bluuebunny/crossref_metadata_2025 huggingface dataset:
MEMS capacitive pressure sensor: analysis, theoretical modeling, simulation and performance comparison of the effect of a conical notch
Authors: Gajula Rukshana Bi , Mahata Sanskriti , Pingali Akhila , Jindal Sumit Kumar
Published: October 2024

Micro-Electro-Mechanical Systems (MEMS) pressure sensors are widely used in various applications due to their high sensitivity, low power consumption, and compactness. This work involves the design and simulation of a MEMS-based Touch Mode Capacitive Pressure Sensor (TMCPS). The proposed sensor is based on a substrate with an integrated conical notch featuring a circular diaphragm, aiming to enhance the key performance parameters of the sensor. The integration of a conical notch in the substrate increases the touch area between the diaphragm and substrate compared to the literature, ensuring increased capacitance and capacitive sensitivity. In this work the mathematical analysis of deflection of a circular diaphragm employing thin plate theory, capacitance, and capacitive sensitivity, along with step-by-step explanations, is provided. The results are obtained from MATLAB simulations. The deflection of the diaphragm is validated through Finite Element Analysis (FEA) using COMSOL Multiphysics. The proposed work demonstrates a significant improvement in sensor sensitivity compared to the existing literature.
Carbon dots induced homeotropic alignment in a negative dielectric nematic liquid crystal material
Authors: P Priscilla , Gathania Arvind K , Kumar Sandeep , Fisch Michael R , Prakash Jai , Supreet  , Kumar Sanjeev , Singh Gautam
Published: October 2024

Recently, doping guest materials such as quantum dots (QDs) into liquid crystals (LCs) has been of great interest since their addition substantially enhances the properties of LC and opens new avenues for scientific advancement. Here, we report the induction of homeotropic alignment in cells without alignment layers of the negative dielectric nematic liquid crystal, N-(4-Methoxybenzylidene)-4-butylaniline (MBBA) by doping with carbon dots (CDs ∼2.8 ± 0.72 nm). The CDs-MBBA composites (CDs concentration: 0.002, 0.01, 0.03, 0.1 and 0.3 wt%) were investigated using optical polarising microscopy, electro-optical and dielectric techniques. Polarizing optical micrographs and voltage dependent optical transmission revealed the induced homeotropic alignment for all the composites under investigation. Interestingly, the least concentrated sample, 0.002 wt% exhibited partial homeotropic alignment. However, due to light leakage, the optical transmission value below threshold voltage was relatively higher than the rest of the composites. MBBA is a negative dielectric material, hence the application of a voltage across the cell was able to switch the alignment from a dark to a bright state for all composites. However, above a certain voltage (>threshold voltage), the bright state produced some instabilities. The value of dielectric permittivity was observed to decrease with increasing concentration, confirming the effect of CDs in producing homeotropic alignment in MBBA. Measurements as a function of temperature were conducted to examine the thermal stability of the induced alignment. The alignment was found to be stable throughout the nematic phase of MBBA. The induction of such alignment without conventional alignment (i.e., rubbing of polyimides) technique can be helpful in addressing the evolving display demands by making liquid crystal displays (LCDs) and other display devices cost effective.
Beyond ADCs: harnessing bispecific antibodies to directly induce apoptosis for targeted tumor eradication
Authors: Goldmacher Victor S , Gershteyn Iosif M , Kovtun Yelena
Published: October 2024

Bispecific apoptosis triggers (BATs) are innovative bispecific antibodies designed to simultaneously target both a tumor-associated antigen and a cancer cell’s death receptor, thereby directly activating the extrinsic apoptotic pathway to induce death of cancer cells. This unique mechanism distinguishes BATs from antibody-drug conjugates (ADCs), which rely on cytotoxic drugs, and bispecific immune cell engagers such as bispecific T-cell engagers (BiTEs) and bispecific natural killer cell engagers (NKCEs), which recruit immune cells to eliminate target cancer cells. BATs offer significant potential advantages in clinical efficacy and safety over ADCs and BiTEs. Although the field is still emerging, recent advancements are highly promising, and analysis of preclinical and clinical data of DR5-targeting antibodies have been pivotal in outlining the criteria for the next generation of effective and safe medicines. Antibodies found inactive in preclinical testing were also found to be clinically ineffective, whereas antibodies with minimal preclinical results demonstrated moderate clinical activity. All clinical DR5-targeting antibodies were well tolerated by patients even at high doses (with the exception of TAS266 due to its unique design). These findings underscore the predictive value of robust preclinical models on clinical outcomes. Notably, first-in-class BAT, Cancerlysin™ IMV-M, demonstrated potent efficacy in diverse xenograft cancer models and safety in non-human primates, marking a significant advancement in developing safe and effective anti-cancer drugs.
Characteristics of incident benzodiazepine recipients among US veterans with posttraumatic stress disorder
Authors: Shahid Komel N , Hadlandsmyth Katherine , Brainerd Delaney R , Lund Brian C
Published: October 2024

Purpose

While benzodiazepine prescribing among veterans with posttraumatic stress disorder (PTSD) declined substantially in the Veterans Health Administration over the past decade, little is known about current incident prescribing. Our objective was therefore to describe patient, provider, facility, and prescribing characteristics among veterans with PTSD who were incident benzodiazepine recipients in 2022 and contrast these to the characteristics for incident recipients in 2012.

Methods

This retrospective observational study included all veterans with PTSD who received an incident benzodiazepine prescription during calendar year 2022 and separately for 2012. The distribution of patient, provider, facility, and benzodiazepine prescribing characteristics was contrasted between years. Stratified subanalyses were conducted by potential non-PTSD benzodiazepine indication, including anxiety and sleep disorders.

Results

A total of 28,310 (6.6%) incident benzodiazepine recipients were identified in 2012, which decreased to 16,776 (1.9%) incident recipients in 2022. The proportion of initial prescriptions written for a days’ supply of 30 or more days decreased from 75.6% to 51.7%, and the proportion who received a second prescription within 6 months decreased from 68.7% to 53.5%. The proportion of patients with diagnoses for potential benzodiazepine indications also increased, including for generalized anxiety disorder (15.1% increase), obsessive compulsive disorders (0.6% increase), panic disorder (6.7% increase), and sleep disorders (22.9% increase).

Conclusion

As incident benzodiazepine prescribing among veterans with PTSD decreased over the past decade, so did the volume of drug dispensed and duration of therapy, while the prevalence of documented prescriptions for non-PTSD indications increased.
Tribunal duties and the exclusion of evidence in international arbitration: the tug-of-war of fairness and efficiency
Authors: Godhe Aleksander
Published: October 2024

Arbitral procedure aims to strike the right balance between fairness and efficiency in the specific and unique circumstances of the case. However, in some difficult cases, both considerations can pull in opposite directions. The exclusion of evidence provides a particularly apt example in which the dilemma arises, aggravated by the considerable evidentiary discretion vested in tribunals and the overall lack of guidance in applicable laws and rules on approaching such circumstances. This article argues that the tug-of-war between fairness and efficiency in the context of the exclusion of evidence can be resolved with the help of relevant tribunal duties, which should guide the exercise of tribunal discretion. These include the duty (i) to resolve the dispute; (ii) to observe due process; (iii) to conduct the procedure efficiently and effectively; (iv) to act with impartiality and independence; and (v) to render an award that is enforceable/not subject to set aside.
Multimodal contrastive learning for spatial gene expression prediction using histology images
Authors: Min Wenwen , Shi Zhiceng , Zhang Jun , Wan Jun , Wang Changmiao
Published: October 2024

In recent years, the advent of spatial transcriptomics (ST) technology has unlocked unprecedented opportunities for delving into the complexities of gene expression patterns within intricate biological systems. Despite its transformative potential, the prohibitive cost of ST technology remains a significant barrier to its widespread adoption in large-scale studies. An alternative, more cost-effective strategy involves employing artificial intelligence to predict gene expression levels using readily accessible whole-slide images stained with Hematoxylin and Eosin (H&E). However, existing methods have yet to fully capitalize on multimodal information provided by H&E images and ST data with spatial location. In this paper, we propose mclSTExp, a multimodal contrastive learning with Transformer and Densenet-121 encoder for Spatial Transcriptomics Expression prediction. We conceptualize each spot as a “word”, integrating its intrinsic features with spatial context through the self-attention mechanism of a Transformer encoder. This integration is further enriched by incorporating image features via contrastive learning, thereby enhancing the predictive capability of our model. We conducted an extensive evaluation of highly variable genes in two breast cancer datasets and a skin squamous cell carcinoma dataset, and the results demonstrate that mclSTExp exhibits superior performance in predicting spatial gene expression. Moreover, mclSTExp has shown promise in interpreting cancer-specific overexpressed genes, elucidating immune-related genes, and identifying specialized spatial domains annotated by pathologists. Our source code is available at https://github.com/shizhiceng/mclSTExp.
MetaboScope: a statistical toolbox for analyzing 1H nuclear magnetic resonance spectra from human clinical studies
Authors: Loo Ruey Leng , Mosquera Javier Osorio , Zasso Michael , Mathews Jacqueline , Johnston Desmond G , Nicholson Jeremy K , Patiny Luc , Holmes Elaine , Wist Julien
Published: October 2024

Motivation

Metabolic phenotyping, using high-resolution spectroscopic molecular fingerprints of biological samples, has demonstrated diagnostic, prognostic, and mechanistic value in clinical studies. However, clinical translation is hindered by the lack of viable workflows and challenges in converting spectral data into usable information.

Results

MetaboScope is an analytical and statistical workflow for learning, designing and analyzing clinically relevant 1H nuclear magnetic resonance data. It features modular preprocessing pipelines, multivariate modeling tools including Principal Components Analysis (PCA), Orthogonal-Projection to Latent Structure Discriminant Analysis (OPLS-DA), and biomarker discovery tools (multiblock PCA and statistical spectroscopy). A simulation tool is also provided, allowing users to create synthetic spectra for hypothesis testing and power calculations.

Availability and implementation

MetaboScope is built as a pipeline where each module accepts the output generated by the previous one. This provides flexibility and simplicity of use, while being straightforward to maintain. The system and its libraries were developed in JavaScript and run as a web app; therefore, all the operations are performed on the local computer, circumventing the need to upload data. The MetaboScope tool is available at https://www.cheminfo.org/flavor/metabolomics/index.html. The code is open-source and can be deployed locally if necessary. Module notes, video tutorials, and clinical spectral datasets are provided for modeling.
Population-aware permutation-based significance thresholds for genome-wide association studies
Authors: John Maura , Korte Arthur , Todesco Marco , Grimm Dominik G
Published: October 2024

Motivation

Permutation-based significance thresholds have been shown to be a robust alternative to classical Bonferroni significance thresholds in genome-wide association studies (GWAS) for skewed phenotype distributions. The recently published method permGWAS introduced a batch-wise approach to efficiently compute permutation-based GWAS. However, running multiple univariate tests in parallel leads to many repetitive computations and increased computational resources. More importantly, traditional permutation methods that permute only the phenotype break the underlying population structure.

Results

We propose permGWAS2, an improved method that does not break the population structure during permutations and uses an elegant block matrix decomposition to optimize computations, thereby reducing redundancies. We show on synthetic data that this improved approach yields a lower false discovery rate for skewed phenotype distributions compared to the previous version and the commonly used Bonferroni correction. In addition, we re-analyze a dataset covering phenotypic variation in 86 traits in a population of 615 wild sunflowers (Helianthus annuus L.). This led to the identification of dozens of novel associations with putatively adaptive traits, and removed several likely false-positive associations with limited biological support.

Availability and implementation

permGWAS2 is open-source and publicly available on GitHub for download: https://github.com/grimmlab/permGWAS.
Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes
Authors: Alías-Segura Sergio , Pazos Florencio , Chagoyen Monica
Published: October 2024

Motivation

Knowledge of the specific cell types affected by genetic alterations in rare diseases is crucial for advancing diagnostics and treatments. Despite significant progress, the cell types involved in the majority of rare disease manifestations remain largely unknown. In this study, we integrated scRNA-seq data from non-diseased samples with known genetic disorder genes and phenotypic information to predict the specific cell types disrupted by pathogenic mutations for 482 disease phenotypes.

Results

We found significant phenotype-cell type associations focusing on differential expression and co-expression mechanisms. Our analysis revealed that 13% of the associations documented in the literature were captured through differential expression, while 42% were elucidated through co-expression analysis, also uncovering potential new associations. These findings underscore the critical role of cellular context in disease manifestation and highlight the potential of single-cell data for the development of cell-aware diagnostics and targeted therapies for rare diseases.

Availability and implementation

All code generated in this work is available at https://github.com/SergioAlias/sc-coex
Modeling longitudinal skewed functional data
Authors: Alam Mohammad Samsul , Staicu Ana-Maria
Published: October 2024

This paper introduces a model for longitudinal functional data analysis that accounts for pointwise skewness. The proposed procedure decouples the marginal pointwise variation from the complex longitudinal and functional dependence using copula methodology. Pointwise variation is described through parametric distribution functions that capture varying skewness and change smoothly both in time and over the functional argument. Joint dependence is quantified through a Gaussian copula with a low-rank approximation-based covariance. The introduced class of models provides a unifying platform for both pointwise quantile estimation and prediction of complete trajectories at new times. We investigate the methods numerically in simulations and discuss their application to a diffusion tensor imaging study of multiple sclerosis patients. This approach is implemented in the R package sLFDA that is publicly available on GitHub.
The incremental value of histogram analysis in the differentiation between hyperdense cysts and solid renal masses on unenhanced CT images
Authors: de Souza Torres Cecília Vidal , de Freitas Secaf André , Maia Vieira David Freire , de Moraes Morgado Alexandre Souto , de Moraes Palma Matheus , Andrade Ramos Gabriel , Elias Jr. Jorge , Reis Rodolfo B , Muglia Valdair F
Published: October 2024

Objective

To investigate the utility of voxel histogram analysis (HA) for differentiating hyperdense renal cysts from small solid masses on unenhanced CT scans.

Methods

A retrospective analysis of 99 hyperdense cystic lesions and 28 solid malignant lesions was conducted using a radiological database (from 2015 to 2021) and a pathological database (from 2010 to 2020). The study investigated the distribution of voxel attenuation values using percentiles to establish reliable criteria for differentiation after drawing a region of interest (ROI) in the centre of the lesions. The standard of reference was a histopathological diagnosis for malignant masses and contrast-enhanced CT or MRI for cysts.

Results

HA provided higher diagnostic accuracy than the conventional mean attenuation value of 70 Hounsfield Units (HU). For the 75th and 90th percentiles ± 1 standard deviation, accuracies of 77.2% (95% confidence interval 68.9%-84.2%) for the 75th and 68.5% (59.7%-76.4%) for the 90th were found, versus 37.0% (28.6%-46.0%) for the 70 HU threshold criterion. A Gaussian distribution of voxel attenuation values was observed in 88.9% of the lesions, suggesting that it is feasible to calculate these parameters from a single measurement.

Conclusion

The study underscores the potential of HA as a valuable tool for characterizing hyperdense cysts on unenhanced CT by using the same ROI for measuring lesion attenuation. HA could offer additional value beyond the 70 HU criterion and possibly influence clinical decisions. Multi-institutional studies are necessary for external validation to confirm its generalizability and more extensive applicability.

Advances in knowledge

(1) A single measurement on unenhanced CT images, using mean attenuation and standard deviation, accurately reflects the voxel distribution of both cystic and solid masses, allowing for the application of histogram analysis. (2) The 75th percentile threshold of 65 HU or higher could potentially increase sensitivity in diagnosing hyperdense cysts, compared to the 70 HU mean attenuation threshold, without compromising specificity.
Asymptomatic slowly progressing erythematous papules with adult onset
Authors: Grechin Cristina , McGrath Sally , O’Brien Odharnaith , O’Kane Marina
Published: October 2024

A 35-year-old woman presented with sudden onset of multiple asymptomatic erythematous papules on her dorsal feet, followed by a 2-year period of additional lesions appearing on her ankles, right forearm and right superior eyelid.
Considerations on Multimorbidity and Frailty in Inflammatory Bowel Diseases
Authors: Carbery Isabel , Selinger Christian P , Todd Oliver , Sebastian Shaji
Published: October 2024

There are growing numbers of older people with inflammatory bowel diseases [IBD]. These older patients are more likely to have other comorbidities and polypharmacy, which can make recognizing and treating IBD complex. Frailty is a newer concept in the IBD field, and we are beginning to recognize the importance of this as a marker of biological age and its association with risk of adverse IBD-related outcomes. In this review article we aim to provide practical insight into the specific challenges facing older patients and their clinicians at each stage of the patient journey. We also discuss the latest understanding of the impact of frailty for these patients with IBD and highlight areas for future research.
Suprarenal interrupted inferior cava with azygos continuation in a patient with pulmonary embolism: a case report
Authors: Shahverdi Ehsan , Keshavarzi Ramtin , Mazandarani Mohammad , Schneider Carsten , Lange Mathias
Published: October 2024

Background

Interrupted inferior vena cava (IVC) is a rare developmental defect characterized by azygos continuation following failure of fusion of one or more of the component parts of the embryological IVC. It occurs in approximately one in 5000 of the general population. It is usually an isolated finding and is generally asymptomatic.

Case summary

A 42-year-old patient presented for further clarification of syncope with a 4-day history of persistent exertional dyspnoea. Computed tomography revealed a central pulmonary artery embolism on both sides, with prominent azygos and hemiazygos veins and paravertebral collaterals. For further clarification, a magnetic resonance imaging (MRI) scan was performed, where hypoplasia or stenosis of the inferior suprarenal vena cava was noted. There were collaterals of the azygos and hemiazygos veins. The finding was consistent with the picture of a venous abnormality in the sense of an ‘interrupted IVC (suprarenal) with azygos continuation’.

Discussion

In the case of an isolated interrupted IVC, the patient is usually asymptomatic, and the vascular anomaly itself does not mandate any treatment. This variation should be considered, especially in young patients with deep venous thrombosis (DVT) when no other reason for thromboembolism is evident. To prevent vascular events such as DVT or pulmonary embolism, lifelong anticoagulation therapy is recommended. An interrupted IVC can also cause procedural difficulties during right heart catheterization, electrophysiological studies, cardiopulmonary bypass surgery, femoral vein catheter advancement, IVC filter placement, and temporary pacing through the transfemoral route.
Artificial intelligence-enabled reconstruction of the right ventricular pressure curve using the peak pressure value: a proof-of-concept study
Authors: Szijártó Ádám , Nicoara Alina , Podgoreanu Mihai , Tokodi Márton , Fábián Alexandra , Merkely Béla , Sárkány András , Tősér Zoltán , Caravita Sergio , Baratto Claudia , Tomaselli Michele , Muraru Denisa , Badano Luigi Paolo , Lakatos Bálint , Kovács Attila
Published: October 2024

Aims

Conventional echocardiographic parameters of right ventricular (RV) function are afterload-dependent. Therefore, incorporating RV pressures may enable the formulation of new parameters that reflect intrinsic RV function accurately. Accordingly, we sought to develop an artificial intelligence–based method to reconstruct the RV pressure curve based on the peak RV pressure.

Methods and Results

We invasively acquired RV pressure in 29 heart failure patients before and after implanting a left ventricular (LV) assist device. Using these tracings, we trained various machine learning models to reconstruct the RV pressure curve of the entire cardiac cycle based on the peak value of the curve. The best-performing model was compared with two other methods that estimated RV pressures based on a reference LV and RV pressure curve, respectively. Seventeen consecutive patients from another centre who underwent right heart catheterization and simultaneous echocardiography served as an external validation cohort. Among the evaluated algorithms, multilayer perceptron (MLP) achieved the best performance with an R2 of 0.887 (0.834–0.941). The RV and LV reference curve–based methods achieved R2 values of 0.879 (0.815–0.943) and 0.636 (0.500–0.771), respectively. During external validation, MLP exhibited similarly good performance [R2 0.911 (0.873–0.948)], which decreased only modestly if the echocardiography-derived peak RV pressure was used instead of the invasively measured peak RV pressure [R2 0.802 (0.694–0.909)].

Conclusions

The proposed method enables the reconstruction of the RV pressure curve using only the peak value as input. Thus, it may serve as a fundamental component for developing new echocardiographic tools targeting the afterload-adjusted assessment of RV function.
Support from Above: International Organizations, Summits, and Leader Survival
Authors: Lee Chia-yi
Published: October 2024

While existing literature indicates a variety of political consequences caused by IO membership, little attention has been paid to IOs’ impact on leaders. This article argues that IO membership has a positive effect on leader survival through two major mechanisms: IOs carrying information and IOs raising national well-being. The beneficial effect of IOs on leader survival, moreover, is stronger for IOs that regularly or periodically hold leader summits. This is not only because these IOs are more important, but also because IO summits increase leaders’ visibility and serve as an endorsement for leaders’ power-consolidating behavior. Using data on leader failures and IO membership, this article shows that IO membership has a negative effect on leader failures, and this effect is much stronger for IOs that hold regular summits.
New mutations in the core Schizosaccharomyces pombe spindle pole body scaffold Ppc89 reveal separable functions in regulating cell division
Authors: Hanna Sarah M , Tavafoghi Bita , Chen Jun-Song , Howard Isaac , Ren Liping , Willet Alaina H , Gould Kathleen L
Published: October 2024

Centrosomes and spindle pole bodies (SPBs) are important for mitotic spindle formation and also serve as signaling platforms. In the fission yeast Schizosaccharomyces pombe, genetic ablation and high-resolution imaging indicate that the α-helical Ppc89 is central to SPB structure and function. Here, we developed and characterized conditional and truncation mutants of ppc89. Alleles with mutations in 2 predicted α-helices near the C-terminus were specifically defective in anchoring Sid4, the scaffold for the septation initiation network (SIN), and proteins dependent on Sid4 (Cdc11, Dma1, Mto1, and Mto2). Artificial tethering of Sid4 to the SPB fully rescued these ppc89 mutants. Another ppc89 allele had mutations located throughout the coding region. While this mutant was also defective in Sid4 anchoring, it displayed additional defects including fragmented SPBs and forming and constricting a second cytokinetic ring in 1 daughter cell. These defects were shared with a ppc89 allele truncated of the most C-terminal predicted α-helices that is still able to recruit Sid4 and the SIN. We conclude that Ppc89 not only tethers the SIN to the SPB but is also necessary for the integrity of the SPB and faithful coordination of cytokinesis with mitosis.
Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus
Authors: Coe Allison , Braakman Rogier , Biller Steven J , Arellano Aldo , Bliem Christina , Vo Nhi N , von Emster Konnor , Thomas Elaina , DeMers Michelle , Steglich Claudia , Huisman Jef , Chisholm Sallie W
Published: October 2024

Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking while attached to particles can, however, transport Prochlorococcus cells below this sunlit zone, depriving them of light for extended periods of time. Previous work has shown that Prochlorococcus by itself cannot survive extended periods of darkness. However, when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, Prochlorococcus cells develop an epigenetically inherited dark-tolerant phenotype that can survive longer periods of darkness. Here we examine the metabolic and physiological changes underlying this adaptation using co-cultures of dark-tolerant and parental strains of Prochlorococcus, each grown with the heterotroph Alteromonas under diel light:dark conditions. The relative abundance of Alteromonas was higher in dark-tolerant than parental co-cultures, while dark-tolerant Prochlorococcus cells were larger, contained less chlorophyll, and were less synchronized to the light:dark cycle. Meta-transcriptome analysis revealed that dark-tolerant co-cultures undergo a joint change, in which Prochlorococcus undergoes a relative shift from photosynthesis to respiration, while Alteromonas shifts toward using more organic acids instead of sugars. Furthermore, the transcriptome data suggested enhanced biosynthesis of amino acids and purines in dark-tolerant Prochlorococcus and enhanced degradation of these compounds in Alteromonas. Collectively, our results demonstrate that dark adaptation involves a strengthening of the metabolic coupling between Prochlorococcus and Alteromonas, presumably mediated by an enhanced, and compositionally modified, carbon exchange between the two species.
Cover crop monocultures and mixtures enhance bacterial abundance and functionality in the maize root zone
Authors: Ghosh Debjyoti , Shi Yijie , Zimmermann Iris M , Stürzebecher Tobias , Holzhauser Katja , von Bergen Martin , Kaster Anne-Kristin , Spielvogel Sandra , Dippold Michaela A , Müller Jochen A , Jehmlich Nico
Published: October 2024

Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Re-utilization of winter cover crop root channels by maize roots during summer allows the cash crop to extract resources from distal regions in the soil horizon. In this study, we investigated how cover cropping during winter followed by maize (Zea mays L.) during summer affects the spatiotemporal composition and function of the bacterial communities in the maize rhizosphere and surrounding soil samples using quantitative polymerase chain reaction (PCR), 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing, and metaproteomics. We found that the bacterial community differed significantly among cover crop species, soil depths, and maize growth stages. Bacterial abundance increased in reused root channels, and it continued to increase as cover crop diversity changed from monocultures to mixtures. Mixing Fabaceae with Brassicaceae or Poaceae enhanced the overall contributions of several steps of the bacterial carbon and nitrogen cycles, especially glycolysis and the pentose phosphate pathway. The deeper root channels of Fabaceae and Brassicaceae as compared to Poaceae corresponded to higher bacterial 16S rRNA gene copy numbers and improved community presence in the subsoil regimes, likely due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel reuse improved the expression of metabolic pathways of the carbon and nitrogen cycles and the bacterial communities, which is beneficial to the soil and to the growing crops.
Does Serendipity Affect Democratic Consequences? Examining the Role of Algorithmic Awareness, Intolerance of Uncertainty in Incidental News Exposure and Online Political Participation
Authors: Chen Zhirui , Guo Wenchen , Zhang Yiwei
Published: October 2024

In the context of social media becoming users' primary access to information, such as news, incidental news exposure under the influence of algorithmic recommendation and its democratic consequences are worth studying. While studies on the relationship between social media users’ incidental news exposure and online political participation have been widely explored, we know little about the current mechanisms of variable association in the context of algorithmic recommendations. This study examines the mediating role of algorithmic awareness and the moderating effect of intolerance of uncertainty on the relationship between incidental news exposure and online political participation among Chinese social media users. Findings indicate that algorithmic awareness negatively mediates this relationship, suggesting that users’ participation in online politics is heightened by their awareness of algorithmic curation. Intolerance of uncertainty positively moderates the link between incidental news exposure and online political participation, emphasizing the impact of personality traits on democratic engagement. This study underscores the importance of transparent algorithmic systems and user-centred design in fostering informed citizen participation in the digital era and offers a comprehensive perspective on the role of serendipity in Chinese democratic participation.
Aetiology, susceptibility and outcomes of fever in patients receiving chemotherapy in Malawi: a prospective study
Authors: Puranam Kaushik , Harrington Meagan , Kasonkanji Edwards , Tegha Gerald , Chikasema Maria J , Chawinga Mena L , Chagomerana Maganizo B , Krysiak Robert , Gopal Satish , van Duin David , Miller Melissa B , Painschab Matthew S
Published: October 2024

Objectives

To evaluate causes of fever, including resistance patterns, in patients undergoing cancer treatment in Malawi.

Methods

In this prospective cohort study, enrolled patients undergoing chemotherapy at Kamuzu Central Hospital in Lilongwe, Malawi were given a thermometer. If a temperature of ≥38°C was recorded, they were instructed to return for hospitalization, standardized fever workup, and antibiotics. All patients were followed through 90 days post-fever event or completion of chemotherapy.

Results

One hundred and five patients were screened and 50 were enrolled. Of the enrollees, 26 (52%) were men and 26 (52%) were HIV positive, with a mean ART duration of 7 years and CD4 count of 293 cells/µL. The most common diagnoses were aggressive non-Hodgkin lymphoma (40%) and Hodgkin lymphoma (22%). Twenty-three febrile events were recorded from 15 patients. Of the 23 events, a causative agent was isolated in 13 cases: Escherichia coli (6), Plasmodium falciparum (3), Streptococcus pneumoniae (2), Pseudomonas aeruginosa (1) and Citrobacter freundii (1). Of the six E. coli isolates, all were found to be resistant to fluoroquinolones and 4/6 (66%) were resistant to cephalosporins. All patients but one survived; the death was attributed to Pseudomonas bacteraemia.

Conclusions

This study describes laboratory-confirmed causes of neutropenic fever (NF) in cancer patients in Malawi. Gram-negative rods, followed by malaria, were the most common source of infection. Gram-negative rods were associated with high rates of antimicrobial resistance. Malaria and resistant bacterial infections should be considered for NF treatment and prevention in sub-Saharan Africa.
Enhancement of a social risk score in the electronic health record to identify social needs among medically underserved patients: using structured data and free-text provider notes
Authors: Hatef Elham , Kitchen Christopher , Gray Geoffrey M , Zirikly Ayah , Richards Thomas , Ahumada Luis M , Weiner Jonathan P
Published: October 2024

Objective

To improve the performance of a social risk score (a predictive risk model) using electronic health record (EHR) structured and unstructured data.

Materials and Methods

We used EPIC-based EHR data from July 2016 to June 2021 and linked it to community-level data from the US Census American Community Survey. We identified predictors of interest within the EHR structured data and applied natural language processing (NLP) techniques to identify patients’ social needs in the EHR unstructured data. We performed logistic regression models with and without information from the unstructured data (Models I and II) and compared their performance with generalized estimating equation (GEE) models with and without the unstructured data (Models III and IV).

Results

The logistic model (Model I) performed well (Area Under the Curve [AUC] 0.703, 95% confidence interval [CI] 0.701:0.705) and the addition of EHR unstructured data (Model II) resulted in a slight change in the AUC (0.701, 95% CI 0.699:0.703). In the logistic models, the addition of EHR unstructured data resulted in an increase in the area under the precision-recall curve (PRC 0.255, 95% CI 0.254:0.256 in Model I versus 0.378, 95% CI 0.375:0.38 in Model II). The GEE models performed similarly to the logistic models and the addition of EHR unstructured data resulted in a slight change in the AUC (0.702, 95% CI 0.699:0.705 in Model III versus 0.699, 95% CI 0.698:0.702 in Model IV).

Discussion

Our work presents the enhancement of a novel social risk score that integrates community-level data with patient-level data to systematically identify patients at increased risk of having future social needs for in-depth assessment of their social needs and potential referral to community-based organizations to address these needs.

Conclusion

The addition of information on social needs extracted from unstructured EHR resulted in an improved prediction of positive cases presented by the improvement in the PRC.
A Polymerase Chain Reaction (PCR) Method to Detect Emerging Multidrug-Resistant Salmonella Infantis Harboring the pESI Plasmid in Seafood
Authors: Veni Krishna , Stephen Jerusha , Lekshmi Manjusha , Nayak Binaya Bhusan , Kumar Sanath H
Published: October 2024

Background

Salmonella Infantis is an emerging multidrug-resistant pathogen worldwide due to the acquisition of a megaplasmid, plasmid of emerging Salmonella Infantis (pESI). Reported initially in poultry, the distribution of pESI-harboring S. Infantis in other food types, including seafood, is unknown.

Objective

This study aimed to develop and optimize a PCR assay for detecting the pESI in Salmonella and non-Salmonella Enterobacterales.

Methods

A duplex PCR targeting the hilA gene and a pESI-associated gene of S. Infantis was designed, and the PCR conditions were optimized. The specificity and sensitivity of the assay were established using 119 Salmonella serovars and 51 non-Salmonella bacterial strains.

Results

All Salmonella isolates yielded hilA PCR product, while only pESI S. Infantis was positive for both hilA and pESI genes. No amplification product was obtained with the DNA of 51 non-Salmonella bacterial strains. The detection limit of the duplex PCR was 104 CFU/mL of pure culture of pESI S. Infantis. The sensitivity of detection in artificially spiked shrimp meat was 1 CFU/g after 6 h of enrichment in lactose broth, followed by 12 h of selective enrichment in the Rappaport-Vassiliadis medium.

Conclusion

The duplex assay will help screen seafood for Salmonella in general and pESI S. Infantis in particular. Given its high sensitivity, the PCR will be a valuable tool for seafood quality assurance. This approach decreases the typical 3–6 day identification time of Salmonella to less than 24 h.

Highlights

S. Infantis carrying the highly transmissible megaplasmid (pESI) is a significant food safety concern. Given its rapid geographical spread and high antimicrobial-resistant traits, it is necessary to have a molecular tool that detects pESI-harboring Salmonella. This study successfully developed a duplex PCR assay that simultaneously detects Salmonella enterica and pESI S. Infantis. This molecular tool will help understand the distribution, sources, and spread of the multidrug-resistance (MDR) plasmid in the food environment.
Validation of the Peel Plate Staphylococcus Aureus (SA) Test for Enumeration of S. aureus in Selected Foods and Non-Cultured Dairy Products: AOAC Performance Tested MethodSM 082401
Authors: Salter Robert S , Durbin Gregory W , Li Sherita , Gilbert McGaughren , Crowley Erin S , Deterding Andrew , Bastin Benjamin
Published: October 2024

Background

The microbial testing platform, Peel Plate™, was developed with Baird Parker ingredients for Staphylococcus aureus (SA) specificity. After rehydrating with 1 mL of the diluted food sample, Peel Plate SA is incubated for 24–48 h at 35–37°C and observed for purple colonies.

Objective

A validation study was performed to evaluate Peel Plate SA for enumeration of SA in selected foods and non-cultured dairy products for Performance Tested MethodSM (PTM) certification.

Methods

Peel Plate SA was evaluated in inclusivity/exclusivity and matrix studies, product consistency and stability studies, and robustness testing. Non-fat dried milk, frozen raw cod fish, corned beef, frozen raw vegetables, potato salad, vegetable soup, frozen unshelled raw shrimp, and baby food (apple, cinnamon, and granola) were evaluated in the matrix studies comparing Peel Plate SA to US and international reference methods. Three levels of contamination along with non-inoculated controls were tested for each matrix.

Results

Peel Plate SA detected 49 of 50 SA isolates tested. Of the 38 exclusivity species tested, none were detected. In the matrix studies, the Peel Plate SA results were determined to be equivalent to the reference method results by paired statistical analysis. In an accelerated stability study, the shelf-life of Peel Plate SA was shown to be stable for 12 months. Equivalence was demonstrated between different production lots. Small changes to critical test parameters did not significantly affect the Peel Plate SA results.

Conclusion

Peel Plate SA is a ready-to-use method for enumeration of SA in a variety of foods and non-cultured dairy products. As with reference methods, Peel Plate SA colonies should be isolated and confirmed with differentiation tests such as catalase and strong coagulase positive.

Highlights

The data were reviewed by the PTM Program and certification was granted for the Peel Plate SA method PTM 082401.
Collagen isolated from human adipose tissue and its cellular affinity
Authors: Yamaoka Hisayo , Yamaoka Keiko , Ishii Hidenori , Tanaka Hideyuki , Yasuda Makoto , Watanabe Shigekazu , Hosoyamada Makoto , Komuro Yuzo
Published: October 2024

The use of collagen in cell cultures promotes cell proliferation and differentiation, and it has been commercialized. In this study, we separated and purified collagen from adipose tissue discarded during liposuction and prepared collagen-coated dishes. After collagen was identified from human adipose tissue, type identification and quantification were performed using SDS-PAGE and FPLC. Collagen type I was used to coat culture dishes. Human skin fibroblasts and human adipose tissue-derived stem cells were seeded at a density of 2.5 × 105 cells/ml on prepared dishes at a collagen concentration of 3 mg/ml and cultured for 7 days. Cell viability was then measured and analyzed. The WST-1 assay was used to evaluate the results. The amount of collagen in 300 g of adipose tissue was 25.5 mg for type I, 41.4 mg for type III, 10.6 mg for type IV, 6.5 mg for type V and 15 mg for type VI. The highest rates were observed for adipose stem cells cultured on human adipose tissue-derived collagen-coated dishes. In cell cultures, cell affinity was higher when cells and the substrate used were of the same origin, and affinity was stronger when the tissue of origin was the same.
The repatriation of wolves to Isle Royale alters the foraging of meso-carnivores
Authors: Lacin Alas Burcu , Rodriguez Curras Mauriel , Smith Matthew M , Potvin Lynette R , Romanski Mark C , Pauli Jonathan N
Published: October 2024

Due to the disproportionate role that large carnivores can have on communities and their global decline over the last century, carnivores are increasingly being repatriated across their historic ranges. The reintroduction of gray wolves (Canis lupus) can precipitate substantive changes to communities and ecosystems. Notably, wolves could have strong effects on smaller and subordinate carnivores, especially in altering their foraging behavior and prey selection. Past studies investigating wolf effects on other carnivores, however, have generally been conducted in relatively complex communities featuring a diverse assemblage of carnivores and prey and have lacked baseline (i.e., pre-repatriation) data. Consequently, researchers have quantified what a community looks like after wolf return, with little information on how the community behaved before. To better understand the effect of large carnivore repatriation on the foraging ecology of a carnivore community, we investigated the impact of reintroduced gray wolves on 2 meso-carnivores: Red Fox (Vulpes vulpes); and American Marten (Martes americana) within an insular and simple vertebrate community at Isle Royale National Park before and after wolf reintroduction. We analyzed >600 scats from 20 individual martens and 63 individual foxes as well as the stable isotopes of 9 and 22 tissue samples from martens and foxes, respectively, at both individual and population levels. We found that the wolf reintroduction had little effect on marten diet but strongly influenced fox diet depending on the analysis conducted. At the population level, our analysis revealed that both foxes and martens were dietary generalists consuming an array of food items including small prey, berries, and human food regardless of wolf presence. However, at the individual level, we found that prior to wolf repatriation foxes primarily consumed berries and small prey but following wolf repatriation the diet of foxes shifted to berries and human foods as well as large carrion. This post-wolf reintroduction shift in diet increased the dietary overlap between foxes and martens. Our work provides new insights into how the return of a large carnivore can alter the foraging ecology of small-bodied carnivores and act both to provision carrion resources as well drive other carnivores to consume more human food and increase dietary overlap.
Neighborhood homicide rate and odds of colorectal adenoma among adult patients seeking colonoscopy
Authors: Hamm Alyshia , Karayeva Evgenia , Oliveira Manoela Lima , Kahouadji Nabil , Grippo Paul , Wolf Patricia G , Mutlu Ece , Tussing-Humphreys Lisa , Kim Sage J
Published: October 2024

Background

Chronic exposure to ambient stressors, including neighborhood crime, may have a detrimental impact on the body’s stress response system with implications for colorectal carcinogenesis.

Methods

We examined associations between the mean neighborhood homicide rates from 2000 and 2018 and diagnosis of colorectal adenoma among patients at the University of Illinois Health and Hospital System in Chicago, Illinois, between 2015 and 2018.

Results

Of the 5225 patients who underwent colonoscopy and were included in the analytic dataset, 60% had colorectal adenoma. Older age, male sex, and higher body mass index (BMI) were associated with greater odds of colorectal adenoma. The neighborhood homicide rate was associated with identifying as Black and Hispanic and higher BMI. A mediation analysis showed that the neighborhood homicide rate effects on colorectal adenoma were mediated through BMI.

Conclusions

The study concluded that older age, male sex, and higher BMI increases the odds of colorectal adenoma, with neighborhood homicide rate indirectly influencing this risk through its association with BMI, particularly among Black and Hispanic individuals.