bluuebunny/crossref_metadata_2025 huggingface dataset:
Acromegaly: Overview and associated temporomandibular joint disorders
Authors: Al‐Hadlaq Malak , Sroussi Herve
Published: January 2024

Objective

To provide a review on acromegaly and its orofacial manifestations, with a focus on associated arthropathies and temporomandibular joint disorders (TMD).

Methods

A review of current literature was performed through an electronic search of three databases: PubMed, ScienceDirect, and Google Scholar. The literature review was focused on the following topics of interest: etiology, diagnosis, and management of acromegaly, orofacial manifestations of acromegaly, acromegalic arthropathies, and acromegaly‐associated TMD.

Results

Acromegaly is a chronic multisystem condition in which excessive production of growth hormone in adults, most commonly caused by benign pituitary adenomas, leads to somatic overgrowth. Orofacial changes are considered hallmarks of the disease. It is important for dentists to recognize signs and symptoms of acromegaly, as this may help to achieve early diagnosis and improve overall disease prognosis. Acromegalic arthropathies typically involve large joints, however, the temporomandibular joints (TMJ) can be affected. TMD associated with acromegaly is under‐recognized and poorly characterized in current literature.

Conclusion

In the appropriate clinical context, acromegaly should be considered as part of the differential diagnosis for patients presenting with TMD. Further studies are needed to better characterize the nature of TMD associated with acromegaly and to define the role of TMJ involvement in early diagnosis.
Extracellular vesicles—Potential link between periodontal disease and diabetic complications
Authors: Huang Shengyuan , Lin Jiang , Han Xiaozhe
Published: January 2024

It has long been suggested that a bidirectional impact exists between periodontitis and diabetes. Periodontitis may affect diabetes glycemic control, insulin resistance, and diabetic complications. Diabetes can worsen periodontitis by delaying wound healing and increasing the chance of infection. Extracellular vesicles (EVs) are heterogeneous particles of membrane‐enclosed spherical structure secreted by eukaryotes and prokaryotes and play a key role in a variety of diseases. This review will introduce the biogenesis, release, and biological function of EVs from a microbial and host cell perspective, discuss the functional properties of EVs in the development of periodontitis and diabetes, and explore their role in the pathogenesis and clinical application of these two diseases. Their clinical implication and diagnostic value are also discussed.
Why future contingents are not all false*
Authors: MacFarlane John
Published: January 2024

Patrick Todd argues for a modified Peircean view on which all future contingents are false. According to Todd, this is the only view that makes sense if we fully embrace an open future, rejecting the idea of actual future history. I argue that supervaluational accounts, on which future contingents are neither true nor false, are fully consistent with the metaphysics of an open future. I suggest that it is Todd's failure to distinguish semantic and postsemantic levels that leads him to suppose otherwise. I also show how one can resist Todd's argument (with Brian Rabern) that the conceptual possibility of omniscience requires us to reject Retro‐closure ().
Restoration of boreal wetlands increases bat activity
Authors: Vasko Ville , Gaultier Simon P. , Blomberg Anna , Lilley Thomas M. , Norrdahl Kai , Brommer Jon E.
Published: January 2024

Wetlands are important habitats for insectivorous bats, as the presence of water promotes insect abundance and provides drinking water for wildlife, and therefore could promote bat conservation. Research on bats and wetlands has mainly focused on constructed wetlands, and with a geographical emphasis on eastern United States and central Europe, whereas relatively little is known about the effects of wetland restoration on bats, especially in the boreal zone. We conducted a Before‐After‐Control‐Impact (BACI) study in 21 wetlands. Using acoustic survey techniques, we collected information on bats both before and after restoration, with 7 of the 21 wetlands acting as control sites and 14 as impact (i.e., restored) sites. Acoustic surveys were conducted in May–September in the years 2018, 2019 (before restoration) and in 2021 and 2022 (after restoration). Species detection for each night was assessed by automated analysis of audio recordings. We assessed the presence and number of active minutes of the Northern bat (Eptesicus nilssonii) and the Myotis species group, using a generalized linear mixed model. Wetland restoration increased the acoustic activity of both taxa, but not their presence. Thus, restoration increased the usage of wetlands as a feeding site for bats. Our BACI study provides strong evidence that wetland restoration caused an increase in bat activity, and can be used as an effective tool for bat conservation.
The moral, the political and social licence in digitally‐driven family policy and intervention: Parents negotiating experiential knowledge and ‘other’ families
Authors: Edwards Rosalind , Gillies Val , Vannier‐Ducasse Hélène , Gorin Sarah
Published: January 2024

The article provides a conceptually informed empirical critique of the pursuit of social licence as a warrant for data linkage and predictive analytics in the field of family policy intervention. It draws on research focusing on parental views of digitally‐driven family governance in the United Kingdom. We identify the notion of consensus that undergirds the concept of social licence that acts to obscure inequalities and silence conflict, and to reframe digital surveillance and prediction as a moral rather than political issue. Using focus group and individual interview material, we show how parents assert professional or lay experiential knowledges in making judgements about the legitimacy of and trust in operational data technologies, involving struggles between positionings as parents like ‘us’ and ‘other’ parents. We demonstrate how parents have different leverages from these unequal and morally charged social locations. Inevitably, the application of social licence in the domain of digital family policy and intervention is fractured by entrenched social divisions and inequalities.
Making futures in Oaxaca: Remittances in the diverse economies of social reproduction
Authors: Smyth Araby
Published: January 2024

In this article, I analyse intermingling economically productive and reproductive work at the global and local scale through the lens of how remittances are folded into the communal social relations of one Indigenous community in Oaxaca. Scholars have illustrated the many ways that social reproduction is reconfigured through transnational labour migration, and troubled the categorisation of economically productive and socially reproductive labour. Expanding on their work, I engage with scholarship about Indigenous communal governance in Guatemala and Mexico, particularly the theories of Gladys Tzul Tzul on reproduction, in order to present new insights into feminist geographical knowledge of diverse economies and social reproduction. Drawing on ethnographic methods, I present three empirical examples, which illustrate how the intermingling of economic production and reproduction of communal life make Indigenous futures. I argue that large‐scale reproductive activities, such as those deployed by the community, produce values beyond capitalist circuits of production and that it is how remittances are inserted into the local communal economies that render the money valuable for reproducing life and securing a future.
MicroPulse™ transscleral cyclophotocoagulation in the equine patient: A case series of four horses
Authors: Sturbaum A. M. , Kaiser K. J. , Riesberg J. S.
Published: January 2024

Objective

To describe the clinical application and outcome of MicroPulse™ transscleral cyclophotocoagulation (MP‐TSCPC) treatment in horses with glaucoma.

Animals Studied

Four client‐owned horses with primary (n = 2) or secondary (n = 2) glaucoma.

Methods

Horses were treated with MP‐TSCPC under standing sedation with a minimum of 30 days of follow‐up (range 30–1241 days). Affected eyes were treated with a 31.3% duty cycle and 3000 mW laser power for a total of 180 s. Data collected included signalment, pre‐ and post‐procedure intraocular pressures (IOPs), laser settings, medications, complications, and repeat therapy.

Results

Four horses (5 eyes) received at least one treatment with MP‐TSCPC. Mean preoperative IOP was 44 mmHg (range 33–49 mmHg). The immediate mean postoperative IOP was 34 mmHg (4 eyes; range 19–55 mmHg). At 1 week, IOP was 38 mmHg (5 eyes; range 21–80 mmHg), at 2 weeks was 40 mmHg (3 eyes, range 17–80 mmHg), at 1 month was 35 mmHg (5 eyes; range 20–50 mmHg), at 3 months was 18 mmHg (2 eyes; range 14–21 mmHg), at 6 months was 35 mmHg (2 eyes; range 30–39 mmHg), and at >300 days was 24 mmHg (3 eyes; range 18–29 mmHg). Complications included corneal ulceration (n = 1 eye), uncontrolled IOP (n = 3 eyes), and need for repeat treatment (n = 2 eyes).

Conclusions

MP‐TSCPC used with the above‐described settings was unsuccessful in treating the majority of cases. Future studies should be targeted at primary glaucoma cases and with use of alternative laser settings.
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
Culture, diversity and deconstruction of prejudices in schools
Authors: Dantas de Paula Luciana , Uchoa-Branco Angela
Published: January 2024

Objective. This research paper is aimed at identifying and analyzing relevant aspects concerning concepts as well as cultural and pedagogical practices related to the intended deconstruction of prejudices proposed by a project in the context of a public elementary school. Method. Participant observation procedures were adopted to investigate activities related to the project and semi-structured individual interviews were conducted with six educators. Furthermore, one focus group session was conducted with a class of 25 students in the 9th grade. Results. indicated successful work to achieve the intended objectives, as well as aspects that were obstacles. It was concluded that lectures are not enough to address sensitive issues linked to the deconstruction of prejudices, for educators’ deep affective-laden values and beliefs can negatively interfere with their dialogical dispositions towards students. Conclusion. We claim that dialogical practices are crucial to help deconstruct prejudices and develop constructive relations among everyone, as they may work to foster social justice and democracy within schools and beyond.
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

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

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.
Documenting and modeling the acoustic variability of intervocalic alveolar taps in conversational Peninsular Spanish
Authors: Perry Scott James , Kelley Matthew C. , Tucker Benjamin V.
Published: January 2024

This study constitutes an investigation into the acoustic variability of intervocalic alveolar taps in a corpus of spontaneous speech from Madrid, Spain. Substantial variability was documented in this segment, with highly reduced variants constituting roughly half of all tokens during spectrographic inspection. In addition to qualitative documentation, the intensity difference between the tap and surrounding vowels was measured. Changes in this intensity difference were statistically modeled using Bayesian finite mixture models containing lexical and phonetic predictors. Model comparisons indicate predictive performance is improved when we assume two latent categories, interpreted as two pronunciation variants for the Spanish tap. In interpreting the model, predictors were more often related to categorical changes in which pronunciation variant was produced than to gradient intensity changes within each tap type. Variability in tap production was found according to lexical frequency, speech rate, and phonetic environment. These results underscore the importance of evaluating model fit to the data as well as what researchers modeling phonetic variability can gain in moving past linear models when they do not adequately fit the observed data.
Freeze-thaw cycles drove chemical weathering and enriched sulfates in the Burns formation at Meridiani, Mars
Authors: Liu Jiacheng , Michalski Joseph R. , Gao Wenyuan , Schröder Christian , Li Yi-Liang
Published: January 2024

Sulfate-rich sedimentary rocks explored by the Opportunity rover during its 14-year surface mission at Meridiani Planum provide an invaluable window into the thousands of sulfate deposits detected on Mars via remote sensing. Existing models explaining the formation of martian sulfates can be generally described as either bottom-up, groundwater-driven playa settings or top-down icy chemical weathering environments. Here, we propose a hybrid model involving both bottom-up and top-down processes driven by freeze-thaw cycles. Freezing leads to cryo-concentration of acidic fluids from precipitations at the surface, facilitating rapid chemical weathering despite low temperatures. Cryosuction causes the upward migration of vadose water and even groundwater with dissolved ions, resulting in the accumulation of ions in near-surface environments. Evaporation precipitates salts, but leaching separates chlorides from sulfates during the thawing period. Freeze-thaw cycles, therefore, can enrich sulfates at the surface. While freeze-thaw is more commonly understood as a mechanism of physical weathering, we suggest that it is a fundamental aspect of chemical weathering on Mars.
DTC: Deep Tracking Control
Authors: Jenelten Fabian , He Junzhe , Farshidian Farbod , Hutter Marco
Published: January 2024

Legged locomotion is a complex control problem that requires both accuracy and robustness to cope with real-world challenges. Legged systems have traditionally been controlled using trajectory optimization with inverse dynamics. Such hierarchical model-based methods are appealing because of intuitive cost function tuning, accurate planning, generalization, and, most importantly, the insightful understanding gained from more than one decade of extensive research. However, model mismatch and violation of assumptions are common sources of faulty operation. Simulation-based reinforcement learning, on the other hand, results in locomotion policies with unprecedented robustness and recovery skills. Yet, all learning algorithms struggle with sparse rewards emerging from environments where valid footholds are rare, such as gaps or stepping stones. In this work, we propose a hybrid control architecture that combines the advantages of both worlds to simultaneously achieve greater robustness, foot-placement accuracy, and terrain generalization. Our approach uses a model-based planner to roll out a reference motion during training. A deep neural network policy is trained in simulation, aiming to track the optimized footholds. We evaluated the accuracy of our locomotion pipeline on sparse terrains, where pure data-driven methods are prone to fail. Furthermore, we demonstrate superior robustness in the presence of slippery or deformable ground when compared with model-based counterparts. Last, we show that our proposed tracking controller generalizes across different trajectory optimization methods not seen during training. In conclusion, our work unites the predictive capabilities and optimality guarantees of online planning with the inherent robustness attributed to offline learning.
A growing soft robot with climbing plant–inspired adaptive behaviors for navigation in unstructured environments
Authors: Del Dottore Emanuela , Mondini Alessio , Rowe Nick , Mazzolai Barbara
Published: January 2024

Self-growing robots are an emerging solution in soft robotics for navigating, exploring, and colonizing unstructured environments. However, their ability to grow and move in heterogeneous three-dimensional (3D) spaces, comparable with real-world conditions, is still developing. We present an autonomous growing robot that draws inspiration from the behavioral adaptive strategies of climbing plants to navigate unstructured environments. The robot mimics climbing plants’ apical shoot to sense and coordinate additive adaptive growth via an embedded additive manufacturing mechanism and a sensorized tip. Growth orientation, comparable with tropisms in real plants, is dictated by external stimuli, including gravity, light, and shade. These are incorporated within a vector field method to implement the preferred adaptive behavior for a given environment and task, such as growth toward light and/or against gravity. We demonstrate the robot’s ability to navigate through growth in relation to voids, potential supports, and thoroughfares in otherwise complex habitats. Adaptive twining around vertical supports can provide an escape from mechanical stress due to self-support, reduce energy expenditure for construction costs, and develop an anchorage point to support further growth and crossing gaps. The robot adapts its material printing parameters to develop a light body and fast growth to twine on supports or a tougher body to enable self-support and cross gaps. These features, typical of climbing plants, highlight a potential for adaptive robots and their on-demand manufacturing. They are especially promising for applications in exploring, monitoring, and interacting with unstructured environments or in the autonomous construction of complex infrastructures.
Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy
Authors: Li Guangyuan , Mahajan Shweta , Ma Siyuan , Jeffery Erin D. , Zhang Xuan , Bhattacharjee Anukana , Venkatasubramanian Meenakshi , Weirauch Matthew T. , Miraldi Emily R. , Grimes H. Leighton , Sheynkman Gloria M. , Tilburgs Tamara , Salomonis Nathan
Published: January 2024

Immunotherapy has emerged as a crucial strategy to combat cancer by “reprogramming” a patient’s own immune system. Although immunotherapy is typically reserved for patients with a high mutational burden, neoantigens produced from posttranscriptional regulation may provide an untapped reservoir of common immunogenic targets for new targeted therapies. To comprehensively define tumor-specific and likely immunogenic neoantigens from patient RNA-Seq, we developed Splicing Neo Antigen Finder (SNAF), an easy-to-use and open-source computational workflow to predict splicing-derived immunogenic MHC-bound peptides (T cell antigen) and unannotated transmembrane proteins with altered extracellular epitopes (B cell antigen). This workflow uses a highly accurate deep learning strategy for immunogenicity prediction (DeepImmuno) in conjunction with new algorithms to rank the tumor specificity of neoantigens (BayesTS) and to predict regulators of mis-splicing (RNA-SPRINT). T cell antigens from SNAF were frequently evidenced as HLA-presented peptides from mass spectrometry (MS) and predict response to immunotherapy in melanoma. Splicing neoantigen burden was attributed to coordinated splicing factor dysregulation. Shared splicing neoantigens were found in up to 90% of patients with melanoma, correlated to overall survival in multiple cancer cohorts, induced T cell reactivity, and were characterized by distinct cells of origin and amino acid preferences. In addition to T cell neoantigens, our B cell focused pipeline (SNAF-B) identified a new class of tumor-specific extracellular neoepitopes, which we termed ExNeoEpitopes. ExNeoEpitope full-length mRNA predictions were tumor specific and were validated using long-read isoform sequencing and in vitro transmembrane localization assays. Therefore, our systematic identification of splicing neoantigens revealed potential shared targets for therapy in heterogeneous cancers.
Mitochondria-mediated ferroptosis contributes to the inflammatory responses of bovine viral diarrhea virus (BVDV)
in vitro
Authors: Li Zhijun , Zhao Bao , Zhang Ying , Fan Wenqi , Xue Qinghong , Chen Xiwen , Wang Jingyu , Qi Xuefeng
Published: January 2024

Bovine viral diarrhea virus (BVDV) threatens a wide range of domestic and wild cattle population worldwide. BVDV causes great economic loss in cattle industry through its immunosuppression and persistent infection. Despite extensive research, the mechanism underlying the pathogenesis of BVDV remains elusive. Our data provide the first direct evidence that mitochondria-mediated ferroptosis and mitophagy are involved in inflammatory responses in both biotypes of BVDV-infected cells. Importantly, we demonstrate that the different degrees of injury of mitochondria and inflammatory responses may attribute to different mitophagy pathways induced by biotypes of BVDV. Overall, our findings uncover the interaction between BVDV infection and mitochondria-mediated ferroptosis, which shed novel light on the physiological impacts of ferroptosis on the pathogenesis of BVDV infection, and provide a promising therapeutic strategy to treat this important infectious disease with a worldwide distribution.
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

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

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

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

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

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.
Erratum to: Air Composition over the Russian Arctic: 1—Methane
Authors: Antokhina O. Yu. , Antokhin P. N. , Arshinova V. G. , Arshinov M. Yu. , Belan B. D. , Belan S. B. , Guruleva E. V. , Davydov D. K. , Ivlev G. A. , Kozlov A. V. , Law K. , Rasskazchikova T. M. , Paris J.-D. , Savkin D. E. , Simonenkov D. V. , Sklyadneva T. K. , Tolmachev G. N. , Fofonov A. V.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1024856023340018
Congenital syphilis: the re-emergence of a forgotten disease
Authors: Foles Ana Isabel , Eiras Dias Mariana , Figueiredo Melissa , Marçal Mónica
Published: January 2024

A preterm newborn presented at birth with generalised oedema, disseminated bullous and desquamative exanthema with palmoplantar involvement and hepatomegaly, admitted to the neonatal intensive care unit with severe multisystemic disease, haemodynamic instability and respiratory distress. The mother had a history of treated latent syphilis before pregnancy. Venereal Disease Research Laboratory screening was negative in the first trimester, titre 1:2 in second trimester and 1:32 in the third trimester, a result only available to the medical team at birth. The mother’s rapid plasma reagin (RPR) titre was 1:64 at birth. The newbon’s RPR titre was 1:256, confirming the diagnosis of early congenital syphilis. The newborn was treated with aqueous penicillin G, with clinical and laboratorial progressive recovery. Congenital syphilis is a preventable disease, but despite prenatal screening programmes, it remains a significant public health issue worldwide with high morbidity and mortality.
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

Background

Human 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.

Study

We present an appraisal of the current UK health professional standards, frameworks and curricula to identify content related to planetary health and environmental sustainability.

Results

No 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.

Conclusion

Update 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.
Coupling of WetSpass-M and MODFLOW models for groundwater flow assessment
Authors: Dowlatabadi Sepideh , Amirabadizadeh Mahdi , Zarei Mahdi
Published: January 2024

Recharge is considered a key parameter in groundwater models for sustainable management of aquifers, which is influenced by factors such as land use, soil and weather. The present study was conducted to couple WetSpass-M and MODFLOW models in the Neyshabur–Rokh Basin. To this aim, the simulated recharge by the WetSpass-M model was applied as an input into MODFLOW to assess the groundwater balance. The hydrodynamic coefficients were determined by calibrating the model, and the model sensitivity to the hydraulic conductivity coefficient, specific yield and recharge was evaluated. The results indicated that the annual average of surface runoff, actual evapotranspiration, interception and recharge during 1991–2017 equalled 18, 36, 7.6 and 42.6% of the average annual precipitation in the basin, respectively. The accurate alignment of simulated and observed water levels, along with the achievement of suitable evaluation criteria values in both steady and transient states, demonstrates the WetSpass-M model's precision in estimating recharge and successfully integrating the two models. The groundwater balance assessment revealed a significant deficit in the aquifer, with the model demonstrating greater sensitivity to the hydraulic conductivity coefficient and providing valuable insights for the sustainable management of the Neyshabur aquifer.

Thematic collection:
This article is part of the Monitoring the aquifers collection available at:
https://www.lyellcollection.org/topic/collections/monitoring-the-aquifers