bluuebunny/crossref_metadata_2025_split huggingface dataset:
A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia
Authors: Hauser S. , Lazarevic V. , Tournoud M. , Ruppé E. , Santiago Allexant E. , Guigon G. , Schicklin S. , Lanet V. , Girard M. , Mirande C. , Gervasi G. , Schrenzel J. 
Published: October 2023

ABSTRACT

The management of ventilator-associated and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen(s). To achieve this, we propose a metagenomics next-generation sequencing (mNGS) assay that includes the use of an internal sample processing control (SPC) for the quantitative detection of 20 relevant bacterial species of interest (SOI) from bronchoalveolar lavage (BAL) samples. To avoid very major errors in the identification of respiratory pathogens due to “false-negative” cases, each sample was spiked with
Bacillus subtilis
, at a precisely defined concentration, using rehydrated BioBall. This SPC ensured the detection and quantification of the pathogen(s) at defined minimum concentrations. In the presented mNGS workflow, absolute quantification of
Staphylococcus aureus
was as accurate as quantitative PCR. We defined a metagenomics threshold at 5.3 × 10
3
genome equivalent unit per milliliter of the sample for each SOI, to distinguish colonization from higher amounts of pathogens that may be associated with infection. Complete mNGS process and metrics were assessed on 40 clinical samples, showing >99.9% sensitivity compared to microbial culture. However, 19 out of the 29 (66%) SOI detections above the metagenomics threshold were not associated with bacterial growth above classical culture-based clinical thresholds. Taxonomic classification of 7 (37%) of the “false-positive” detections was confirmed by finding specific 16S/MetaPhlAn2 markers, the 12 other “false-positive” detections did not yield enough reads to check their taxonomic classification. Our SPC design and analytical workflow allowed efficient detection and absolute quantification of pathogens from BAL samples, even when the bacterial DNA quantity was largely below the manufacturer’s recommendations for NGS. The frequent “false-positive” detections suggested the presence of nonculturable cells within the tested BAL samples. Furthermore, mNGS detected mixed infections, including bacterial species not reported by routine cultures.

IMPORTANCE
The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.
Fusobacterium nucleatum
and its metabolite hydrogen sulfide alter gut microbiota composition and autophagy process and promote colorectal cancer progression
Authors: Wang Minyu , Wang Zheng , Lessing Duncan James , Guo Min , Chu Weihua 
Published: October 2023

ABSTRACT

Fusobacterium nucleatum
is a harmful bacterium that produces hydrogen sulfide by metabolizing sulfur-containing amino acids, both of which have been shown to promote/initiate the development of various cancers, such as colorectal cancer, liver cancer, as well as lung cancer. However, few studies have reported how
F. nucleatum
acts on gut microbiota, influences the autophagy process, and promotes the development of colorectal cancer through the metabolite hydrogen sulfide. It was found that HCT116 cells secreted more inflammatory factors and showed higher survival as well as migration rate when given a pathological concentration of hydrogen sulfide. Using cellular transcriptome sequencing, it could be seen that after giving HCT116 cells
F. nucleatum
or
F. nucleatum
with L-cysteine, many inflammation-related signaling pathways, including autophagic pathways, were elevated compared to the control group.
In vivo
, the mice in the model groups displayed cancer progression, and the expression of some of the autophagy-related genes,
DRAM1
,
NBR1
,
ATG7
,
MAP1LC3A
were also increased in mice given
F. nucleatum
or
F. nucleatum
with L-cysteine when compared to the untreated control mice. The number of certain probiotic bacteria and fungi in the mice given
F. nucleatum
or
F. nucleatum
and L-cysteine decreased significantly; in contrast, the number of potentially pathogenic bacteria and fungi increased. These findings suggest that
F. nucleatum
and its metabolite hydrogen sulfide can modulate intestinal microbiota and autophagy as well as promote the development and progression of colorectal cancer.

IMPORTANCE

Colorectal cancer (CRC) is the second most common cancer in the world; the main treatment for CRC is immunosuppressive therapy, but this therapy is only effective for a small percentage of CRC patients, so there is an urgent need for a treatment with fewer side effects and higher efficacy. This study demonstrated that
Fusobacterium nucleatum
with increased abundance in CRC can regulate the autophagy process and disrupt normal intestinal microbiota by producing hydrogen sulfide, factors that may be involved in the development and progression of CRC. This study may provide a reference for future CRC treatment options that are efficient and have fewer side effects.
Structural insights on the nucleoprotein C-terminal domain of Měnglà virus
Authors: Ferrero Diego Sebastian , Tomás Gilabert Omar , Verdaguer Nuria 
Published: October 2023

ABSTRACT

Filoviruses depend on the nucleoprotein (NP) to accomplish multiple functions during the viral life cycle. NP is the most abundantly expressed viral protein in infected cells and the main component of the viral nucleocapsid. It can be structurally divided into amino- and carboxy- terminal domains (NTD and CTD). The NTD can homo-oligomerize to interact and protect the (−) ssRNA genome, forming long helical structures. The flexible CTD is responsible for the binding of other nucleocapsid proteins and is involved in the formation of inclusion bodies (IBs)—the cytoplasmic sites of nucleocapsid formation and genome replication. The CTD ends in a ~100-residue globular tail. Měnglà virus (MLAV) is the only member of the new
Dianlovirus
genus within the
Filoviridae
family. Their differential characteristics and the possibility of becoming a threat for human health justify the interest in better understanding of its structure and function. In this work, we present the structure of the globular tail of the MLAV NP CTD, showing an overall conformation closely related to that previously reported for the equivalent NP region in MARV. Moreover, analyses of the CTD-CTD interactions in the crystal asymmetric unit revealed a higher-order helicoidal structure. Mutational studies underscore the crucial role of a number of residues, located at the CTD-CTD contact interface, for IB formation. Site-directed mutagenesis of amino acids L653 and F687, involved in the formation of these helicoidal assemblies, abrogate the growth of IBs when the full-length MLAV NP was ectopically expressed in cells. Our findings confirm the role of NP CTD in IB formation, also for MLAV, and focus the attention on particular residues as starting point for further analysis.

IMPORTANCE
Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
Morphological and Genetic Identification of Harpacticella inopinata (Harpacticoida, Copepoda) from Lake Baikal and the Yenisei River (Russia)
Authors: Fefilova E. B. , Popova E. I. , Mayor T. Y. , Novikov A. A. , Velegzhaninov I. O. , Golubev M. A. , Bakashkina A. S. 
Published: October 2023

Abstract
The results of studies of the morphology and genetics of the Baikal subendemic (Harpacticella inopinata Sars, 1908 harpacticoid) are presented. The collections of 1969 and 2017–2022 from the southern part of Lake Baikal and the Yenisei River within the city of Krasnoyarsk are used as material. It is demonstrated that morphological variability within the species is most pronounced in the structure of the antenna exopodite and the number of pores and sensilla on the integument of thoracic somites. The genetic variability of the studied H. inopinata sample is described by three clades with an average distance between them of 0.24; genetic distances between individuals within the detected genetic groups do not exceed 0.005. It is found that H. inopinata from geographically distant habitats (Lake Baikal and the Yenisei River) form a single morphological and genetic group. The analysis of genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei River, probably associated with an anthropogenic invasion.
Intervention targets for reducing mortality between mid-adolescence and mid-adulthood: a protocol for a machine-learning facilitated systematic umbrella review
Authors: Kerr Jessica A , Gillespie Alanna N , O'Connor Meredith , Deane Camille , Borschmann Rohan , Dashti S Ghazaleh , Spry Elizabeth A , Heerde Jessica A , Möller Holger , Ivers Rebecca , Boden Joseph M , Scott James G , Bucks Romola S , Glauert Rebecca , Kinner Stuart A , Olsson Craig A , Patton George C 
Published: October 2023

IntroductionA rise in premature mortality—defined here as death during the most productive years of life, between adolescence and middle adulthood (15–60 years)—is contributing to stalling life expectancy in high-income countries. Causes of mortality vary, but often include substance misuse, suicide, unintentional injury and non-communicable disease. The development of evidence-informed policy frameworks to guide new approaches to prevention require knowledge of early targets for intervention, and interactions between higher level drivers. Here, we aim to: (1) identify systematic reviews with or without meta-analyses focused on intervention targets for premature mortality (in which intervention targets are causes of mortality that can, at least hypothetically, be modified to reduce risk); (2) evaluate the review quality and risk of bias; (3) compare and evaluate each review’s, and their relevant primary studies, findings to identify existing evidence gaps.Methods and analysisIn May 2023, we searched electronic databases (MEDLINE, PubMed, Embase, Cochrane Library) for peer-reviewed papers published in the English language in the 12 years from 2012 to 2023 that examined intervention targets for mortality. Screening will narrow these papers to focus on systematic reviews with or without meta-analyses, and their primary papers. Our outcome is death between ages 15 and 60 years; with potential intervention targets measured prior to death. A MeaSurement Tool to Assess systematic Reviews (AMSTAR 2) will be used to assess quality and risk of bias within included systematic reviews. Results will be synthesised narratively due to anticipated heterogeneity between reviews and between primary studies contained within included reviews.Ethics and disseminationThis review will synthesise findings from published systematic reviews and meta-analyses, and their primary reviewed studies, meaning ethics committee approval is not required. Our findings will inform cross-cohort consortium development, be published in a peer-reviewed journal, and be presented at national and international conferences.PROSPERO registration numberCRD42022355861.
Physical activity interventions for inpatients in secure mental health settings: what works, for whom, in what circumstances and why? A protocol for a realist synthesis
Authors: Keel Toby , Machaczek Katarzyna , King James A , Breen Kieran , Stubbs Brendon , Kinnafick Florence 
Published: October 2023

IntroductionThe physical health of individuals with severe mental illness (SMI) is a cause for concern. While the purpose of inpatient mental health settings is rehabilitation and treatment, the physical health of hospitalised patients commonly deteriorates. Physical activity (PA) has been identified as an appropriate intervention to help improve the psychological and physical health of inpatients. We aim to address the gaps in the current literature by exploring how, why, for whom and in what contexts PA interventions help patients with SMI, who receive inpatient treatment, to increase their PA engagement.Methods and analysisRealist synthesis: Six steps will be followed: (1) identification of the review question and scope of the review; (2) searching for evidence; (3) screening and appraisal; (4) extraction of data; (5) synthesis of the data and (6) dissemination. Five databases will be searched: Web of Science, PubMed, PsycINFO, PsychArticles and EmBase. A total of 10–15 stakeholders made up of academics and people living with SMI, sport and exercise therapists, psychiatrists, physiotherapists of low, medium and highly secure inpatient settings, will form an expert advisory group. They will provide their insight and knowledge of the secure setting contexts and perceived principles of how PA initiatives being undertaken in their hospitals for patients with SMI work, or not. The results will be published in accordance with the Realist And Meta-narrative Evidence Syntheses-Evolving Standards publication standards.Ethics and disseminationEthical approval has been granted. The review will produce context-specific guidance for Clinical Commissioning Groups and practitioners on how to optimise the provision of PA interventions for people with SMI in inpatient settings.
Preoperative percutaneous or transvascular marking for curative resection of small liver tumours with potential for missing during hepatectomy: a study protocol for an open-label, single-arm phase II study
Authors: Fukuhara Sotaro , Kuroda Shintaro , Kobayashi Tsuyoshi , Takei Daisuke , Namba Yosuke , Oshita Ko , Matsubara Keiso , Honmyo Naruhiko , Nakano Ryosuke , Sakai Hiroshi , Tahara Hiroyuki , Ohira Masahiro , Kawaoka Tomokazu , Tsuge Masataka , Chosa Keigo , Awai Kazuo , Ohdan Hideki 
Published: October 2023

IntroductionSmall liver tumours are difficult to identify during hepatectomy, which prevents curative tumour excision. Preoperative marking is a standard practice for small, deep-seated tumours in other solid organs; however, its effectiveness for liver tumours has not been validated. The objective of this study is to evaluate the effectiveness of preoperative markings for curative resection of small liver tumours.Methods and analysisThis is an open-label, single-arm, single-centre, phase II study. Patients with liver tumours of ≤15 mm requiring hepatectomy will be enrolled and will undergo preoperative marking by placing a microcoil near the tumour using either the percutaneous or transvascular approach. The tumours, including the indwelling markers, will be excised. The primary endpoint will be the successful resection rate of liver tumours, defined as achieving a surgical margin of ≥5 mm and ≤15 mm. Secondary endpoints will include the results of preoperative marking and hepatectomy.Ethics and disseminationEthical approval for this trial was obtained from the Ethical Committee for Clinical Research of Hiroshima University, Japan. The results will be published at an academic conference or by submitting a paper to a peer-reviewed journal.Trial registration numberjRCTs062220088.
Youth partnership in suicide prevention research: moving beyond the safety discourse
Authors: Michail Maria , Morgan Jamie , Lavis Anna 
Published: October 2023

ObjectiveIn this communication article, we discuss coproduction in suicide prevention research, with an emphasis on involving young people. We critically reflect on the lessons we have learned by working alongside young people, and how these lessons may be useful to other research teams.SummaryThe meaningful involvement of young people in the design, implementation and translation of mental health research has received significant attention over the last decade. For most funding bodies, the involvement of patients and the public in the planning and delivery of research is advised and, in many cases, mandatory. When it comes to suicide prevention research, however, things are slightly different in practice. Involvement of young people in suicide prevention research has often been considered a controversial, unfeasible and even risky endeavour. In our experiences of working in this field, such concerns are expressed by funders, Higher Education Health and Safety committees and practitioners. By presenting an example from our research where the involvement of young people as experts by experience was integral, we highlight key lessons learnt that could maximise the potential of youth partnership in suicide prevention research. These lessons take on particular importance in mental health research against the background of long-entrenched power differences and the silencing of service user voices. Professional knowledge, obtained through education and vocational training, has historically taken priority over experiential knowledge obtained through lived experience, in psychiatric practice and research. Although this hierarchy has widely been challenged, any account of coproduction in mental health research is positioned against that background, and the remnants of those inequitable power relationships arguably take on greater resonance in suicide prevention research and require careful consideration to ensure meaningful involvement.ConclusionWe conclude that progress in suicide research cannot be fulfilled without the meaningful involvement of, and partnership with, young people with lived experience.
Intravenous alteplase before endovascular therapy for acute large vessel occlusion with large ischemic core: subanalysis of a randomized clinical trial
Authors: Shindo Seigo , Uchida Kazutaka , Yoshimura Shinichi , Sakai Nobuyuki , Yamagami Hiroshi , Toyoda Kazunori , Matsumaru Yuji , Matsumoto Yasushi , Kimura Kazumi , Ishikura Reiichi , Inoue Manabu , Sakakibara Fumihiro , Nakajima Makoto , Ueda Mitsuharu , Morimoto Takeshi 
Published: October 2023

BackgroundThe efficacy of endovascular therapy (EVT) in patients with large ischemic core has been reported, but it remains unclear whether IV alteplase (IVT) has beneficial effects in addition to EVT in such patients. We evaluated the efficacy and safety of EVT with or without IVT.MethodsThe RESCUE-Japan LIMIT was an open-label, prospective, multicenter, randomized clinical trial to evaluate the efficacy and safety of EVT in stroke patients with large ischemic core, defined as Alberta Stroke Program Early CT Score (ASPECTS) 3–5. This subanalysis evaluated the differences in the effects of EVT with medical care (EVT group) compared with medical care alone (No-EVT group) between those who received IVT (IVT stratum) and those who did not (No-IVT stratum) before EVT.ResultsAmong 202 enrolled patients, 147 (73%) did not receive IVT. In the No-IVT stratum, the modified Rankin Scale (mRS) score of 0–3 at 90 days was significantly higher in the EVT group than in the No-EVT group (31.1% vs 12.3%, OR 3.21 (95% CI 1.37 to 7.53)). In the IVT stratum, the mRS score of 0–3 was 30.8% in the EVT group and 13.8% in the No-EVT group (OR 2.78 (95% CI 0.72 to 10.7)) (interaction p=0.77). The incidence of symptomatic intracranial hemorrhage was not different between the two groups in the No-IVT stratum (OR 1.20 (95% CI 0.35 to 4.12)), but it was significantly higher in the EVT group than in the No-EVT group in the IVT stratum (11.5% vs 0%, p=0.03).ConclusionsThere was no difference in efficacy of EVT with or without IVT, while IVT before EVT might increase symptomatic intracranial hemorrhage in patients with large ischemic core.Trial registration informationNCT03702413.
Crystal field, electronegativity and magnetic behavior of Mn-, Fe-, Co- and Ni-doped LiMgN half-Heusler: KKR-CPA approximation
Authors: Ziat Younes , Zarhri Zakaryaa , Belkhanchi Hamza 
Published: October 2023

This paper aims to investigate the behavior of LiMgN half-Heusler (HH) semiconductor doped by transition metals (TM [Formula: see text] Mn, Fe, Co and Ni). HHs belong to the [Formula: see text] space group (No. 216) and have a zinc blende structure that can be described by the chemical symbol XYZ. The research methodology utilized in this investigation involves theoretical analysis based on the principles of density functional theory (DFT). The studied LiMg[Formula: see text]TM[Formula: see text]N alloy displayed the half-metallicity behavior when TM [Formula: see text] Fe, Co and Ni. Hence, these systems could be a promising candidate in spintronic application thanks to their ferromagnetism. The principal contribution to magnetism in the full LiMg[Formula: see text]TM[Formula: see text]N alloys comes from the Mn, Fe, Co and Ni doping. The partial magnetic moments of these elements are significantly greater than the combined partial magnetic moments of Li, Mg and N. When comparing LiMg[Formula: see text]Mn[Formula: see text]N to LiMg[Formula: see text]Fe[Formula: see text]N, 5Co[Formula: see text]N and LiMg[Formula: see text]Ni[Formula: see text]N, it is important to note that the exchange splitting energy [Formula: see text] associated to their spin up and spin down were discussed. The variation of Mn(3d) in relation to ([Formula: see text]) is larger than that of Fe, Co and Ni. Therefore, [Formula: see text]. Furthermore, there is a correlation between the magnetic moment and electronegativity trend of the TM dopant. Specially, the electronegativity trend ([Formula: see text] is well matched with the total spin moment trend, where [Formula: see text].