research topic of microbial ecology has evolved from the analysis of community composition to community assembly, including the relative contribution of deterministic and stochastic processes for the formation and maintenance of community diversity. Many studies have reported the microbial assembly mechanisms in various habitats, but the assembly regularities of global microbial communities remain unknown. In this study, we analyzed the EMP data set using a combined pipeline to explore the assembly mechanisms of global microbial communities, microbial sources to construct communities, core microbes in different environment types, and community-internal factors influencing assembly. The results provide a panoramic picture and rules of global and environment-typical microbial community assemblies, which enhances our understandings of the mechanisms globally controlling community diversity and species coexistence.
In Vivo
Genome-Wide Gene Expression Profiling Reveals That
Haemophilus influenzae
Purine Synthesis Pathway Benefits Its Infectivity within the Airways
Authors: Euba Begoña , Gil-Campillo Celia , Asensio-López Javier , López-López Nahikari , Sen-Kilic Emel , Díez-Martínez Roberto , Burgui Saioa , Barbier Mariette , Garmendia Junkal
Published: May 2023

In vivo
-omic strategies offer great opportunities for increased understanding of host-pathogen interplay and for identification of therapeutic targets. Here, using transcriptome sequencing, we profiled host and pathogen gene expression during
H. influenzae
infection within the murine airways.
Clinical Significance of a 16S-rDNA Analysis of Heart Valves in Patients with Infective Endocarditis: a Retrospective Study
Authors: Johansson Gustav , Sunnerhagen Torgny , Ragnarsson Sigurdur , Rasmussen Magnus
Published: May 2023

This work demonstrates that it can be of importance to perform both cultures and analysis using 16S-rDNA PCR and sequencing of valves excised from patients undergoing surgery for infective endocarditis. 16S-analysis may help both to establish a microbiological etiology in cases of blood culture negative endocarditis and to provide help in situations where there are discrepancies between valve and blood cultures. In addition, our results show a high degree of concordance between blood cultures and 16S-analyses, indicating that the latter has a high sensitivity and specificity for the etiological diagnosis of endocarditis in patients who were subjected to heart valve surgery.
Synergistic Interactions among
Burkholderia cepacia
Complex-Targeting Phages Reveal a Novel Therapeutic Role for Lysogenization-Capable Phages
Authors: Lauman Philip , Dennis Jonathan J.
Published: May 2023

The spread of antimicrobial resistance is an imminent threat to public health around the world. Particularly concerning are species of the
Burkholderia cepacia
complex (Bcc), which cause life-threatening respiratory infections and are notoriously resistant to antibiotics.
The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria
Authors: Morales Grace , Abelson Benjamin , Reasoner Seth , Miller Jordan , Earl Ashlee M. , Hadjifrangiskou Maria , Schmitz Jonathan
Published: May 2023

Escherichia coli
is the most common etiological agent of urinary tract infections (UTIs), with UTI-associated strains designated “uropathogenic”
E. coli
or UPEC. Across urinary strains of
E. coli
, the global landscape of MGEs and its relationship to virulence factor carriage and clinical symptomatology require greater clarity.
White Collar 1 Modulates Oxidative Sensitivity and Virulence by Regulating the HOG1 Pathway in Fusarium asiaticum
Authors: Tang Ying , Tang Yan , Ren Dandan , Wang Congcong , Qu Yao , Huang Li , Xue Yongjun , Jiang Yina , Wang Yiwen , Xu Ling , Zhu Pinkuan
Published: May 2023

The well-conserved fungal blue-light receptor White Collar complex (WCC) is known to regulate virulence of several pathogenic species for either plant or human hosts, but how WCC determines fungal pathogenicity remains largely unknown. The WCC component FaWC1 in the cereal pathogen
Fusarium asiaticum
was previously found to be required for full virulence.
Mapping the available evidence on the impact of ingested live microbes on health: a scoping review protocol
Authors: Mukherjee Arghya , Iyer Ajay , Gómez-Sala Beatriz , O’Connor Eibhlis , Kenny John G , Cotter Paul D
Published: May 2023

Introduction

It has been hypothesised that the regular consumption of safe, live microbes confers health-promoting attributes, including the prevention of disease. To address this hypothesis, we propose a scoping review approach that will systematically assess the large corpus of relevant literature that is now available on this research topic. This article outlines a protocol for a scoping review of published studies on interventions with live microbes in non-patient populations across eight health categories. The scoping review aims to catalogue types of interventions, measured outcomes, dosages, effectiveness, as well as current research gaps.

Methods and analysis

The scoping review will follow the six-staged protocol as proposed by Arksey and O’Malley and will include the following stages: defining the research questions (stage 1); defining the eligibility criteria and finalising search strategy (stage 2); selection of studies based on the eligibility criteria (stage 3); development of a data extraction framework and charting of data (stage 4); aggregation of results and summarisation of findings (stage 5); and the optional consultation with stakeholders (stage 6), which will not be performed.

Ethics and dissemination

Since the scoping review synthesises information from existing literature, no separate ethical approval is required. The findings of the scoping review will be communicated for publication to an open-access, peer-reviewed scientific journal, presented at relevant conferences, and disseminated at future workshops with all relevant data and documents being available online through the Open Science Framework (https://osf.io/kvhe7).
Experiences of patients and their relatives of postoperative radiological surveillance and surveillance intensity following primary resection of a soft tissue sarcoma and its impact on their quality of life: a systematic review protocol
Authors: Maes Danielle , McMullan Christel , Ford Samuel J , Wilson Roger , Oppong Raymond , Aiyegbusi Olalekan Lee
Published: May 2023

Introduction

Postoperative radiological surveillance following primary resection of a soft tissue sarcoma (sarcoma of the retroperitoneum, abdomen, pelvis, trunk or extremities) is standard of care in all international high-volume sarcoma centres in the world. The intensity of postoperative surveillance imaging is highly varied and knowledge of the impact of surveillance and surveillance intensity on patients’ quality of life is limited. The aim of this systematic review is to summarise the experiences of patients and their relatives/caregivers of postoperative radiological surveillance following resection of a primary soft tissue sarcoma and its impact on their quality of life.

Methods and analysis

We will systematically search MEDLINE, EMBASE, PsycINFO, CINAHL Plus and Epistemonikos. Hand searching of reference lists of included studies will be conducted. Further searches will be performed via Google Scholar, to reveal further studies within unpublished ‘grey’ literature. Two reviewers will independently screen the titles and abstracts following the eligibility criteria. After retrieval of the full text of the selected studies, the methodological quality will be appraised using the Joanna Briggs Institute Critical Appraisal Checklist for Qualitative Research and the Center for Evidence-Based Management checklist for Critical Appraisal of a Cross-Sectional Study. Data on the study population, relevant themes and conclusions will be extracted from the selected papers, and a narrative synthesis will be conducted.

Ethics and dissemination

The systematic review does not require ethics approval. The findings of the proposed work will be published in a peer-reviewed journal and disseminated widely to patients, clinicians and allied health professionals through the Sarcoma UK website, the Sarcoma Patient Advocacy Global Network and the Trans-Atlantic Australasian Retroperitoneal Sarcoma Working Group. In addition, the outcomes of this research will be presented at national and international conferences.

PROSPERO registration number

CRD42022375118.
Cohort profile: a longitudinal study of HIV infection in the central nervous system with focus on cerebrospinal fluid – the Gothenburg HIV CSF Study Cohort
Authors: Hagberg Lars , Gisslén Magnus
Published: May 2023

Purpose

In order to enable long-term follow-up of the natural course of HIV infection in the central nervous system, a longitudinal cohort study with repeated cerebrospinal fluid (CSF) analyses at intervals over time was initiated in 1985. When antiretrovirals against HIV were introduced in the late 1980s, short-term and long-term effects of various antiretroviral treatment (ART) regimens were added to the study.

Participants

All adult people living with HIV (PLWH) who were diagnosed at or referred to the Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden were asked to participate in the Gothenburg HIV CSF Study Cohort. PLWH with neurological symptoms or other clinical symptoms of HIV, as well as those with no symptoms of HIV infection, were included. Most participants were asymptomatic, which distinguishes this cohort from most other international HIV CSF studies. In addition, HIV-negative controls were recruited. These included people on HIV pre-exposure prophylaxis who served as lifestyle-matched controls to HIV-infected men who have sex with men. Since lumbar puncture (LP) is an invasive procedure, some PLHW only consented to participate in one examination. Furthermore, at the beginning of the study, several participants were lost to follow-up having died from AIDS. Of 662 PLWH where an initial LP was done, 415 agreed to continue with follow-up. Among the 415, 56 only gave permission to be followed with LP for less than 1 year, mainly to analyse the short-term effect of ART. The remaining 359 PLWH were followed up with repeated LP for periods ranging from >1 to 30 years. This group was defined as the ‘longitudinal cohort’. So far, on 7 April 2022, 2650 LP and samplings of paired CSF/blood had been performed, providing a unique biobank.

Findings to date

A general finding during the 37-year study period was that HIV infection in the central nervous system, as mirrored by CSF findings, appears early in the infectious course of the disease and progresses slowly in the vast majority of untreated PLWH. Combination ART has been highly effective in reducing CSF viral counts, inflammation and markers of neural damage. Minor CSF signs of long-term sequels or residual inflammatory activity and CSF escape (viral CSF blips) have been observed during follow-up. The future course of these changes and their clinical impact require further studies.

Future plans

PLWH today have a life expectancy close to that of non-infected people. Therefore, our cohort provides a unique opportunity to study the long-term effects of HIV infection in the central nervous system and the impact of ART and is an ongoing study.
ADAMS project: a genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis based in the UK
Authors: Jacobs Benjamin M , Schalk Luisa , Dunne Angie , Scalfari Antonio , Nandoskar Ashwini , Gran Bruno , Mein Charles A , Sellers Charlotte , Spilker Cord , Rog David , Visentin Elisa , Bezzina Elizabeth Lindsey , Uzochukwu Emeka , Tallantyre Emma , Wozniak Eva , Sacre Eve , Hassan-Smith Ghaniah , Ford Helen L , Harris Jade , Bradley Joan , Breedon Joshua , Brooke Judith , Kreft Karim L , Tuite Dalton Katherine , George Katila , Papachatzaki Maria , O'Malley Martin , Peter Michelle , Mattoscio Miriam , Rhule Neisha , Evangelou Nikos , Vinod Nimisha , Quinn Outi , Shamji Ramya , Kaimal Rashmi , Boulton Rebecca , Tanveer Riffat , Middleton Rod , Murray Roxanne , Bellfield Ruth , Hoque Sadid , Patel Shakeelah , Raj Sonia , Gumus Stephanie , Mitchell Stephanie , Sawcer Stephen , Arun Tarunya , Pogreban Tatiana , Brown Terri-Louise , Begum Thamanna , Antoine Veronica , Rashid Waqar , Noyce Alastair J , Silber Eli , Morris Huw , Giovannoni Gavin , Dobson Ruth
Published: May 2023

Purpose

Genetic studies of multiple sclerosis (MS) susceptibility and severity have focused on populations of European ancestry. Studying MS genetics in other ancestral groups is necessary to determine the generalisability of these findings. The genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis (ADAMS) project aims to gather genetic and phenotypic data on a large cohort of ancestrally-diverse individuals with MS living in the UK.

Participants

Adults with self-reported MS from diverse ancestral backgrounds. Recruitment is via clinical sites, online (https://app.mantal.co.uk/adams) or the UK MS Register. We are collecting demographic and phenotypic data using a baseline questionnaire and subsequent healthcare record linkage. We are collecting DNA from participants using saliva kits (Oragene-600) and genotyping using the Illumina Global Screening Array V.3.

Findings to date

As of 3 January 2023, we have recruited 682 participants (n=446 online, n=55 via sites, n=181 via the UK MS Register). Of this initial cohort, 71.2% of participants are female, with a median age of 44.9 years at recruitment. Over 60% of the cohort are non-white British, with 23.5% identifying as Asian or Asian British, 16.2% as Black, African, Caribbean or Black British and 20.9% identifying as having mixed or other backgrounds. The median age at first symptom is 28 years, and median age at diagnosis is 32 years. 76.8% have relapsing–remitting MS, and 13.5% have secondary progressive MS.

Future plans

Recruitment will continue over the next 10 years. Genotyping and genetic data quality control are ongoing. Within the next 3 years, we aim to perform initial genetic analyses of susceptibility and severity with a view to replicating the findings from European-ancestry studies. In the long term, genetic data will be combined with other datasets to further cross-ancestry genetic discoveries.
Epidemiological characteristics of pulmonary tuberculosis among students in Guizhou, China: a retrospective study from 2010 to 2020
Authors: Zhou Jian , Ma Xiaoxue , Lu Ting-Jia , Zhuang Yan , Li Jin-Lan , Chen Huijuan
Published: May 2023

Objective

We described epidemiological characteristics of pulmonary tuberculosis (PTB) among students and evaluated susceptible populations and areas in Guizhou province and also to provide scientific suggestions for prevention and control.

Setting

Guizhou, China.

Design

This is a retrospective epidemiological study on PTB in students.

Methods

Data are from the China Information System for Disease Control and Prevention. We collected all PTB cases among the student population from 2010 to 2020 in Guizhou. Incidence, composition ratio and hotspot analysis were used to describe epidemiological and some clinical characteristics.

Results

A total of 37 147 new student PTB cases were registered among the population aged 5–30 years during 2010–2020. The proportions of men and women were 53.71% and 46.29%, respectively. Cases aged 15–19 years dominated (63.91%), and the proportion of ethnic groups was increasing during the period. Generally, the raw annual incidence of PTB among the population was increasing from 32.585 per 100 000 persons in 2010 to 48.872 per 100 000 persons in 2020 (c2trend=1283.230, p<0.001). March and April were the peak months of a year, and cases were clearly grouped in Bijie city. New cases were mainly identified via physical examination, and cases from active screening were still low (0.76%). Additionally, secondary PTB accounted for 93.68%, positive rate of pathogen was only 23.06%, and the recovery rate was 94.60%.

Conclusions

The population aged 15–19 years is the vulnerable population, and Bijie city is the susceptible area. BCG vaccination and promotion for active screening should be the priority of futural PTB prevention and control. Tuberculosis laboratory capacity should be improved.
Evaluating an audit and feedback intervention for reducing overuse of pathology test requesting by Australian general practitioners: protocol for a factorial cluster randomised controlled trial
Authors: O'Connor Denise A , Glasziou Paul , Schram Dina , Gorelik Alexandra , Elwick Amelia , McCaffery Kirsten , Thomas Rae , Buchbinder Rachelle
Published: May 2023

Introduction

Consistent evidence shows pathology services are overused worldwide and that about one-third of testing is unnecessary. Audit and feedback (AF) is effective for improving care but few trials evaluating AF to reduce pathology test requesting in primary care have been conducted. The aim of this trial is to estimate the effectiveness of AF for reducing requests for commonly overused pathology test combinations by high-requesting Australian general practitioners (GPs) compared with no intervention control. A secondary aim is to evaluate which forms of AF are most effective.

Methods and analysis

This is a factorial cluster randomised trial conducted in Australian general practice. It uses routinely collected Medicare Benefits Schedule data to identify the study population, apply eligibility criteria, generate the interventions and analyse outcomes. On 12 May 2022, all eligible GPs were simultaneously randomised to either no intervention control or to one of eight intervention groups. GPs allocated to an intervention group received individualised AF on their rate of requesting of pathology test combinations compared with their GP peers. Three separate elements of the AF intervention will be evaluated when outcome data become available on 11 August 2023: (1) invitation to participate in continuing professional development-accredited education on appropriate pathology requesting, (2) provision of cost information on pathology test combinations and (3) format of feedback. The primary outcome is the overall rate of requesting of any of the displayed combinations of pathology tests of GPs over 6 months following intervention delivery. With 3371 clusters, assuming no interaction and similar effects for each intervention, we anticipate over 95% power to detect a difference of 4.4 requests in the mean rate of pathology test combination requests between the control and intervention groups.

Ethics and dissemination

Ethics approval was received from the Bond University Human Research Ethics Committee (#JH03507; approved 30 November 2021). The results of this study will be published in a peer-reviewed journal and presented at conferences. Reporting will adhere to Consolidated Standards of Reporting Trials.

Trial registration number

ACTRN12622000566730.
Voice of persons with a life-limiting illness in conversation with healthcare professionals: systematic review and meta-synthesis
Authors: Sikhosana Nqobile , Whitehead Dean , Moxham Lorna , Karacsony Sara , Namasivayam Pathmavathy , Fernandez Ritin
Published: May 2023

Background

Healthcare organisations are transforming the way care is delivered to people with a life-limiting illness with an increased focus on recognising the voice of the persons experiencing the illness and putting them in the centre of decision-making. However, the clinical practice remains largely based on the views of healthcare professionals and families or carers of the person with the illness.

Objectives

To synthesise the best available evidence on the experience of persons living with a life-limiting illness about expressing their voice during communication with healthcare professionals.

Design

Systematic review and meta-synthesis.

Data sources

CINAHL, Embase, Medline, PsycINFO, ProQuest Dissertations and Theses.

Review methods

A structured search was conducted to identify qualitative studies that reported on the experience of persons living with a life-limiting illness. The methodological quality of included studies was assessed using the Joanna Briggs Institute (JBI) critical appraisal checklists. The review was undertaken using the JBI and PRISMA guidelines.

Results

The expression of the voice of persons living with a life-limiting illness is influenced by: (1) the uncertain future surrounding illness trajectory and prognosis; (2) what is known from experience, media, family and friends; (3) emotional and psychological factors and (4) control and personal autonomy.

Conclusions

In the early stages of a life-limiting illness, the voice of those experiencing the disease is not always audible. Instead, this voice is potentially present but silent and carried and promoted within healthcare professionals’ values of accountability, professionalism, respect, altruism, equality, integrity and morality.
Status report of the n_TOF facility after the 2nd CERN long shutdown period
Authors: Patronis N. , Mengoni A. , Goula S. , Aberle O. , Alcayne V. , Altieri S. , Amaducci S. , Andrzejewski J. , Babiano-Suarez V. , Bacak M. , Balibrea Correa J. , Beltrami C. , Bennett S. , Bernardes A. P. , Berthoumieux E. , Beyer R. , Boromiza M. , Bosnar D. , Caamaño M. , Calviño F. , Calviani M. , Cano-Ott D. , Casanovas A. , Castelluccio D. M. , Cerutti F. , Cescutti G. , Chasapoglou S. , Chiaveri E. , Colombetti P. , Colonna N. , Console Camprini P. , Cortés G. , Cortés-Giraldo M. A. , Cosentino L. , Cristallo S. , Dellmann S. , Di Castro M. , Di Maria S. , Diakaki M. , Dietz M. , Domingo-Pardo C. , Dressler R. , Dupont E. , Durán I. , Eleme Z. , Fargier S. , Fernández B. , Fernández-Domínguez B. , Finocchiaro P. , Fiore S. , García-Infantes F. , Gawlik-Ramiega A. , Gervino G. , Gilardoni S. , González-Romero E. , Guerrero C. , Gunsing F. , Gustavino C. , Heyse J. , Hillman W. , Jenkins D. G. , Jericha E. , Junghans A. , Kadi Y. , Kaperoni K. , Kaur G. , Kimura A. , Knapová I. , Kokkoris M. , Krtička M. , Kyritsis N. , Ladarescu I. , Lederer-Woods C. , Lerendegui-Marco J. , Lerner G. , Manna A. , Martínez T. , Masi A. , Massimi C. , Mastinu P. , Mastromarco M. , Maugeri E. A. , Mazzone A. , Mendoza E. , Michalopoulou V. , Milazzo P. M. , Mucciola R. , Murtas F. , Musacchio-Gonzalez E. , Musumarra A. , Negret A. , Pérez de Rada A. , Pérez-Maroto P. , Pavón-Rodríguez J. A. , Pellegriti M. G. , Perkowski J. , Petrone C. , Pirovano E. , Plaza del Olmo J. , Pomp S. , Porras I. , Praena J. , Quesada J. M. , Reifarth R. , Rochman D. , Romanets Y. , Rubbia C. , Sánchez-Caballero A. , Sabaté-Gilarte M. , Schillebeeckx P. , Schumann D. , Sekhar A. , Smith A. G. , Sosnin N. V. , Stamati M. E. , Sturniolo A. , Tagliente G. , Tarifeño-Saldivia A. , Tarrío D. , Torres-Sánchez P. , Vagena E. , Valenta S. , Variale V. , Vaz P. , Vecchio G. , Vescovi D. , Vlachoudis V. , Vlastou R. , Wallner A. , Woods P. J. , Zarrella R. , Zugec P.
Published: May 2023

During the second long shutdown period of the CERN accelerator complex (LS2, 2019-2021), several upgrade activities took place at the n_TOF facility. The most important have been the replacement of the spallation target with a next generation nitrogen-cooled lead target. Additionally, a new experimental area, at a very short distance from the target assembly (the NEAR Station) was established. In this paper, the core commissioning actions of the new installations are described. The improvement in the n_TOF infrastructure was accompanied by several detector development projects. All these upgrade actions are discussed, focusing mostly on the future perspectives of the n_TOF facility. Furthermore, some indicative current and future measurements are briefly reported.
Spectral collocation technique for solving fractional generalized Cattaneo model
Authors: Abdelkawy M. A. , Soluma E. M. , Tedjani A. H. , Hassan E. I.
Published: May 2023

This paper discusses a numerical study of a category of fractional generalized Cattaneo models. Non-Newtonian fluids have been widely used in engineering and industry throughout the last decades. The above model is treated using two autonomous consecutive spectral collocation strategies. For the current model, our technique has proven to be more accurate, efficient, and workable. The analysis indicates that the spectral method is exponentially convergent.
Software Testing Integration-Based Model (I-BM) Framework for Recognizing Measure Fault Output Accuracy Using Machine Learning Approach
Authors: Zulkifli Zulkifli , Gaol Ford Lumban , Trisetyarso Agung , Budiharto Widodo
Published: May 2023

In software development, the software testing phase is an important process in determining the quality level of the software. Software testing is a process of executing a program aimed at finding errors in module access, units, and involves the execution of the system being tested on a number of test inputs, and determining whether the output produced is correct. In this study, a model-based testing (MBT) called integration-based model (I-BM) framework will be developed. This I-BM framework integrates testing variables from several software testing methods, namely black-box testing, white-box testing, unit testing, system testing, and acceptance testing. The integrated variables are function, interface, structure, performance, requirement, documentation, positives, and negatives. Then, this framework will document software errors to form a dataset, which will be measured for the level of accuracy of expected manual fault output using neural network algorithm and support vector machine. From the experiment results, it shows that the accuracy level of predicting fault output values from the I-BM framework using the neural network algorithm is on average 80%, and it produces a superior SVM architecture model in predicting I-BM framework output errors with an accuracy value of 0.99, precision of 0.99, recall of 0.99, and [Formula: see text]-score of 0.99. Compared to other MBT, the IBM framework has the advantage of being a more comprehensive software testing model because it starts from the identification of problems, analysis, design, documentation of software testing, and recommendations for each fault output found. Thus, software errors can be classified systematically in the form of a dataset, and not only focus on software testing for product lines and module mappings.
MODEL TO STUDY INTERDEPENDENT CALCIUM AND IP3 DISTRIBUTION REGULATING NFAT PRODUCTION IN T LYMPHOCYTE
Authors: BHARDWAJ HEMANT , ADLAKHA NEERU
Published: May 2023

The cooperative system of calcium (Ca[Formula: see text]) and inositol 1,4,5-trisphosphate (IP3) plays a crucial role in maintaining structure and functions of T lymphocyte cells including the production of nuclear factor of activated T cells (NFAT) as an immunological response. NFAT regulates several mechanisms and dysregulation in this process can lead to various disorders like inflammatory bowel diseases, etc. In this study, the two-way feedback model of Ca[Formula: see text] and IP3 dynamics regulating NFAT production in T lymphocytes has been constructed. A system of nonlinear reaction-diffusion equations for calcium and IP3 for a one-dimensional case has been employed in this proposed model. The numerical simulation is performed using finite element and the Crank–Nicholson method. The effects of the parameters like Ryanodine Receptor (RyR), source amplitude and buffers on active NFAT production have been analyzed. The novel insights about regulatory and dysregulation events and mechanisms of Ca[Formula: see text], IP3 and NFAT are concluded from these results.
Licorice-Based Biosynthesis of Gold Nanoparticles and Evaluation of Some Pathogenic Bacteria’s Resistance to Antibacterial Agents
Authors: Fezaa Abeer H. , Al-Haddad Raad M. S. , Ali Abduallah M.
Published: May 2023

This research aims to prepare gold nanoparticles by the biological method, using the licorice as a reduced agent, and to investigate the potential of gold nanoparticles as antibacterial agents. Nanoparticles of the distinctive gold peak have been observed at a wavelength of 515–518[Formula: see text]nm before and after adding the plant extract; this is known as plasmonic surface resonance, where the particles were synthesized and tested using several techniques such as using ultraviolet–visible radiation, zeta potentials, FT-IR, TEM, XRD FTIR measurement detection that shows peaks Absorption at 1388[Formula: see text]cm[Formula: see text] C–O extension of a carboxylic acid. TEM measurements show particles with a size of 39[Formula: see text]nm under ideal conditions, the crystallization phase of the XRD patterns of the produced Au NPs was (38.41, 44.6, 64.72, 77.618), correspond to (111), (200), (220), and (311) plane of metallic Au, confirming the crystal structure of Au. The generated AuNPs are relatively stable, due to the coating process, licorice extract is critical to maintaining the stability of the nanoparticles and preventing them from agglomerating. Compared to the uncoated gold nanoparticles, the coated licorice extract shows a larger zeta capacity (15.8 mV). For two pathogenic bacteria of Streptococcus mutans, Mirabilis proteome was (6–22) and (6–25)[Formula: see text]mm. The results show that licorice extract can be used for more environmentally friendly production of AuNPs with homogeneous particle sizes.
Intelligent Decision-Making Framework for Evaluating and Benchmarking Hybridized Multi-Deep Transfer Learning Models: Managing COVID-19 and Beyond
Authors: Ahmed M. A. , Al-Qaysi Z. T. , Albahri A. S. , Alqaysi M. E. , Kou Gang , Albahri O. S. , Alamoodi A. H. , Albahri Suad A. , Alnoor Alhamzah , Al-Samarraay Mohammed S. , Hamid Rula A. , Garfan Salem , Alotaibi Fahd S.
Published: May 2023

In this study, we developed a novel multi-criteria decision-making (MCDM) framework for evaluating and benchmarking hybrid multi-deep transfer learning models using radiography X-ray coronavirus disease (COVID-19) images. First, we collected and pre-processed eight public databases related to the targeted datasets. Second, convolutional neural network (CNN) models extracted features from 1,338 chest X-ray (CXR) frontal view image data using six pre-trained models: VGG16, VGG19, painters, SqueezeNet, DeepLoc, and Inception v3. Then, we used the intersection between the six CNN models and eight classical machine learning (ML) methods, including AdaBoost, Decision Tree, logistic regression, random forest, kNN, neural network, and Naive Bayes, to introduce 48 hybrid classification models. In this study, eight supervised ML methods were used to classify COVID-19 CXR images. The classifiers were implemented using the TensorFlow2 and Keras libraries in Python. A feature vector was extracted from each image, and a five-fold cross-validation technique was used to evaluate the performance. The cost parameter [Formula: see text] was set to 1 and the gamma parameter [Formula: see text] was set to 0.1 for all classifiers. The experiments were run on a Windows-based computer with dual Intel I CoITM i7 processors at 2.50[Formula: see text]GHz, 8[Formula: see text]GB of RAM, and a graphical processing unit of 2[Formula: see text]GB. The performance metrics of the 48 hybrid models, including the classification accuracy (CA), specificity, area under the curve (AUC), F1 score, precision, recall, and log loss, were used as efficient evaluation criteria. Third, the MCDM approach was used, which included (i) developing a dynamic decision matrix based on seven evaluation metrics and the developed hybrid models, (ii) developing the fuzzy-weighted zero-inconsistency method for determining the weight coefficients for the seven-evaluation metrics with zero inconsistency, and (iii) developing the Višekriterijumsko Kompromisno Rangiranje method for benchmarking the 48 hybrid models. Our experimental results reveal that (i) CA and AUC obtained the highest importance weights of 0.164 and 0.147, respectively, whereas F1 and specificity obtained the lowest weights of 0.134 and 0.134, respectively, and (ii) the highest three hybrid model scores were painters neural network, painters logistic regression, and VGG16-logistic regression, making them the highest ranking scores. Finally, the developed framework was validated using sensitivity analysis and comparison analysis.
Minimizing Employee Walking through Clustering of Tools in Fixed-Position Layouts
Authors: Shih Yung-Chin
Published: May 2023

The objective of this research work was to study the performance of fixed-position layouts when working with different tools. We developed a computational model to obtain two performance indicators, the distance traveled and the training costs of employees. A Simulated Annealing algorithm was specifically developed and embedded in the developed model to define the best types of tools that minimize the total distance traveled. The results indicate that it is statistically advantageous to group different types of tools in carts, not only to reduce displacement but also to reduce the costs for training employees. Moreover, increasing the number of working centers, in most cases, contributes to a reduction in the distance traveled. There is no evidence that training costs increase as the number of components increases, and it is observed that the number of components has a negative influence on the performance.
Tachyonic dark energy in general relativity and teleparallel frameworks
Authors: Bellucci S. , Banijamali A.
Published: May 2023

This paper is intended to review the consequences of assuming tachyon scalar field as a candidate for dark energy from dynamical system technique and observational cosmology point of views. In the contexts of general relativity and teleparallel gravity, a variety of non-minimally coupled tachyon fields have been taken into consideration. These models provide us subclasses of scalar-tensor and scalar-torsion theories. This review covers the tachyonic chameleon, the non-minimally coupled tachyon field to the Gauss–Bonnet invariant and the tachyonic teleparallel dark energy models. Type Ia supernovae and baryonic acoustic oscillations datasets are the observational data that have been used to constrain the model parameters.
Economic and Political Cycles in China: Leadership Uncertainty and Local Government’s Water Resources Governance Performance
Authors: Niu Yanfang , Chen Mangmang , Yang Jie , Ying Limeng , Sun Yu
Published: May 2023

There is ample evidence indicating that political institutions and official mobility influence the economy, finance, and environment. Specifically, political turnovers have been found to be essential for the functioning and oversight of economic institutions. Chinese cities, where the party secretary frequently changes every few years, provide an interesting context for studying political turnovers. In this study, we investigated the effects of political turnovers on urban sewage discharge in 242 Chinese cities between 2003 and 2018. The findings revealed a significant impact of the timing of the Chinese Communist Party Congress on urban sewage discharge. Leading up to and including the year of the Party Congress, there was a marked reduction in urban sewage discharge. Conversely, discharge increased substantially during the year or two years following the Party Congress. These results suggest that political turnovers play a critical role in environmental governance performance in China.
Policy Uncertainties, Water Technology and Economic Growth
Authors: Yang Fan , Ge Jingyi , Wang Xiaomin
Published: May 2023

Environmental economists have long been interested in the relationship between policy enforcement, technological progress, and economic growth. A multidirectional process exists where factors such as the economy, policy, technology, and environment interactively work. Based on the balanced panel data of 261 prefecture-level cities in China from 2000 to 2020, this study innovatively examines the diversified channels in the policy–technology system within the structural equation modeling framework. Conclusions can be drawn as follows. First, the policy uncertainties curb the technological improvement in the water sector, particularly in southern Chinese cities. Second, the incubation and adoption of water technology are closely intertwined, significantly affecting water quality. By clarifying the interaction of the factors in water technology diffusion, this study provides a comprehensive framework to investigate China’s water economics and policy uncertainties.
VLSP 2022 Abmusu Task Dataset: A Resource for Vietnamese Abstractive Multi-Document Summarization
Authors: Nguyen Quoc-An , Can Duy-Cat , Le Hoang-Quynh , Tran Mai-Vu
Published: May 2023

The performance of automatic summarization systems has improved significantly with the development of supervised approaches. However, in the Vietnamese abstractive multi-document summarization task, the available datasets are insufficient for training the model. With this motivation, we contribute a new gold standard Vietnamese abstractive multi-document summarization dataset, named Abmusu. Following the collecting and clustering of articles, we have built a hierarchical annotation process to generate summaries, with three roles: annotator, supervisor, and curator. As a result, the dataset contains 600 news clusters formed from 1839 articles and the corresponding human-generated summaries. To the best of our knowledge, Abmusu dataset is the biggest dataset for Vietnamese abstractive multi-document summarization that is freely available for research. Moreover, summaries are more concise, making it challenging to train the summarization models. We also used various summarization baselines to benchmark the Abmusu dataset.
Ordovician–Silurian deformation of the Neoproterozoic upper gneiss unit in the northern Seve Nappe Complex: implications for subduction of the Baltican margin
Authors: Barnes C. J. , Majka J. , Callegari R. , Walczak K. , Ziemniak G. , Bukała M.
Published: May 2023

The upper gneiss unit is exposed in the northernmost Seve Nappe Complex (SNC) in the Scandinavian Caledonides. To investigate the Caledonian tectonic history of the unit,
in situ
white mica and biotite
40
Ar/
39
Ar geochronology was applied to a leucogranite and two paragneisses. The leucogranite exhibits low-strain traits. Biotite porphyroblasts yielded a cooling age of 459 ± 2 Ma. White mica that replace biotite and plagioclase provided a crystallization age of 436 ± 5 Ma. White mica in both paragneisses exhibit high-strain characteristics associated with top-to-the-east sense of shear. One paragneiss provided dispersed late Cambrian to Late Ordovician dates with the youngest approximating deformation at 459 ± 2 Ma. The older dates are interpreted to reflect
40
Ar inherited from a previous metamorphic event. The second paragneiss yielded a deformation age of 434 ± 2 Ma. The collective dataset is interpreted to record exhumation of the upper gneiss unit at
c.
459 Ma and deformation and fluid infiltration at
c.
434 Ma during continental collision. The events closely resemble the deformation histories of other northern SNC terranes. Synthesizing these results with those for other northern SNC terranes suggests that the Baltican margin underwent oblique, south-to-north subduction during late Cambrian time.

Supplementary material:
Tables providing mineral chemistry of white mica and biotite and
40
Ar/
39
Ar geochemistry results are available at
https://doi.org/10.6084/m9.figshare.c.6639993

Thematic collection:
This article is part of the Caledonian Wilson cycle collection available at:
https://www.lyellcollection.org/topic/collections/the-caledonian-wilson-cycle
Improving Automated Labeling for ATT&CK Tactics in Malware Threat Reports
Authors: Domschot Eva , Ramyaa Ramyaa , Smith Michael R.
Published: May 2023

Once novel malware is detected, threat reports are written by security companies that discover it. The reports often vary in the terminology describing the behavior of the malware making comparisons of reports of the same malware from different companies difficult. To aid in the automated discovery of novel malware, it was recently proposed that novel malware could be detected by identifying behaviors. This assumes that a core set of behaviors are present in most, if not all, malware variants. However, there is a lack of malware datasets that are labeled with behaviors. Motivated by a need to label malware with a common set of behaviors, this work examines automating the process of labeling malware with behaviors identified in malware threat reports despite the variability of terminology. To do so, we examine several techniques from the natural language processing (NLP) domain. We find that most state-of-the-art word embedding NLP methods require large amounts of data and are trained on generic corpora of text data—missing the nuances related to information security. To address this, we use simple feature selection techniques. We find that simple feature selection techniques generally outperform word embedding methods and achieve an increase of 6% in the
F
.5
-score over prior work when used to predict MITRE ATT&CK tactics in threat reports. Our work indicates that feature selection, which has commonly been overlooked by sophisticated methods in NLP tasks, is beneficial for information security related tasks, where more sophisticated NLP methodologies are not able to pick out relevant information security terms.
Remote Perception Attacks against Camera-based Object Recognition Systems and Countermeasures
Authors: Man Yanmao , Li Ming , Gerdes Ryan
Published: May 2023

In vision-based object recognition systems, imaging sensors perceive the environment and then objects are detected and classified for decision-making purposes, e.g., to maneuver an automated vehicle around an obstacle or to raise alarms for intruders in surveillance settings. In this work we demonstrate how camera-based perception can be unobtrusively manipulated to enable an attacker to create spurious objects or alter an existing object, by remotely projecting adversarial patterns into cameras, exploiting two common effects in optical imaging systems, viz., lens flare/ghost effects and auto-exposure control. To improve the robustness of the attack, we generate optimal patterns by integrating adversarial machine learning techniques with a trained end-to-end channel model. We experimentally demonstrate our attacks using a low-cost projector on three different cameras, and under different environments. Results show that, depending on the attack distance, attack success rates can reach as high as 100%, including under targeted conditions. We develop a countermeasure that reduces the problem of detecting ghost-based attacks into verifying whether there is a ghost overlapping with a detected object. We leverage spatiotemporal consistency to eliminate false positives. Evaluation on experimental data provides a worst-case equal error rate of 5%.
Security Aspects of Cryptocurrency Wallets—A Systematic Literature Review
Authors: Houy Sabine , Schmid Philipp , Bartel Alexandre
Published: May 2023

Cryptocurrencies are gaining prominence among individuals and companies alike, resulting in the growing adoption of so-called cryptocurrency wallet applications, as these simplify transactions. These wallets are available in a myriad of different forms and specifications. All of them are susceptible to various ways the attacker can exploit the vulnerabilities and steal money from victims. Cryptocurrency wallets create a unique field as they combine features of password managers, banking applications, and the need to keep their users and their transactions anonymous. We collect the findings from previous literature to provide an overview of the different attack surfaces, possible countermeasures, and further research. Existing literature focused on one of the features mentioned before, while we considered all of them. Our systematic study shows that there is a considerable variety of attack vectors, which we have divided into six subcategories, (i) Memory and Storage, (ii) Operating Systems, (iii) Software Layer, (iv) Network Layer, (v) Blockchain Protocol, and (vi) Others. We have found a large gap between the possible countermeasures and their actual adoption. Therefore, we provide a list of possible directions for future research to tackle this gap.
COVID-19: Epidemiological Models
Authors: Atkeson Andrew
Published: May 2023

The world has been confronted in recent decades with several infectious disease outbreaks caused by novel pathogens, with the COVID-19 pandemic being the most severe of these. In this article, I review some of the main elements of epidemiological models used to forecast the trajectory of a new epidemic and to guide public health policy responses to a new infectious disease. I argue that economists have a lot to contribute to the discussion of public health policies, particularly in regard to assessing the costs and benefits of alternative policies and in improving the modeling of changes in human behavior in response to new infectious diseases. This survey is intended to serve economists interested in starting research in these areas.
Major Gaps in Understanding Dietary Supplement Use in Health and Disease
Authors: Bailey Regan L. , Jun Shinyoung , Cowan Alexandra E. , Eicher-Miller Heather A. , Gahche Jaime J. , Dwyer Johanna T. , Hartman Terryl J. , Mitchell Diane C. , Seguin-Fowler Rebecca A. , Carroll Raymond J. , Tooze Janet A.
Published: May 2023

Precise dietary assessment is critical for accurate exposure classification in nutritional research, typically aimed at understanding how diet relates to health. Dietary supplement (DS) use is widespread and represents a considerable source of nutrients. However, few studies have compared the best methods to measure DSs. Our literature review on the relative validity and reproducibility of DS instruments in the United States [e.g., product inventories, questionnaires, and 24-h dietary recalls (24HR)] identified five studies that examined validity ( n = 5) and/or reproducibility ( n = 4). No gold standard reference method exists for validating DS use; thus, each study's investigators chose the reference instrument used to measure validity. Self-administered questionnaires agreed well with 24HR and inventory methods when comparing the prevalence of commonly used DSs. The inventory method captured nutrient amounts more accurately than the other methods. Reproducibility (over 3 months to 2.4 years) of prevalence of use estimates on the questionnaires was acceptable for common DSs. Given the limited body of research on measurement error in DS assessment, only tentative conclusions on these DS instruments can be drawn at present. Further research is critical to advancing knowledge in DS assessment for research and monitoring purposes.