bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biopsychosocial risk factors for intimate partner violence perpetration and victimization in adolescents and adults reported after the COVID-19 pandemic onset: a scoping review protocol
Authors: Moghimi Elnaz , Godfrey Christina , Hilton N. Zoe , Wintermute Jolene , McKeown Sandra , Melvin Ashley , Rajack Natalie , Asadpour Kimia , Duquette Matthew 
Published: January 2024

Objective:
This scoping review aims to provide a comprehensive summary of the biological, psychological, and sociological risk factors for intimate partner violence (IPV) victimization and perpetration reported after the onset of the COVID-19 pandemic.

Introduction:
IPV is a significant public health concern, characterized by various forms of violence inflicted by intimate partners. The onset of the COVID-19 pandemic significantly increased the global prevalence of IPV. While prior research has identified factors linked to IPV, the risk factors reported in the literature during this period have not been systematically mapped. Additionally, the similarities and differences in risk factors between perpetration and victimization have not been well delineated.

Inclusion criteria:
This review will focus on individuals aged 12 years or older involved in dyadic romantic relationships. Primary studies and systematic reviews published from the year 2020 will be included. Full-text papers, preprints, theses, and dissertations published in English will be included. Studies focusing on factors unrelated to IPV risk will be excluded. Non-systematic reviews, opinion pieces, and protocols will also be excluded.

Methods:
Following the JBI methodology for scoping reviews, systematic searches will be conducted for both peer-reviewed and gray literature. Independent reviewers will screen records, select eligible studies, and extract data using a standardized form. Key risk factors will be mapped to explore their interplay.

Review registration:
Open Science Framework https://osf.io/c2hkm
A Joint Probability Distribution for Multivariate Wind-Wave Conditions and Discussions on Uncertainties
Authors: Vanem Erik , Fekhari Elias , Dimitrov Nikolay , Kelly Mark , Cousin Alexis , Guiton Martin 
Published: January 2024

Abstract
This article presents a joint statistical model, which is needed in probabilistic design and structural risk assessment, that has been fitted to data of wind and wave conditions for an offshore location off South Brittany. The data are from a numerical model and contain hourly values for several wind and wave variables over a period of 32 years. The joint distribution presented in this article considers the variables wind direction, mean wind speed, significant wave height, wave direction, and peak period. A conditional model for turbulence given wind speed is introduced to yield an additional variable for the joint model. The joint model is constructed as a product of marginal and conditional models for the various variables. Additionally, the fitted models will be used to construct environmental contours for some of the variables. For significant wave height, various models are used to obtain different extreme value estimates, illustrating the uncertainties involved in extrapolating statistical models beyond the support of the data, and a discussion on the use of nonparametric copulas for the joint distribution is presented. Moreover, bootstrap has been performed to estimate the uncertainty in estimated model parameters from sampling variability. The effect of changing which variable to model as the marginal in a conditional model is illustrated by switching from wind speed to significant wave height. Such joint distribution models are important inputs for design of offshore structures, and in particular for offshore wind turbines, and the influence of the joint model in design is illustrated by a simple case study. This article is an extension of the conference paper by Vanem et al. (2023, “A Joint Probability Distribution Model for Multivariate Wind and Wave Conditions,” 42nd International Conference on Ocean, Offshore and Arctic Engineering).
Large-Bore Locomotive Engines – Numerical Simulations of Natural Gas/Diesel Dual-Fuel Operation
Authors: Kazmouz Samuel J. , Wu Sicong , Klingbeil Adam , Lavertu Thomas , Jayakar Vijayaselvan , Sheth Pushkar , Wijeyakulasuriya Sameera , Ameen Muhsin 
Published: January 2024

Abstract
US DOE has identified hard-to-decarbonize sectors like rail, marine, and aviation as candidates for sustainable low carbon fuels. Along with diesel or biodiesel, hydrogen or natural gas can be burned in a dual-fuel setup. In this paper, numerical simulations of natural gas and diesel dual-fuel combustion in a large-bore rail engine are discussed. The numerical results are investigated to determine best practices that guide future simulations with different fuels. Previous experimental results of a single cylinder Wabtec engine at four different operating conditions; from pure diesel up to 80% natural gas energy-based substitution rate, were used for validation. Natural gas is port injected while diesel is directly injected into the cylinder. First, previous numerical work involving large-bore diesel engines is covered. Then, for every case, the temporal pressure and temperature boundary conditions at the intake and exhaust ports, in addition to the diesel rate of injection, are discussed. The boundary conditions are generated using 1D engine models and the rate of injection are extracted from data of a similar injector with different nozzle flow. The results investigate the effect of turbulence model and grid size on computational results. Global in-cylinder pressure, heat release rate, and combustion phasing in addition to local flame-wall interactions are investigated to determine the best grid and turbulence model setups. The results show that RSM turbulence model provides better results than RNG k-ε turbulence model. In addition, a finer grid is required as substitution rate increases to account for increased mixed-mode combustion. Finally, potential additional challenges in modeling Hydrogen/Diesel dual-fuel combustion in locomotive engines are discussed.
Effects of the invasion of
Ralstonia solanacearum
on soil microbial community structure in Wuhan, China
Authors: Wu Qian-Yu , Ma Rong , Wang Xing , Ma Yi-Nan , Wang Zhi-Shan , Wei Hai-Lei , Zhang Xiao-Xia 
Published: January 2024

ABSTRACT

This study investigated the change in the microbiome of tomato rhizosphere soils after the invasion of
Ralstonia solanacearum
and analyzed the correlation between microbes and soil physicochemical properties. Diversity analyses of the bacteria in healthy and diseased rhizosphere soil samples (HRS and DRS) revealed that HRS had a higher species diversity and were compositionally different from DRS (
P
≤ 0.05). Substantial differences in the relative abundance of Actinobacteria (37.52% vs 28.96%,
P
≤ 0.05) and Proteobacteria (29.20% vs 35.59%,
P
≤ 0.05) were identified in HRS and DRS, respectively. Taxonomic composition analysis showed ten differentially abundant genera, and seven of them (
Gaiella
,
Roseisolibacter
,
Solirubrobacter
,
Kribbella
,
Acidibacter
,
Actinomarinicola
, and
Marmoricola
) are more abundant in HRS. Soil pH and enzyme activities were negatively correlated with the abundance of
R. solanacearum
. The contents of total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkaline nitrogen (alkaline N), available phosphorus (AP), available potassium (AK), NO3—N(NN), NH4
+
-N (AN), and organic matter (OM) were all significantly increased in DRS. The composition and richness of protozoa in the samples show significant differences.
Cephalobus
,
Acrobeles
,
Heteromita
, norank_Tylenchida, and
Rotylenchulus
were enriched in DRS. Microbial interaction networks revealed that the HRS networks were more complex than the DRS networks. Overall, the results of this study demonstrate that healthy soil has a more complex microbial community structure and higher enzyme activity, and the invasion of
R. solanacearum
damages the soil microbial system.

IMPORTANCE

How does the invasion of
Ralstonia solanacearum
affect tomato rhizosphere bacteria and protozoa? Which microbial changes can affect the growth of
R. solanacearum
? To date, most research studies focus on bacteria, with little research on protozoa, and even less on the synergistic effects between protozoa and bacteria. Here, we analyzed the correlation between tomato rhizosphere bacterial and protozoan communities and soil physicochemical properties during the invasion of
R. solanacearum
. We found that the diversity and abundance of rhizosphere microorganisms in healthy rhizosphere soil samples (HRS) were significantly higher than those in diseased rhizosphere soil samples (DRS), and there were significant changes in soil pH and enzyme activity. Overall, in this study, the analysis of microbial changes during the invasion of
R. solanacearum
provides a theoretical basis for the prevention and control of bacterial wilt.
Conversion of a classical microbiology laboratory to a total automation laboratory enhanced by the application of lean principles
Authors: Trigueiro Graça , Oliveira Carlos , Rodrigues Alexandra , Seabra Sofia , Pinto Rui , Bala Yohann , Gutiérrez Granado Monica , Vallejo Sandra , Gonzalez Victoria , Cardoso Carlos 
Published: January 2024

ABSTRACT
Laboratory automation in microbiology improves productivity and reduces sample turnaround times (TATs). However, its full potential can be unlocked through the optimization of workflows by adopting lean principles. This study aimed to explore the relative impact of laboratory automation and continuous improvement events (CIEs) on productivity and TATs. Laboratory automation took place in November 2020 and consisted of the introduction of WASPLab and VITEK MS systems. CIEs were run in May and September 2021. Before the conversion, the laboratory processed about ~492 samples on weekdays and had 10 full-time equivalent (FTE) staff for a productivity of 49 samples/FTE/day. In March 2021, after laboratory automation, the caseload went up to ~621 while the FTEs decreased to 8.5, accounting for productivity improvement to 73 samples/FTE/day. The hypothetical productivity went up to 110 samples/FTE/day following CIEs, meaning that the laboratory could at that point deal with a caseload increase to ~935 with unchanged FTEs. Laboratory conversion also led to an improvement in TATs for all sample types. For vaginal swabs and urine samples, median TATs decreased from 70.3 h [interquartile range (IQR): 63.5–93.1] and 73.7 h (IQR: 35.6–50.7) to 48.2 h (IQR: 44.8–67.7) and 40.0 h (IQR: 35.6–50.7), respectively. Automation alone was responsible for 37.2% and 75.8% of TAT reduction, respectively, while the remaining reduction of 62.8% and 24.2%, respectively, was achieved due to CIEs. The laboratory reached productivity and TAT goals predefined by the management after CIEs. In conclusion, automation substantially improved productivity and TATs, while the subsequent implementation of lean management further unlocked the potential of laboratory automation.

IMPORTANCE
In this study, we combined total laboratory automation with lean management to show that appropriate laboratory work organization enhanced the benefit of the automation and substantially contributed to productivity improvements. Globally, the rapid availability of accurate results in the setting of a clinical microbiology laboratory is part of patient-centered approaches to treat infections and helps the implementation of antibiotic stewardship programs backed by the World Health Organization. Locally, from the point of view of laboratory management, it is important to find ways of maximizing the benefits of the use of technology, as total laboratory automation is an expensive investment.
Salmonella
-induced microbiome profile in response to sanitation by quaternary ammonium chloride
Authors: Chen Qiyue , Palanisamy Vignesh , Wang Rong , Bosilevac Joseph M. , Chitlapilly Dass Sapna 
Published: January 2024

ABSTRACT

Salmonella enterica
is a prominent cause of foodborne disease in the United States. However, the mechanism and route of pathogen transmission that leads to
Salmonella
infection in commercial processing plants are poorly understood. This study aimed to investigate the effect of mixed-species biofilms on
S. enterica
survival and persistence under sanitizer stress [Quaternary ammonium compounds (QACs)] by analyzing 78 floor drain samples from a meat processing facility and three
S
.
enterica
strains (serovars Cerro, Montevideo, and Typhimurium) isolated from that facility and an unrelated source. The four test groups were as follows: control, QAC treatment,
Salmonella
addition, and QAC treatment with
Salmonella
addition. DNAs were extracted, and 16S rRNA gene based on the variable region V4 amplicon sequencing was performed to analyze the relative abundance, core microbiome, and Alpha and Beta diversity using the qiime2 pipeline. At the genus level, the
Brochothrix
(45.56%),
Pseudomonas
(38.94%),
Carnobacterium
(6.18%),
Lactococcus
(4.68%),
Serratia
(3.14%), and
Staphylococcus
(0.82%) were shown to be the most prevalent in all drain samples. The results demonstrate that the relative abundance of different bacterial genera was affected by both QAC treatment and
Salmonella
addition, with some genera showing increases or decreases in abundance. Notably, the correlation network was constructed to understand the relationships between the different bacteria.
Nitrospira
had the greatest number of connections in the floor drain environment network, with two negative and eight positive correlations. The results suggest that
Nitrospira
in the mixed-species biofilm community may play a role in converting ammonium in the QAC sanitizer into nitrites. Thus,
Nitrospira
could be a potentially important genus in providing sanitizer resistance to pathogen-encompassed mixed-species biofilms.

IMPORTANCE

Salmonella
contamination in meat processing facilities can lead to foodborne illness outbreaks. Our study characterized the microbiome dynamics in beef facility drains and their response to
Salmonella
addition and common sanitizer (QAC).
Nitrospira
could be an important genus in providing sanitizer resistance to pathogen-encompassed mixed-species biofilms. The results provide insight into the impact of mixed-species biofilms on
Salmonella
survival and persistence under sanitizer stress in meat processing facilities.
The results
highlight the need to consider mixed-species biofilm effects when developing targeted interventions to enhance food safety.
Molecular detection and characterization of the
Mycobacterium tuberculosis
complex subspecies responsible for bovine tuberculosis in Punjab, Pakistan
Authors: Maqsood Rubab , Duffy Shannon C. , Bin Rashid Hamad , Gill Shakera Sadiq , Jabeen Chanda , Arshad Nimra , Umbreen Gulshan , Behr Marcel A. , Kapur Vivek , Chaudhry Mamoona 
Published: January 2024

ABSTRACT

Bovine tuberculosis (bTB), traditionally associated with
Mycobacterium bovis
, presents significant public health and economic challenges worldwide. This study investigated the causative agents of bTB in slaughtered cattle and buffalo in Lahore, Pakistan. Of the 3,581 animals screened, 34 were identified with gross TB-like lesions. The lesions were processed for culture, PCR, and Sanger sequencing to identify the causative agents of the disease. The results identified 10
Mycobacterium orygis
and 8
Mycobacterium tuberculosis sensu stricto
isolates. Whole-genome sequencing was performed on two
M
.
orygis
isolates, and the sequences were phylogenetically compared to 93 publicly available
M. orygis
sequences. The results also demonstrated that the JB21 and JB22 primers, which have been previously commonly applied to detect
M. bovis
in Pakistan, are unable to distinguish between
M. tuberculosis
complex subspecies. The identification of
M. orygis
and
M. tuberculosis
as causative agents of bTB in this slaughterhouse in Punjab may have important implications in identifying cases of zoonotic TB in humans and applying appropriate molecular tools to identify the prevalence of the disease. The data from this study align with recent findings suggesting
M. orygis
is the predominant cause of bTB in South Asia.

IMPORTANCE

The study findings hold significant relevance to the Journal of Clinical Microbiology, as they directly impact the field. The first-time identification of
Mycobacterium orygis
and
Mycobacterium tuberculosis
as the predominant causative agents of bovine tuberculosis in Lahore, Pakistan underscores the urgent need for enhanced diagnostic methods. The study emphasizes the importance of improved assays for the accurate detection and differentiation of Mycobacterium subspecies. Additionally, the research addresses zoonotic risk assessment and public health implications, advocating for a multidisciplinary approach that integrates clinical microbiology with veterinary and human health sectors. These insights contribute to clinical microbiology knowledge, shaping effective strategies for disease prevention, surveillance, and control. The study’s potential to advance the field makes it well suited for publication in the Microbiology Spectrum journal.
Detection of rare carbapenemases in Enterobacterales—comparison of two colorimetric and three CIM-based carbapenemase assays
Authors: Schaffarczyk Lukas , Noster Janina , Stelzer Yvonne , Sattler Janko , Gatermann Sören , Hamprecht Axel 
Published: January 2024

ABSTRACT

Rapid and reliable detection of carbapenemase-producing Enterobacterales (CPE) is crucial for prompt treatment and infection control. Most assays target the primary four enzymes (KPC, OXA-48-like, VIM, and NDM), often missing less common variants (e.g., GES, IMI, OXA-23, and OXA-58). Therefore, assays based on the hydrolysis of carbapenems are recommended in addition to differentiation tests such as PCR or immunochromatographic assays. The aim of this study was to compare the currently Clinical and Laboratory Standards Institute (CLSI)-recommended tests mCIM (modified carbapenem inactivation method) and Carba NP with new colorimetric tests (NitroSpeed-Carba NP) and novel variations of the carbapenem inactivation method (CIM) such as simplified CIM (sCIM) or modified zinc-supplemented CIM (mzCIM). The challenge collection included 205 clinical isolates, 139 CPE vs 66 non-CPE. Among all 205 isolates, the sensitivity/specificity of mCIM was 81.3%/98.5%, Carba NP 76.3%/100%, NitroSpeed-Carba NP 86.3%/78.8%, sCIM 100%/94%, and mzCIM 97.8%/98.5%. For rare carbapenemases (
n
= 48), the sensitivity of mzCIM (98.3%) and sCIM (100%) was higher than that of mCIM (60.4%), Carba NP (50%), or NitroSpeed-Carba NP (70.2%). Most indeterminate results occurred for mCIM (14.4%), Carba NP (8.2%), and sCIM (6.3%). The detection of rare carbapenemases remains challenging with the currently recommended assays. The CIM-based tests demonstrated superior sensitivity, with sCIM and mzCIM outperforming the currently recommended mCIM and Carba NP, especially among isolates with weakly hydrolyzing carbapenemases (e.g., OXA-23 and OXA-58). Although colorimetric assays provide more rapid results, laboratories have to be aware of the low sensitivity for rare carbapenemases. Both sCIM and the new mzCIM performed well, are cost-effective, and can easily be implemented in any laboratory.

IMPORTANCE
Detection of so-called rare carbapenemases (e.g., GES, IMI, OXA-23, and OXA-58) in Enterobacterales is challenging, and data on the performance of currently available assays are scarce. This study systematically assessed the performance of currently recommended and novel hydrolysis-based assays on a set of molecularly characterized isolates. It demonstrates that the currently recommended assays mCIM and Carba NP perform well on isolates producing common carbapenemases such as KPC, VIM, NDM, and OXA-48, but have only a moderate sensitivity in the detection of rare carbapenemases. In contrast, the newer CIM-based variants, sCIM and mzCIM, are equally capable of detecting frequent and uncommon carbapenemases. These assays could potentially help to improve our knowledge on the epidemiology of these “rare” enzymes.
Dietary fibre intake and its association with ultraprocessed food consumption in the general population of Switzerland: analysis of a population-based, cross-sectional national nutrition survey
Authors: Schönenberger Katja A , Huwiler Valentina V , Reber Emilie , Mühlebach Stefan , Stanga Zeno , Pestoni Giulia , Faeh David 
Published: January 2024

Objectives
The objective of this study was to describe the compliance to dietary fibre recommendations of the Swiss population and to investigate the association between dietary fibre intake and ultraprocessed food (UPF) consumption.

Methods

Data were obtained from the cross-sectional Swiss National Nutrition Survey
menuCH
. We summarised the sociodemographic, lifestyle and anthropometric parameters as well as dietary data collected with two 24-hour dietary recalls for the whole population and subgroups according to absolute and relative dietary fibre intake. We analysed the associations between dietary fibre intake and UPF consumption by fitting multinomial logistic regression models. Data were weighted according to the
menuCH
weighting strategy to achieve a representation of the Swiss population.

Results

Data obtained from 2057 adults were included in the analysis, of which 87% had a dietary fibre intake of <30 g/day. Participants with high UPF consumption had lower odds of being in the medium or high dietary fibre intake groups than participants with low UPF consumption. The odds of being in the medium or high dietary fibre intake groups decreased linearly across quartiles of UPF consumption (
p
for trend ≤0.004).

Conclusions
Dietary fibre intake is insufficient in all population groups in Switzerland. UPF consumption is inversely and dose dependently associated with dietary fibre intake. To increase dietary fibre intake, public health measures should discourage UPF consumption and increase dietary fibre intake via unprocessed or minimally processed foods.
Health and social care professional standards need to be updated to advance leadership and action for environmental sustainability and planetary health
Authors: Walpole Sarah , Popat Aneka , Blakey Emma Pascale , Holden Eleanor , Whittaker Ben , Saggu Ravijyot , Fennell-Wells Amarantha , Armit Kirsten , Hothi Daljit 
Published: January 2024

BackgroundHuman health is inextricably linked to planetary health. The desire to nurture and protect both concurrently requires the mitigation of healthcare-associated environmental harms and global initiatives that support sustainable lifestyles. Health leadership is important to bring adequate attention and action to address planetary health challenges. Health professionals are central to this endeavour, but the will and energy of a few will not be adequate to address this urgent challenge.StudyWe present an appraisal of the current UK health professional standards, frameworks and curricula to identify content related to planetary health and environmental sustainability.ResultsNo current UK health professional standard provides statements and competencies to guide practising and trainee health professionals to focus on and advance the sustainability agenda within their clinical practice and across wider healthcare systems.ConclusionUpdate of health professional standards is needed to ensure that health professionals in every specialty are supported and encouraged to lead the implementation of environmentally sustainable practices within the health sector and advocate for planetary health.