bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of rock mass units using a non-invasive geophysical approach
Authors: Hasan Muhammad , Shang Yanjun , Meng Qingsen
Published: September 2023

Thorough and accurate assessment of rock mass units is important for development of engineering infrastructures and groundwater resources assessments. Rock mass units are widely evaluated by reliable geomechanical parameters namely rock quality designation (RQD) and rock core index (RCI). Conventionally, these parameters are acquired via an extensive number of geotechnical tests. Such tests, however, suffer efficiency for data coverage, cost, equipment and topographic constrictions, and hence cause ambiguity in geological models for a detailed evaluation of rock mass integrity. Conversely, geophysical surveys offer fast, more user-friendly, less invasive, more cost-effective and less time-consuming approach for geological investigations. The past research confirms a useful link between geophysical and geotechnical parameters. But, none of the past studies provides a suitable and generalized relation between these parameters which can reduce geotechnical model uncertainty mostly caused by inadequate data and subsurface heterogeneity. This paper proposes a meaningful and feasible method to obtain geomechanical parameters using a certain number of drillings and geophysical data of four different sites. Based on electrical resistivity obtained from electrical resistivity tomography (ERT) and controlled-source audio-frequency magneto telluric (CSAMT), this research provides the general and adaptable formulas for geotechnical parameter estimation and reduces geological model uncertainty for more detailed 2D/3D imaging of RQD and RCI covering the whole sites where even no drilling data exists. Thus, the investigated sites are assessed laterally and vertically along each geophysical profile via distinct value ranges of geological parameters for a thorough and reliable evaluation of rock mass units in highly heterogeneous setting. Our research reduces the ambiguity caused by structural heterogeneities and scarce data, fills the gap between inadequate well tests and the true geological models, and gives new insights into the rock mass units for proper engineering design and groundwater exploitation.
Real-time rate of penetration prediction for motorized bottom hole assembly using machine learning methods
Authors: Shokry Amir , Elkatatny Salaheldin , Abdulraheem Abdulazeez
Published: September 2023

Drilling rate of penetration (ROP) is one of the most important factors that have their significant effect on the drilling operation economically and efficiently. Motorized bottom hole assembly (BHA) has different applications that are not limited to achieve the required directional work but also it could be used for drilling optimization to enhance the ROP and mitigate the downhole vibration. Previous work has been done to predict ROP for rotary BHA and for rotary steerable system BHA; however, limited studies considered to predict the ROP for motorized BHA. In the present study, two artificial intelligence techniques were applied including artificial neural network and adaptive neurofuzzy inference system for ROP prediction for motorized assembly in the rotary mode based on surface drilling parameters, motor downhole output parameters besides mud parameters. This new robust model was trained and tested to accurately predict the ROP with more than 5800 data set with a 70/30 data ratio for training and testing respectively. The accuracy of developed models was evaluated in terms of average absolute percentage error, root mean square error, and correlation coefficient (R). The obtained results confirmed that both models were capable of predicting the motorized BHA ROP on Real-time. Based on the proposed model, the drilling parameters could be optimized to achieve maximum motorized BHA ROP. Achieving maximum ROP will help to reduce the overall drilling cost and as well minimize the open hole exposure time. The proposed model could be considered as a robust tool for evaluating the motorized BHA performance against the different BHA driving mechanisms which have their well-established models.
Bioparameter-directed nanoformulations as MRI CAs enable the specific visualization of hypoxic tumour
Authors: Lu Xinyi , Wang Xin , Gao Susu , Chen Ziwei , Bai Ru , Wang Yaling
Published: September 2023

The significant development of bioparameter-directed nanoformulations as MRI contrast agents for tumour diagnosis has been explained.
Advances and challenges in scalable carbon dioxide electrolysis
Authors: Sun Ji Wei , Fu Huai Qin , Liu Peng Fei , Chen Aiping , Liu Porun , Yang Hua Gui , Zhao Huijun
Published: September 2023

This perspective illustrates ways to achieve scalable CO2 electrolysis by designing efficient electrolyzers and regulating the catalytic reaction environments.
CT-Guided Percutaneous Thrombin Injection of Posttraumatic Aortic Branch Pseudoaneurysm
Authors: Devane Aron Michael , Schammel Christine Marie Gilligan
Published: September 2023

A pseudoaneurysm of an aortic branch artery is a potentially life-threatening uncommon occurrence, which may result in retroperitoneal hemorrhage. Imaging-guided percutaneous thrombin injection has a high technical success and effectiveness rate for treating pseudoaneurysms of the femoral, iliac, and popliteal arteries. We present a case of a retroperitoneal hemorrhage in a patient with a periaortic branch pseudoaneurysm, potentially from an avulsed lumbar artery. Anatomy prevented fixation with a covered stent; the comorbidities eliminated safe surgical repair, and endovascular embolization was not an option due to the avulsion. Computed tomography (CT) fluoroscopy-guided thrombin injection provided a safe, successful embolization with no postprocedural complications.
Freezing and thawing of cells on a microfluidic device: a simple and time-saving experimental procedure
Authors: Lv Xiaoqing , Ma Zhengtai , Guo Lin
Published: September 2023

Developing cell cryopreservation methods on chips is not only crucial for biomedical science but also represents an innovative approach for preserving traditional cell samples. This study presents a simple method for direct cell freezing and thawing on chip, allowing for long-term storage of cells. During the freezing process, cells were injected into the microchannel along with a conventional cell cryopreservation solution, and the chip was packed using a self-sealing bag containing isopropyl alcohol and then stored in a –80°C refrigerator until needed. During the thawing process, microcolumn arrays with a spacing of 8 µm were strategically incorporated into the microfluidic chip design to effectively inhibit cells from the channel. The breast cancer cell lines MDA-MB-231 and B47D demonstrated successful thawing and growth after cryopreservation for 1 month to 1 year. These findings offer a direct cell freezing and thawing method on a microfluidic chip for subsequent experiments.
Genome-wide multimediator analyses using the generalized Berk–Jones statistics with the composite test
Authors: Lai En-Yu , Huang Yen-Tsung
Published: September 2023

Motivation

Mediation analysis is performed to evaluate the effects of a hypothetical causal mechanism that marks the progression from an exposure, through mediators, to an outcome. In the age of high-throughput technologies, it has become routine to assess numerous potential mechanisms at the genome or proteome scales. Alongside this, the necessity to address issues related to multiple testing has also arisen. In a sparse scenario where only a few genes or proteins are causally involved, conventional methods for assessing mediation effects lose statistical power because the composite null distribution behind this experiment cannot be attained. The power loss hence decreases the true mechanisms identified after multiple testing corrections. To fairly delineate a uniform distribution under the composite null, Huang (Genome-wide analyses of sparse mediation effects under composite null hypotheses. Ann Appl Stat 2019a;13:60–84; AoAS) proposed the composite test to provide adjusted P-values for single-mediator analyses.

Results

Our contribution is to extend the method to multimediator analyses, which are commonly encountered in genomic studies and also flexible to various biological interests. Using the generalized Berk–Jones statistics with the composite test, we proposed a multivariate approach that favors dense and diverse mediation effects, a decorrelation approach that favors sparse and consistent effects, and a hybrid approach that captures the edges of both approaches. Our analysis suite has been implemented as an R package MACtest. The utility is demonstrated by analyzing the lung adenocarcinoma datasets from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium. We further investigate the genes and networks whose expression may be regulated by smoking-induced epigenetic aberrations.

Availability and implementation

An R package MACtest is available on https://github.com/roqe/MACtest.
An intersectional framework for counterfactual fairness in risk prediction
Authors: Wastvedt Solvejg , Huling Jared D , Wolfson Julian
Published: September 2023

Along with the increasing availability of health data has come the rise of data-driven models to inform decision making and policy. These models have the potential to benefit both patients and health care providers but can also exacerbate health inequities. Existing “algorithmic fairness” methods for measuring and correcting model bias fall short of what is needed for health policy in two key ways. First, methods typically focus on a single grouping along which discrimination may occur rather than considering multiple, intersecting groups. Second, in clinical applications, risk prediction is typically used to guide treatment, creating distinct statistical issues that invalidate most existing techniques. We present novel unfairness metrics that address both challenges. We also develop a complete framework of estimation and inference tools for our metrics, including the unfairness value (“u-value”), used to determine the relative extremity of unfairness, and standard errors and confidence intervals employing an alternative to the standard bootstrap. We demonstrate application of our framework to a COVID-19 risk prediction model deployed in a major Midwestern health system.
Variable selection in high dimensions for discrete-outcome individualized treatment rules: Reducing severity of depression symptoms
Authors: Moodie Erica E M , Bian Zeyu , Coulombe Janie , Lian Yi , Yang Archer Y , Shortreed Susan M
Published: September 2023

Despite growing interest in estimating individualized treatment rules, little attention has been given the binary outcome setting. Estimation is challenging with nonlinear link functions, especially when variable selection is needed. We use a new computational approach to solve a recently proposed doubly robust regularized estimating equation to accomplish this difficult task in a case study of depression treatment. We demonstrate an application of this new approach in combination with a weighted and penalized estimating equation to this challenging binary outcome setting. We demonstrate the double robustness of the method and its effectiveness for variable selection. The work is motivated by and applied to an analysis of treatment for unipolar depression using a population of patients treated at Kaiser Permanente Washington.
Safety, tolerability, pharmacokinetics and efficacy of HB0017, a humanized monoclonal antibody that targets interleukin-17A, in healthy participants and patients with moderate-to-severe plaque psoriasis
Authors: Jiang Congjun , Du Yu , Liu Xiaoyan , Wang Jingjing , Ge Cuizhu , Xu Jingyue , Wang Shuoxiong , Li Benke , Zhu Gege , Zhang Wanlu , Qian Qiaoxiao , Ma Chi , Zhu Xiangyang , Zhan Yifan , Yang Yongmin
Published: September 2023

Background

Several interleukin (IL)-17 inhibitors have been approved for the treatment of moderate-to-severe plaque psoriasis (PsO). There is still scope for the development of affordable treatments for PsO.

Objectives

To assess, in a phase Ia study, the safety, tolerability and pharmacokinetics (PK) of HB0017, a humanized monoclonal antibody that targets IL-17A, in healthy participants and patients with moderate-to-severe plaque PsO; and, in a phase Ib study, to assess the efficacy of HB0017 in patients with moderate-to-severe plaque PsO.

Methods

The phase Ia study (NCT04505033) was a randomized double-blind placebo-controlled dose-escalation study in healthy participants. Each cohort of 10 volunteers was randomly assigned to receive either a single dose of HB0017 (50 mg, 150 mg, 300 mg or 450 mg) or the matching placebo at a ratio of 4 : 1. The phase Ib study (NCT05442788) was a randomized double-blind placebo-controlled dose-escalation study in enrolled patients with moderate-to-severe plaque PsO. Each cohort of 10 patients was randomly assigned to receive either multiple doses of HB0017 (150 mg, 300 mg or 450 mg) or the matching placebo at a ratio of 4 : 1.

Results

HB0017 demonstrated dose-proportional linear PK and was tolerated across the dose range assessed. In the phase Ia and Ib studies, participants in both the HB0017 and placebo groups experienced treatment-emergent adverse events (69% vs. 87%, 96% vs. 100%, respectively). HB0017 demonstrated clinically meaningful effects in patients with moderate-to-severe plaque PsO. PASI 75 [≥ 75% improvement in Psoriasis Area and Severity Index (PASI)], PASI 90 (≥ 90% improvement in PASI) and static Physician Global Assessment (sPGA) 0/1 (i.e. ‘clear’ or ‘almost clear’) responses were 100% for the HB0017 300-mg group, with maximal improvements (100% or near 100% reductions from baseline) in PASI score observed at week 12, while the duration of effect was evident up to week 20. There was no clinical response in any participant in the placebo group in the phase Ib study.

Conclusions

Overall, HB0017 showed acceptable safety and tolerability in both healthy participants and patients with moderate-to-severe plaque PsO. An encouraging signal of efficacy with a longer half-life provides HB0017 with the potential to be added to the currently available range of biologics targeting IL-17A.
Hidradenitis suppurativa tarda: defining an understudied elderly population
Authors: van der Weijden Deveny A Y , Koerts Nicole D K , van Munster Barbara C , van der Zee Hessel H , Horváth Barbara
Published: September 2023

Background

Hidradenitis suppurativa (HS) is a chronic, devastating, multifactorial skin disease. Patients generally develop HS after puberty and the prevalence of the disease is assumed to decrease with higher age. Data outside the usual age range are limited, especially for elderly patients.

Objectives

To investigate the prevalence, clinical characteristics and associated comorbidities among the elderly HS population.

Methods

Data were collected through a population-wide survey-based study within the Lifelines Cohort Study in the Netherlands. The clinical characteristics of elderly patients with HS (≥ 60 years) were compared with an adult population (< 60 years) with HS. The comorbidities in elderly patients with HS were compared with those of a non-HS sex- and age-matched elderly population in a 1 : 4 ratio. HS in the elderly was defined as active HS in patients aged 60 years and older. Within the HS elderly group, two subgroups were defined, late-onset HS (HS developed after 60 years of age) and persistent HS (HS developed from a younger age but continuing after 60 years of age).

Results

Within the Lifelines cohort 209 elderly patients with HS were identified as well as an adult (< 60 years) group with HS (n = 793) and a non-HS sex- and age-matched control elderly group (n = 810). The prevalence of HS among the elderly bootstrap analysis population was 0.8% [95% confidence interval (CI) 0.4–1.2]. A significantly higher age of HS symptom onset was found compared with the adult HS group: respectively, 40 vs. 23 years (odds ratio 1.056, 95% CI 1.05–1.07). Among the elderly HS cohort (in the Discussion, the HS tarda cohort) a female : male ratio of 1.7 : 1.0 and a higher family history for HS were found. Moreover, elderly patients with HS had a significantly higher risk of having HS-associated comorbidities compared with the sex- and age-matched controls.

Conclusions

The prevalence of HS in the elderly is not rare. Among the elderly a shift from female predominance towards a lower female : male ratio in HS is observed. In addition, HS in the elderly showed significant variation in age of onset and involved body areas. Moreover, elderly patients with HS were more susceptible to multimorbidity. Finally, we propose defining HS in the elderly as ‘HS tarda’ and subdividing it as late-onset and persistent HS tarda.
Cross-seeding by prion protein inactivates TDP-43
Authors: Polido Stella A , Stuani Cristiana , Voigt Aaron , Banik Papiya , Kamps Janine , Bader Verian , Grover Prerna , Krause Laura J , Zerr Inga , Matschke Jakob , Glatzel Markus , Winklhofer Konstanze F , Buratti Emanuele , Tatzelt Jörg
Published: September 2023

A common pathological denominator of various neurodegenerative diseases is the accumulation of protein aggregates. Neurotoxic effects are caused by a loss of the physiological activity of the aggregating protein and/or a gain of toxic function of the misfolded protein conformers. In transmissible spongiform encephalopathies or prion diseases, neurodegeneration is caused by aberrantly folded isoforms of the prion protein (PrP). However, it is poorly understood how pathogenic PrP conformers interfere with neuronal viability. Employing in vitro approaches, cell culture, animal models and patients’ brain samples, we show that misfolded PrP can induce aggregation and inactivation of TAR DNA-binding protein-43 (TDP-43).

Purified PrP aggregates interact with TDP-43 in vitro and in cells and induce the conversion of soluble TDP-43 into non-dynamic protein assemblies. Similarly, mislocalized PrP conformers in the cytosol bind to and sequester TDP-43 in cytosolic aggregates. As a consequence, TDP-43-dependent splicing activity in the nucleus is significantly decreased, leading to altered protein expression in cells with cytosolic PrP aggregates. Finally, we present evidence for cytosolic TDP-43 aggregates in neurons of transgenic flies expressing mammalian PrP and Creutzfeldt–Jakob disease patients.

Our study identified a novel mechanism of how aberrant PrP conformers impair physiological pathways by cross-seeding.
Optimal subthalamic stimulation sites and related networks for freezing of gait in Parkinson’s disease
Authors: Fan Houyou , Guo Zijian , Jiang Yin , Xue Tao , Yin Zixiao , Xie Hutao , Diao Yu , Hu Tianqi , Zhao Baotian , Wu Delong , An Qi , Xu Yichen , Gao Yuan , Bai Yutong , Zhang Jianguo
Published: September 2023

Freezing of gait is a common and debilitating symptom in Parkinson’s disease. Although high-frequency subthalamic deep brain stimulation is an effective treatment for Parkinson’s disease, post-operative freezing of gait severity has been reported to alleviate, deteriorate or remain constant. We conducted this study to explore the optimal stimulation sites and related connectivity networks for high-frequency subthalamic deep brain stimulation treating freezing of gait in Parkinson’s disease. A total of 76 Parkinson’s disease patients with freezing of gait who underwent bilateral high-frequency subthalamic stimulation were retrospectively included. The volumes of tissue activated were estimated based on individual electrode reconstruction. The optimal and sour stimulation sites were calculated at coordinate/voxel/mapping level and mapped to anatomical space based on patient-specific images and stimulation settings. The structural and functional predictive connectivity networks for the change of the post-operative Freezing of Gait-Questionnaire were also identified based on normative connectomes derived from the Parkinson’s Progression Marker Initiative database. Leave-one-out cross-validation model validated the above results, and the model remained significant after including covariates. The dorsolateral two-thirds of the subthalamic nucleus was identified as the optimal stimulation site, while the ventrocentral portion of the right subthalamic nucleus and internal capsule surrounding the left central subthalamic nucleus were considered as the sour stimulation sites. Modulation of the fibre tracts connecting to the supplementary motor area, pre-supplementary motor area and pedunculopontine nucleus accounted for the alleviation of freezing of gait, whereas tracts connecting to medial and ventrolateral prefrontal cortices contributed to the deterioration of freezing of gait. The optimal/sour stimulation sites and structural/functional predictive connectivity networks for high-frequency subthalamic deep brain stimulation treating freezing of gait are identified and validated through sizable Parkinson’s disease patients in this study. With the growing understanding of stimulation sites and related networks, individualized deep brain stimulation treatment with directional leads will become an optimal choice for Parkinson’s disease patients with freezing of gait in the future.
Red-faced lies: a qualitative analysis of online misinformation and conspiracy theories in rosacea
Authors: Fuller James , Murphy Michelle , O’Connor Cathal
Published: September 2023

Rosacea is a common chronic inflammatory skin disease with a complex aetiology and major psychological impact, rendering patients susceptible to misinformation. We aimed to assess the content of rosacea-related misinformation online. A formal review of PubMed was performed, using the terms ‘rosacea’ AND ‘misinformation’ OR ‘disinformation’ OR ‘conspiracy theory’, along with informal Google searches using combinations of these terms, and further targeted searches on Twitter, Facebook, Instagram and TikTok. Key areas of misinformation identified in the search included mislabelling of rosacea as adult acne; falsehoods about rosacea only occurring in older adults or in individuals with lightly pigmented skin; incorrect causes of rosacea such as makeup or diet; and misleading ‘cures’, some of which may lead to exacerbation of the underlying rosacea. Dermatologists must be aware of the large amount of rosacea misinformation trending online and be prepared to counteract them with evidence to optimize patient care.
A cost-effectiveness analysis of hypertrophic cardiomyopathy sudden cardiac death risk algorithms for implantable cardioverter defibrillator decision-making
Authors: Green Nathan , Chen Yang , O'Mahony Constantinos , Elliott Perry M , Barriales-Villa Roberto , Monserrat Lorenzo , Anastasakis Aristides , Biagini Elena , Gimeno Juan Ramon , Limongelli Giuseppe , Pavlou Menelaos , Omar Rumana Z
Published: September 2023

Aims

To conduct a contemporary cost-effectiveness analysis examining the use of implantable cardioverter defibrillators (ICDs) for primary prevention in patients with hypertrophic cardiomyopathy (HCM).

Methods

A discrete-time Markov model was used to determine the cost-effectiveness of different ICD decision-making rules for implantation. Several scenarios were investigated, including the reference scenario of implantation rates according to observed real-world practice. A 12-year time horizon with an annual cycle length was used. Transition probabilities used in the model were obtained using Bayesian analysis. The study has been reported according to the Consolidated Health Economic Evaluation Reporting Standards checklist.

Results

Using a 5-year SCD risk threshold of 6% was cheaper than current practice and has marginally better total quality adjusted life years (QALYs). This is the most cost-effective of the options considered, with an incremental cost-effectiveness ratio of £834 per QALY. Sensitivity analyses highlighted that this decision is largely driven by what health-related quality of life (HRQL) is attributed to ICD patients and time horizon.

Conclusion

We present a timely new perspective on HCM-ICD cost-effectiveness, using methods reflecting real-world practice. While we have shown that a 6% 5-year SCD risk cut-off provides the best cohort stratification to aid ICD decision-making, this will also be influenced by the particular values of costs and HRQL for subgroups or at a local level. The process of explicitly demonstrating the main factors, which drive conclusions from such an analysis will help to inform shared decision-making in this complex area for all stakeholders concerned.
Transapical beating-heart septal myectomy for recurrent left ventricular outflow tract obstruction after septal reduction therapy in hypertrophic obstructive cardiomyopathy
Authors: Li Jiangtao , Li Chenhe , Wei Xiang
Published: September 2023

We present a case of a 58-year-old man for surgical myectomy due to recurrent left ventricular outflow tract (LVOT) obstruction, who had prior transaortic septal myectomy and embolization of the septal branch. On admission, transthoracic echocardiography showed a typical hypertrophic obstructive cardiomyopathy (HOCM) with asymmetric septal hypertrophy, significant LVOT obstruction and severe mitral regurgitation due to the systolic anterior movement of the anterior mitral valve leaflet. We performed a novel procedure of the transapical beating-heart septal myectomy, following which the LVOT obstruction was resolved. And a decreased grade of systolic anterior movement and a reduction in the severity of mitral regurgitation were observed.
Mineral substrate quality determines the initial soil microbial development in front of the Nordenskiöldbreen, Svalbard
Authors: Luláková Petra , Šantrůčková Hana , Elster Josef , Hanáček Martin , Kotas Petr , Meador Travis , Tejnecký Václav , Bárta Jiří
Published: September 2023

Substrate geochemistry is an important factor influencing early microbial development after glacial retreat on nutrient-poor geological substrates in the High Arctic. It is often difficult to separate substrate influence from climate because study locations are distant. Our study in the retreating Nordenskiöldbreen (Svalbard) is one of the few to investigate biogeochemical and microbial succession in two adjacent forefields, which share the same climatic conditions but differ in their underlying geology. The northern silicate forefield evolved in a classical chronosequence, where most geochemical and microbial parameters increased gradually with time. In contrast, the southern carbonate forefield exhibited high levels of nutrients and microbial biomass at the youngest sites, followed by a significant decline and then a gradual increase, which caused a rearrangement in the species and functional composition of the bacterial and fungal communities. This shuffling in the early stages of succession suggests that high nutrient availability in the bedrock could have accelerated early soil succession after deglaciation and thereby promoted more rapid stabilization of the soil and production of higher quality organic matter. Most chemical parameters and bacterial taxa converged with time, while fungi showed no clear pattern.
Role of host ciliate Paramecium bursaria mitochondria and trichocysts for symbiotic Chlorella variabilis attachment beneath the host cell cortex
Authors: Kodama Yuuki , Fujishima Masahiro
Published: September 2023

Symbiotic Chlorella variabilis is encased in the perialgal vacuole (PV) membrane of ciliate Paramecium bursaria. The PV membrane is stably anchored below the host cell cortex by adhesion to host mitochondria. Host trichocysts, which are defensive organelles against predators, are present in the mitochondria and PV membrane vicinity. The mechanism by which PV attaches beneath the host cell cortex remains unknown. When P. bursaria is centrifuged at high speed, the symbiotic algae are displaced from the host cell cortex and concentrate at the posterior end. When centrifugation is stopped, the dislocated algae reattach beneath the host cell cortex with fast cytoplasmic streaming. The densities of mitochondria and trichocysts before and after centrifugation were compared using indirect immunofluorescence microscopy with monoclonal antibodies. Almost all trichocysts were shed by high-speed centrifugation, but dislocated algae could reattach even in the absence of trichocysts. In contrast, host mitochondria were unaffected in localization and number, and the dislocated algae also reattached. These findings suggest trichocysts are unnecessary for algal relocalization and that mitochondria are colocalized with the algae. However, many mitochondria were also present in the cell’s anterior region without symbiotic algae. Therefore, not all areas with mitochondria contained algae, but there was an algal localization bias within the host cell.
High prevalence of GR2 and GR4 plasmids in Acinetobacter baumannii strains from Brazil
Authors: de Melo Beatriz Souza Toscano , Xavier Danilo Elias , Leal Nilma Cintra , Campos Túlio de Lima
Published: September 2023

Acinetobacter baumannii is Gram-negative pathogen with extensive role in healthcare-associated infections (HAIs). Plasmids in this species are important carriers of antimicrobial resistance genes. In this work, we investigated the plasmids of 227 Brazilian A. baumannii genomes. A total of 389 plasmid sequences with 424 Rep proteins typed to 22 different homology groups (GRs) were identified. The GR2 plasmid group was the most predominant (40.6%), followed by the GR4 group (16.7%), representing ∼57% of all plasmids. There is a wide distribution of plasmids among the isolates and most strains carry more than one plasmid. Our analyses revealed a significant prevalence of GR4 plasmids in Brazilian A. baumannii genomes carrying several antimicrobial resistance genes, notably to carbapenem (39.43%). These plasmids harbor a MOBQ relaxase that might confer increased spreading potential in the environment. Most plasmids of the predominant groups belong to the same plasmid taxonomic unit (PTU-Pse7) and have a AbkA/AbkB toxin–antitoxin system that has a role in plasmid stability and dissemination of carbapenem resistance genes. The results of this work should contribute to our understanding of the molecular content of plasmids in a large and populous country, highlighting the importance of genomics for enhanced epidemiological surveillance.
An information theoretic Bayesian uncertainty analysis of AEM systems over Menindee Lake, Australia
Authors: Ray Anandaroop , Ley-Cooper Yusen , Brodie Ross C , Taylor Richard , Symington Neil , Moghaddam Negin F
Published: September 2023

Long-range, active-source airborne electromagnetic (AEM) systems for near-surface conductivity imaging fall into two categories: helicopter (rotary-wing) borne or fixed-wing aircraft borne. A multitude of factors such as flying height, transmitter loop area and current, source waveforms, aerodynamic stability and data stacking times contribute to the geological resolvability of the subsurface. A comprehensive comparison of the relative merits of each system considering all such factors is difficult, but test flights over well-constrained subsurface geology with downhole induction logs are extremely useful for resolution studies. However, given the non-linear nature of the electromagnetic inverse problem, handling transmitter–receiver geometries in fixed-wing aircraft is especially challenging. As a consequence of this non-linearity, inspecting the closeness of downhole conductivities to deterministic inversion results is not sufficient for studying resolvability. A more comprehensive picture is provided by examining the variation in probability mass of the depth-wise Bayesian posterior conductivity distributions for each kind of AEM system within an information theoretic framework. For this purpose, probabilistic inversions of data must be carried out. Each acquiring system should fly over the same geology, survey noise levels must be measured and the same prior probabilities on conductivity must be used. With both synthetic models as well as real data from over the Menindee calibration range in New South Wales, Australia, we shed new light on the matter of AEM inverse model uncertainty. We do this using two information theoretic attributes derived from different Kullback–Leibler divergences—Bayesian information gain, and a strictly proper scoring rule, to assess posterior probabilities estimated by a novel Bayesian inversion scheme. The inversion marginalizes fixed-wing geometry attributes as generic nuisance parameters during Markov chain sampling. This is the first time-domain AEM study we know of, that compares nuisance marginalized subsurface posterior conductivities from a fixed-wing system, with rotary-wing derived posterior conductivities. We also compare field results with induction log data where available. Finally, we estimate the information gain in each case via a covariate shift adaptation technique that has not been used before in geophysical work. Our findings have useful implications in AEM system selection, as well as in the design of better deterministic AEM inversion algorithms.
An efficient algorithm to measure arrival times of weak seismic phases
Authors: Li Lei , Durand Stéphanie , Ricard Yanick , Debayle Eric
Published: September 2023

In seismic tomography, traveltime information of seismic body phases is commonly used to invert the seismic velocities of the subsurface structure. At long periods or for later seismic phases, the arrival time of seismic phases lack definitive onset and a direct picking of the absolute arrival time has large uncertainty and reproducibility. A common practice is to estimate the relative delay between the observed and synthetic signals that maximizes the correlation coefficient. For that aim, we must first select appropriate time windows around the candidate signals. To improve the ability to detect and extract weak signals, we develop a new morphological time window selection (MTWS) algorithm that adapts to the shape of signals and has robust performance in automated processing of massive data. The MTWS method consists of two successive steps. First, we detect the major peaks on the waveform envelope using a maximum filter. Secondly, we solve for the beginning and end of the time windows surrounding the peaks straightforwardly from simple geometrical equations. The efficiency and robustness of the MTWS algorithm make it very suitable for automated processing of huge data sets. We demonstrate the implementation of the method with both synthetic and observed long period (20–40 s) SH waves. From ∼100 000 traces of transverse-component seismograms recorded by global seismic networks over the course of a year, we obtain ∼15 000 Sdiff, ∼7500 ScS and also some ScS multiples. The global map of Sdiff correlation time delays shows consistent patterns with the shear wave velocity perturbations on the core–mantle boundary in the recent tomographic models.
Elastic deformation resulting from internal mass loading: semi-analytical solution
Authors: Tang He , Sun Wenke , Liu Tai
Published: September 2023

Numerous physical processes are responsible for mass exchange between the surface and the interior of the Earth, including but not limited to the conversion of surface water and groundwater, volcanic eruptions and the consequent outflow of magma to the surface, and underground mining of mineral resources, among others. These mass transport phenomena influence the deformation of the Earth's crust. In this study, we extend the conventional loading theory to analyse the extent of crustal deformation by obtaining Green's functions due to internal mass loading in a layered elastic spherical earth model. For the surface source and internal source, the displacement and gravity change show significant differences within a specific horizontal range several times the source depth. Compared with other physical quantities, horizontal displacement is more sensitive to source depth. Furthermore, the utilization of a disc-like load example serves to illustrate the distinctions in displacement deformation between internal and surface loadings. We also published the code for calculating Green's function for internal mass loading in the public repository GitHub.
The impact of crustal scattering on body-wave reflection interferometry by cross-correlation and multidimensional deconvolution
Authors: Hartstra Iris , Wapenaar Kees
Published: September 2023

Previous studies indicate that scattering may pose a trade-off for the performance of seismic interferometry (SI) applications for retrieving body-wave reflections of a target reflector. While it has been demonstrated that a higher scattering strength of the overburden improves the Green’s function estimated by cross-correlation SI, other theoretical and empirical studies showed that multiple scattering also gives rise to more artefacts. The implications of this trade-off are analysed in this numerical study for a lithospheric scenario with varying crustal scattering strength and passive illumination conditions. In this scenario, we apply SI by cross-correlation to elastodynamic responses to double-couple sources to reconstruct virtual Moho primary reflections. We include multidimensional deconvolution (MDD) methods in the analysis to investigate whether scattering-induced artefacts affect MDD methods in a similar way as was shown for the cross-correlation method. Our results show that there indeed exists a trade-off between the quality of the virtual primary reflection of the target that can be obtained by SI and the scattering strength of the overburden. Furthermore, we find that the full-field MDD method proves to be most resilient to the negative effects of multiple scattering for all illumination conditions and scattering strengths analysed.
Mediastinal perigraft seroma after thoracic aortic surgery
Authors: Suzuki Ryo , Akita Masafumi , Miyazaki Suguru , Shimano Ryo
Published: September 2023

OBJECTIVES

We investigated pertinent factors associated with mediastinal perigraft seroma (PGS) after thoracic aortic surgery. In addition, we provided a clinical review of this entity, as reports reviewing abundant mediastinal PGS cases are rare.

METHODS

Eighty-two patients who underwent either ascending aortic replacement or aortic arch replacement between 2016 and 2022 in our institution were enrolled in the present study. Postoperative computed tomography scans were performed to detect fluid capsules with a diameter ≥3.0 cm and radiodensity ≤25 Hounsfield units. Patients who did and who did not develop PGS formation were compared. Variables with a statistically significant difference between these groups were included in a multiple logistic regression analysis along with other factors associated with PGS in the literature.

RESULTS

The incidence rate of PGS was 14.6% (12/82). The average radiodensity of the mass was 16.6 ± 6.3 Hounsfield units. The average onset of PGS was 8.5 months post-surgery. Multivariate logistic regression analysis revealed that ejection fraction [odds ratio (OR): 1.25, 95% confidence interval (CI): 1.03–1.50, P = 0.021], aortic dissection (versus degenerative aortic aneurysm) (OR: 6.61, 95% CI: 1.35–32.4, P = 0.02) and warfarin use (OR: 6.67, 95% CI: 1.19–37.1, P = 0.03) significantly contributed to mediastinal PGS after thoracic aortic surgery.

CONCLUSIONS

High ejection fraction, warfarin use and aortic dissection (versus degenerative aortic aneurysm) contributed significantly to mediastinal PGS formation after thoracic aortic surgery. Careful serial postoperative imaging studies and fluid analysis can be used to guide treatment plans.

Clinical trial registration

UMIN-CTR (University hospital Medical Information Network-Clinical Trial Registry) Registration number: UMIN000050764.
Genome-wide Association Study of Susceptibility to Respiratory Syncytial Virus Hospitalization in Young Children <5 Years of age
Authors: Egeskov-Cavling Amanda Marie , van Wijhe Maarten , Yakimov Victor , Johannesen Caroline Klint , Pollard Andrew J , Trebbien Ramona , Bybjerg-Grauholm Jonas , Fischer Thea Kølsen ,   for the Respiratory Syncytial Virus Consortium in Europe (RESCEU) investigators, Nair Harish , Campbell Harry , Beutels Philippe , Bont Louis , Pollard Andrew , Openshaw Peter , Martinon-Torres Federico , Heikkinen Terho , Meijer Adam , Fischer Thea , van den Berge Maarten , Giaquinto Carlo , Abram Michael , Swanson Kena , Rizkalla Bishoy , Vernhes Charlotte , Gallichan Scott , Aerssens Jeroen , Kumar Veena , Molero Eva
Published: September 2023

Background

Worldwide, respiratory syncytial virus (RSV) infections are among the most common causes of infant hospitalization. Host genetic factors influencing the risk and severity of RSV infection are not well known.

Methods

We conducted a genome-wide association study (GWAS) to investigate single-nucleotide polymorphisms (SNPs) associated with severe RSV infections using a nested case-control design based on 2 Danish cohorts. We compared SNPs from 1786 children hospitalized with RSV to 45 060 controls without an RSV-coded hospitalization. We performed gene-based testing, tissue enrichment, gene-set enrichment, and a meta-analysis of the 2 cohorts. Finally, an analysis of potential associations between the severity of RSV infection and genetic markers was performed.

Results

We did not detect any significant genome-wide associations between SNPs and RSV infection or the severity of RSV. We did find potential loci associated with RSV infections on chromosome 5 in 1 cohort but failed to replicate any signals in both cohorts.

Conclusions

Despite being the largest GWAS of severe RSV infection, we did not detect any genome-wide significant loci. This may be an indication of a lack of power or an absence of signal. Future studies might include mild illness and need to be larger to detect any significant associations.
How to Survive a (Juvenile) Piranha Attack: An Integrative Approach to Evaluating Predator Performance
Authors: Lowe A , Kolmann M A , Paig-Tran E W M
Published: September 2023

Figures

Synopsis

There is an evolutionary arms race between predators and prey. In aquatic environments, predatory fishes often use sharp teeth, powerful bites, and/or streamlined bodies to help capture their prey quickly and efficiently. Conversely, prey are often equipped with antipredator adaptations including: scaly armor, sharp spines, and/or toxic secretions. This study focused on the predator–prey interactions between the armored threestripe cory catfish (Corydoras trilineatus) and juvenile red-bellied piranha (Pygocentrus nattereri). Specifically, we investigated how resistant cory catfish armor is to a range of natural and theoretical piranha bite forces and how often this protection translated to survival from predator attacks by Corydoras. We measured the bite force and jaw functional morphology of P. nattereri, the puncture resistance of defensive scutes in C. trilineatus, and the in situ predatory interactions between the two. The adductor mandibulae muscle in juvenile P. nattereri is robust and delivers an average bite force of 1.03 N and maximum bite force of 9.71 N, yet its prey, C. trilineatus, survived 37% of confirmed bites without any damage. The C. trilineatus armor withstood an average of nine bites before puncture by P. nattereri. Predation was successful only when piranhas bit unarmored areas of the body, at the opercular opening and at the caudal peduncle. This study used an integrative approach to understand the outcomes of predator–prey interactions by evaluating the link between morphology and feeding behavior. We found that juvenile P. nattereri rarely used a maximal bite force and displayed a net predation success rate on par with other adult vertebrates. Conversely, C. trilineatus successfully avoided predation by orienting predator attacks toward their resilient, axial armor and behavioral strategies that reduced the predator's ability to bite in less armored regions of the body.
Turtle Shell Kinesis Underscores Constraints and Opportunities in the Evolution of the Vertebrate Musculoskeletal System
Authors: Cordero G A
Published: September 2023

Synopsis

Species groups that feature traits with a low number of potentially variable (evolvable) character states are more likely to repeatedly evolve similar phenotypes, that is, convergence. To evaluate this phenomenon, this present paper addresses anatomical alterations in turtles that convergently evolved shell kinesis, for example, the movement of shell bones to better shield the head and extremities. Kinesis constitutes a major departure from the evolutionarily conserved shell of modern turtles, yet it has arisen independently at least 8 times. The hallmark signature of kinesis is the presence of shell bone articulations or “hinges,” which arise via similar skeletal remodeling processes in species that do not share a recent common ancestor. Still, the internal biomechanical components that power kinesis may differ in such distantly related species. Complex diarthrodial joints and modified muscle connections expand the functional boundaries of the limb girdles and neck in a lineage-specific manner. Some lineages even exhibit mobility of thoracic and sacral vertebrae to facilitate shell closure. Depending on historical contingency and structural correlation, a myriad of anatomical alterations has yielded similar functional outcomes, that is, many-to-one mapping, during the convergent evolution of shell kinesis. The various iterations of this intricate phenotype illustrate the potential for the vertebrate musculoskeletal system to undergo evolutionary change, even when constraints are imposed by the development and structural complexity of a shelled body plan. Based on observations in turtles and comparisons to other vertebrates, a hypothetical framework that implicates functional interactions in the origination of novel musculoskeletal traits is presented.
Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage
Authors: Li Rongrong , Hu Ming , Jiang Xin , Xu Chuncheng
Published: September 2023

Aims

Lactate and butyrate are important indicators of silage quality. However, the microorganisms and mechanisms responsible for lactate and butyrate production in silage are not well documented.

Methods and results

whole-metagenomic sequencing was used to analyse metabolic pathways, microbiota composition, functional genes, and their contributions to lactate and butyrate production in alfalfa silage with (SA) and without (CK) sucrose addition. Carbon metabolism was the most abundant metabolic pathway. We identified 11 and 2 functional genes associated with lactate and butyrate metabolism, respectively. Among them, D-lactate dehydrogenase (ldhA) and L-lactate dehydrogenase (ldhB) were most important for the transition between D/L-lactate and pyruvate and were primarily related to Lactobacillus in the SA group. The genes encoding L-lactate dehydrogenase (lldD), which decomposes lactate, were the most abundant and primarily associated with Enterobacter cloacae. Butyrate-related genes, mainly encoding butyryl-CoA: acetate CoA-transferase (but), were predominantly associated with Klebsiella oxytoca and Escherichia coli in the CK group.

Conclusions

Enterobacteriaceae and Lactobacillaceae were mainly responsible for butyrate and lactate formation, respectively.