bluuebunny/crossref_metadata_2025 huggingface dataset:
Soybean-mediated suppression of BjaI/BjaR
1
quorum sensing in
Bradyrhizobium diazoefficiens
impacts symbiotic nitrogen fixation
Authors: Han Fang , Li Huiquan , Lyu Ermeng , Zhang Qianqian , Gai Haoyu , Xu Yunfang , Bai Xuemei , He Xueqian , Khan Abdul Qadir , Li Xiaolin , Xie Fang , Li Fengmin , Fang Xiangwen , Wei Min
Published: January 2024

The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR
1
QS system in
Bradyrhizobium diazoefficiens
USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR
1
showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR
1
systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR
1
exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR
1
QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by
B. diazoefficiens
.

IMPORTANCE

The present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes’ role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.
Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Authors: Liu Yingying , Wu Dan , Kan Yongjun , Zhao Li , Jiang Chang , Pang Wensheng , Hu Juan , Zhou Meilan
Published: January 2024

Pseudostellaria heterophylla of the Caryophyllaceae family is an important medicinal herb in traditional Chinese medicine, but it encounters continuous cropping obstacle during cultivation. This study aimed to study the differences in the response of Pseudostellaria heterophylla cultivation to soil microorganisms and phenolic substances in different types of soil (Loamy soil and Clayey soil). The analysis of soil metabolites using HPLC-ESI-Q/TOF-MS and HPLC-DAD techniques revealed that the content of various phenolic components in the rhizosphere soil increased significantly after Pseudostellaria heterophylla cultivation. Pseudostellaria heterophylla cultivation in yellow soil could increase the abundance of Proteobacteria, Ascomycota, and Thermoplasmatota, while in brown soil, the abundance of Ascomycota significantly decreased. In addition, Pseudostellaria heterophylla cultivation could increase the α-diversity of bacteria and fungi in yellow soil, while reducing the α-diversity of archaea, and the impact on diversity in brown soil was relatively small. Correlation analysis showed that phenolic compounds were more likely to regulate the genera Bradyrhizobium, Calcarisporiella, Boothiomyces and Methanocella. Pseudostellaria heterophylla may regulate rhizosphere microbial diversity and community structure by secreting phenolic. However, in different types of soil environments, the response mechanism of soil microorganisms to Pseudostellaria heterophylla planting might vary. Our study provides new insights that the variability in the response of different soil types to Pseudostelariae heterophylla cultivation should be taken into account when developing strategies for reducing continuous cropping obstacles in medicinal plants.
One-year effectiveness of high-load compared with low-load strengthening exercise on self-reported function in patients with hypermobile shoulders: a secondary analysis from a randomised controlled trial
Authors: Liaghat Behnam , Juul-Kristensen Birgit , Faber Daniel A , Christensen Emil O , Søgaard Karen , Skou Søren T , Søndergaard Jens , Juhl Carsten B
Published: January 2024

Objectives

To investigate the long-term effectiveness of high-load versus low-load strengthening exercise on self-reported function in patients with hypermobility spectrum disorder (HSD) and shoulder symptoms.

Methods

A secondary analysis of a superiority, parallel-group, randomised trial (balanced block randomisation 1:1, electronic concealment) including adult patients (n=100) from primary care with HSD and shoulder pain and/or instability ≥3 months. Patients received 16 weeks of shoulder exercises (three sessions/week): HEAVY (n=50, full-range, high-load, supervised twice/week) or LIGHT (n=50, neutral/mid-range, low-load, supervised three times in total). The 1-year between-group difference in change in self-reported function was measured using the Western Ontario Shoulder Instability Index (WOSI, scale 0–2100, 0=best). Secondary outcomes were self-reported measures including changes in shoulder-related symptoms, function, emotions and lifestyle, quality of life, patient-perceived effect, treatment utility and adverse events. A blinded analyst conducted the analyses using linear mixed model repeated measurements analysis.

Results

One-year data were available in 86 out of 100 participants (79% women, mean age 37.8 years) (LIGHT 84%, HEAVY 88%). The mean WOSI score between-group difference favoured HEAVY (−92.9, 95% CI −257.4 to 71.5, p=0.268) but was not statistically significant. The secondary outcomes were mostly inconclusive, but patients in HEAVY had larger improvement in the WOSI emotions subdomain (−36.3; 95% CI −65.4 to −7.3, p=0.014). Patient-perceived effect favoured HEAVY anchored in WOSI-emotions (55% vs 31%, p=0.027) and WOSI-lifestyle (50% vs 29%, p=0.042).

Conclusion

High-load shoulder strengthening exercise was not superior to low-load strengthening exercise in improving self-reported function at 1 year. High-load strengthening exercise may be more effective in improving patient emotions about shoulder pain and function, but more robust data are needed to support these findings.

Trial registration number

NCT03869307.
Incorporating biological and clinical insights into variant choice for Mendelian randomisation: examples and principles
Authors: Burgess Stephen , Cronjé Héléne Toinét
Published: January 2024

Mendelian randomisation is an accessible and valuable epidemiological approach to provide insight into the causal nature of relationships between risk factor exposures and disease outcomes. However, if performed without critical thought, we may simply have replaced one set of implausible assumptions (no unmeasured confounding or reverse causation) with another set of implausible assumptions (no pleiotropy or other instrument invalidity). The most critical decision to avoid pleiotropy is which genetic variants to use as instrumental variables. Two broad strategies for instrument selection are a biologically motivated strategy and a genome-wide strategy; in general, a biologically motivated strategy is preferred. In this review, we discuss various ways of implementing a biologically motivated selection strategy: using variants in a coding gene region for the exposure or a gene region that encodes a regulator of exposure levels, using a positive control variable and using a biomarker as the exposure rather than its behavioural proxy. In some cases, a genome-wide analysis can provide important complementary evidence, even when its reliability is questionable. In other cases, a biologically-motivated analysis may not be possible. The choice of genetic variants must be informed by biological and functional considerations where possible, requiring collaboration to combine biological and clinical insights with appropriate statistical methodology.
Abstracts from international Emergency Medicine journals
Authors: Production EMJ
Published: January 2024

Editor’s note: EMJ has partnered with the journals of multiple international emergency medicine societies to share from each a highlighted research study, as selected by their editors. This edition will feature an abstract from each publication.
Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study)
Authors: Kean Iain Robert Louis , Clark John A , Zhang Zhenguang , Daubney Esther , White Deborah , Ferrando-Vivas Paloma , Milla Gema , Cuthbertson Brian , Pappachan John , Klein Nigel , Mouncey Paul , Rowan Kathy , Myburgh John , Gouliouris Theodore , Baker Stephen , Parkhill Julian , Pathan Nazima , ARCTIC research team
Published: January 2024

Objective

Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control.

Design

We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care.

Results

SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specificallyBifidobacterium,at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment.

Conclusion

Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.
Seroconversion in syphilis screening without positive confirmatory tests points at early infection
Authors: Nieuwenburg Silvia Achia , Jongen Vita Willemijn , Schim van der Loeff Maarten , de Vries Henry , van Dam Alje
Published: January 2024

Introduction

The chemiluminescence immunoassay (CLIA) is a widely used screening test for syphilis. A CLIA seroconversion in the absence of a positive line immunoassay (LIA) or rapid plasma reagin (RPR) could indicate either an early incubating syphilis or a false positive result. We aimed to evaluate the diagnostic value of such seroconversions.

Methods

We retrospectively analysed data of clients visiting the Centre for Sexual Health Amsterdam between July 2013 and August 2021 with a positive CLIA and a negative RPR and negative or indeterminate LIA (at time To), and a preceding visit (T−1) with a negative CLIA <6 months of To(‘unconfirmed CLIA seroconversion’). If available, data of follow-up visits (T1) <2 months of Towere also included. A syphilis diagnosis was confirmed if darkfield microscopy or PCR forTreponema pallidumwas positive at T0or T1, or if RPR and/or LIA were positive at T1.

Results

We included data of 107 clients with unconfirmed CLIA seroconversion. The value of CLIA seroconversion could not be established in 13 (12.1%) clients. In the remaining 94 clients, the unconfirmed CLIA seroconversion was confirmed as early syphilis in 72 (76.6%) clients and probable syphilis in 6 (6.4%) clients. In 16 (17.0%) clients, the unconfirmed CLIA seroconversion was regarded as a false positive reaction of whom 4 (5.3%) clients had a seroreversion of the CLIA at T1.

Conclusion

The majority of unconfirmed CLIA seroconversions represented early syphilis infections. Therefore, additionalT. pallidumPCR, a follow-up consultation or early treatment is recommended.
The jelly report: Forecasting jellyfish using email and social media
Authors: Record Nicholas R. , Tupper Benjamin , Pershing Andrew J.
Published: January 2024

Ecosystem forecasting has potential societal value, for industry, recreation, and human health applications to name a few. The complexities of ecological systems, the expenses associated with monitoring them, and the suddenness at which forecasts become needed often make forecasts impractical. We tested a novel rapid spin-up daily forecasting system for jellyfish — Cyanea capillata (lion’s mane jellyfish), Aurelia aurita (moon jellyfish), and Staurostoma mertensii (whitecross jellyfish) — in the Gulf of Maine. The system blended satellite data with citizen reports collected via email and social media. The forecasting system took 1–3 weeks of tuning before performance plateaued, after which forecast performance was consistently high. Good model performance did not always correspond with good forecast performance, and predictor variables whose contribution improved model performance in some cases had the opposite effect on forecast performance. An adaptive learning mode provided a very modest improvement in performance. In a test of forecast range, forecast performance decreased significantly at a forecast range of around 1 week. Overall, the approach appeared to be a promising avenue toward rapid spin-up of forecasts for undermonitored systems.
Implications of the 2020 National Building Code of Canada updates on the design demands for reinforced concrete shear wall buildings
Authors: Dehghani S. , Tobber L.
Published: January 2024

The seismic demands of the Reinforced Concrete Shear Walls (RCSWs) system are determined based on Canada’s National Building Code (NBC). NBC 2020 features the revised Canadian Seismic Hazard Model and presents the possibility of enhancing demand’s accuracy by determining design spectra based on the specific average shear wave velocity, instead of specified site classes. This paper investigates the changes in design demands for RCSWs compared to the previous edition. To do so, fifty-five RCSW prototypes were modelled using distributed mass and stiffness procedure, and their dynamic response was assessed through Modal Response Spectrum Analysis at five locations across Canada. The results highlight significant changes in deformation and force demands, where the majority of cases experienced an increase in 2020 compared to 2015 when demands were determined based on specified site classes. This study also evaluates the log-log interpolation method recommended by NBC 2020 for the design spectral acceleration.
Factors that influence measurements of sweet cherry (Prunus avium) flower bud cold hardiness obtained using differential thermal analysis
Authors: Houghton Elizabeth , Hannam Kirsten , Neilsen Denise , Nelson Louise M.
Published: January 2024

Differential thermal analysis (DTA) is a technique commonly used to evaluate the cold hardiness of plant organs that supercool as a means for cold survival. The aim of this study was to evaluate the effect of different pretest bud storage conditions, cooling rates, and bud excision techniques on dormant sweet cherry flower bud low temperature exotherms (LTEs) measured using DTA. Furthermore, this study compared cold hardiness estimates made using DTA and controlled freezing tests. We determined that buds stored at warmer temperatures (12.5 °C and room temperature) for 2–6 h prior to DTA or transported to the lab in a moist environment underwent biologically relevant changes in their apparent sensitivity to cold, as indicated by LTEs produced at warmer temperatures. The DTA cooling rate also significantly affected LTEs, with faster cooling resulting in the production of LTEs at warmer temperatures. Overall, LTEs were comparable among buds with varying amounts of plant material remaining attached to the bud base. It is important to note that the region directly subtending the primordia was always left intact on the buds being compared. This study demonstrated that overall, DTA and controlled freezing tests resulted in comparable measures of cold hardiness. The findings presented in this study are pertinent to researchers interested in conducting cold hardiness measurements in sweet cherry and highlight that consistency in DTA pretest conditions and bud preparation are required to achieve reliable LTE results that can be compared among studies.
Electromagnetic extension of Buchdahl bound in f(R, T) gravity
Authors: Bhattacharya Soumik , Sharma Ranjan , Maharaj Sunil D.
Published: January 2024

We develop a static charged stellar model in f(R, T) gravity where the modification is assumed to be linear in T which is the trace of the energy momentum tensor. The exterior spacetime of the charged object is described by the Reissner–Nordström metric. The interior solution is obtained by invoking the Buchdahl–Vaidya–Tikekar ansatz, for the metric potential $$g_{rr}$$

g

rr

, which has a clear geometric interpretation. A detailed physical analysis of the model clearly shows distinct physical features of the resulting stellar configuration under such a modification. We find the maximum compactness bound for such a class of compact stars which is a generalization of the Buchdahl bound for a charged sphere described in f(R, T) gravity. Our result shows physical behaviour that is distinct from general relativity.
The effective potential in Fermi gauges beyond the standard model
Authors: Zuk Jonathan , Balázs Csaba , Papaefstathiou Andreas , White Graham
Published: January 2024

We derive the field-dependent masses in Fermi gauges for arbitrary scalar extensions of the Standard Model. These masses can be used to construct the effective potential for various models of new physics. We release a flexible notebook () which performs these calculations and renders large-scale phenomenological studies of various models possible. Motivated by the debate on the importance of gauge dependence, we show that, even in relatively simple models, there exist points where the global minimum is discontinuous in the gauge parameter. Such points require some care in discovering, indicating that a gauge-dependent treatment might still give reasonable results when examining the global features of a model.
Black hole surrounded by the pseudo-isothermal dark matter halo
Authors: Yang Yi , Liu Dong , Övgün Ali , Lambiase Gaetano , Long Zheng-Wen
Published: January 2024

In this paper, we obtain a new spherically symmetric black hole surrounded by the pseudo-isothermal dark matter halo. Furthermore, to explore the effects of the pseudo-isothermal halo profile on a rotating black hole at the M87 galactic center, we derive a rotating black hole solution encompassed by the pseudo-isothermal halo by using the Newman-Janis method. Our investigation focuses on the impact of the pseudo-isothermal halo on the black hole event horizon, time-like and null orbits, as well as the black hole shadow. We find that as the spin parameter a increases, the interval between the inner event horizon and the outer event horizon of the rotating black hole surrounded by the pseudo-isothermal halo in M87 diminishes. This leads to the formation of an extreme black hole. The presence of dark matter, however, has minimal effect on the event horizon. Moreover, in the M87 as the spin parameter a increases, the black hole shadow deviates increasingly from a standard circle, with larger spin parameters causing more pronounced distortion relative to the standard circle. Surprisingly, we observe that the dark matter density has very little influence on the shadow of the black hole surrounded by the pseudo-isothermal halo in the M87. This study contributes to a deeper understanding of black hole structures and the role of dark matter in the universe.
Knowing What You Need to Know
Authors: Limoncelli Thomas A.
Published: January 2024

Personal, team, and organizational effectiveness can be improved with a little preparation.
Security Mismatch
Authors: Vachon Phil
Published: January 2024

Security must be a business enabler, not a hinderer.
Semantic-Consistency-guided Learning on Deep Features for Unsupervised Salient Object Detection
Authors: Zhang Ying Ying , Zhang Shuo , Hui Ming
Published: January 2024

Unsupervised salient object detection is an important task in many real-world scenarios where pixel-wise label information is of scarce availability. Despite its significance, this problem remains rarely explored, with a few works that consider unsupervised salient object detection methods based on the fused graph from the sum fusion of multiple deep feature similarity matrices. However, these methods ignore the interrelation of the low-level feature similarity matrices and the high-level semantic similarity matrice, which degrades the quality of the fused graph. In this article, we propose a semantic-consistency-guided multi-graph fusion learning algorithm for unsupervised saliency detection, where the consistency and inconsistency between multiple low-level feature similarity matrices and the high-level semantic similarity matrice are explored to promote the robustness and quality of the fused graph. In the first stage, a semantic-consistency-guided multi-graph fusion learning method is proposed to exploit consistency and inconsistency of multiple low-level deep features and the high-level semantic feature. The semantic-consistency-guided similarity matrices are computed for preliminary saliency ranking. In the following saliency refinement stage, the semantic-enhanced similarity matrices are built by the cross diffusion to fuse the multiple low-level deep features and the high semantic deep feature. Based on the semantic-enhanced similarity matrices, the refinement saliency maps are calculated in a semantic-enhanced cellular automata manner. Furthermore, the final ensemble stage of the large margin semi-supervised classification views the preliminary ranking results and refinement results as features, adopts the large margin graphs for saliency ensemble. Extensive evaluations over four benchmark datasets show that the proposed unsupervised method performs favorably against the state-of-the-art approaches and is competitive with some supervised deep learning-based methods.
Width Helps and Hinders Splitting Flows
Authors: Cáceres Manuel , Cairo Massimo , Grigorjew Andreas , Khan Shahbaz , Mumey Brendan , Rizzi Romeo , Tomescu Alexandru I. , Williams Lucia
Published: January 2024

Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow/circulation
X
on a directed graph
G
into weighted source-to-sink paths whose weighted sum equals
X
. We show that, for acyclic graphs, considering the
width
of the graph (the minimum number of paths needed to cover all of its edges) yields advances in our understanding of its approximability. For the version of the problem that uses only non-negative weights, we identify and characterise a new class of
width-stable
graphs, for which a popular heuristic is a
O
(log
Val
(
X
))-approximation (
Val
(
X
) being the total flow of
X
), and strengthen its worst-case approximation ratio from

\(\Omega (\sqrt {m})\)

to Ω (
m
/log
m
) for sparse graphs, where
m
is the number of edges in the graph. We also study a new problem on graphs with cycles, Minimum Cost Circulation Decomposition (MCCD), and show that it generalises MFD through a simple reduction. For the version allowing also negative weights, we give a (⌈ log ‖ X ‖ ⌉ +1)-approximation (‖
X
‖ being the maximum absolute value of
X
on any edge) using a power-of-two approach, combined with parity fixing arguments and a decomposition of unitary circulations (‖
X
‖ ≤ 1), using a generalised notion of width for this problem. Finally, we disprove a conjecture about the linear independence of minimum (non-negative) flow decompositions posed by Kloster et al. [
2018
], but show that its useful implication (polynomial-time assignments of weights to a given set of paths to decompose a flow) holds for the negative version.
Report on the 9th ACM SIGIR / the 13th International Conference on the Theory of Information Retrieval (ICTIR 2023)
Authors: Yoshioka Masaharu , Aliannejadi Mohammad , Kiseleva Julia
Published: January 2024

The 9th ACM SIGIR / The 13th International Conference on the Theory of Information Retrieval (ICTIR 2023) held in Taiwan co-located with SIGIR 2023. This brief report provides an overview of ICTIR 2023 and introduces the student reviewer program, which provides an opportunity for the students to understand and contribute to the conference review process.

Date
: 23 July 2023.

Website
: https://sigir.org/ictir2023/.
Rethinking E-Commerce Search
Authors: Wang Haixun , Na Taesik
Published: January 2024

E-commerce search and recommendation usually operate on structured data such as product catalogs and taxonomies. However, creating better search and recommendation systems often requires a large variety of unstructured data including customer reviews and articles on the web. Traditionally, the solution has always been converting unstructured data into structured data through information extraction, and conducting search over the structured data. However, this is a costly approach that often has low quality. In this paper, we envision a solution that does entirely the opposite. Instead of converting unstructured data (web pages, customer reviews, etc) to structured data, we instead convert structured data (product inventory, catalogs, taxonomies, etc) into textual data, which can be easily integrated into the text corpus that trains LLMs. Then, search and recommendation can be performed through a Q/A mechanism through an LLM instead of using traditional information retrieval methods over structured data.
A gel-coated air-liquid-interface culture system with tunable substrate stiffness matching healthy and diseased lung tissues
Authors: He Zhi-Jian , Chu Catherine , Dickson Riley , Okuda Kenichi , Cai Li-Heng
Published: January 2024

In a conventional ALI system, cells are cultured on a plastic membrane that is much stiffer than human airway tissues. We develop a gel-ALI system by coating the plastic membrane with a thin layer of hydrogel with tunable stiffness matching that of healthy and fibrotic airway tissues. We discover that human bronchial epithelial cells migrate significantly faster on hydrogel substrates with pathological stiffness, highlighting the importance of mechanical cues in human airway remodeling.
Brg1/PRMT5 nuclear complex epigenetically regulates FOXO1 in IPF mesenchymal progenitor cells
Authors: Jbeli Aiham H. , Yang Libang , Xia Hong , Gilbertsen Adam J. , Bitterman Peter B. , Henke Craig A.
Published: January 2024

Our research offers valuable understanding regarding the epigenetic control of IPF MPC. The data we obtained strongly support the idea that the coordination between chromatin remodeling and histone methylation plays a key role in regulating transcription factors. Specifically, our findings indicate that FOXO1, an essential transcription factor, likely governs the self-renewal of IPF MPC, which is crucial for maintaining a critical pool of fibrogenic MPCs. This interplay could be an important therapeutic target.
The Self-Perception and Political Biases of ChatGPT
Authors: Rutinowski Jérôme , Franke Sven , Endendyk Jan , Dormuth Ina , Roidl Moritz , Pauly Markus
Published: January 2024

This contribution analyzes the self-perception and political biases of OpenAI’s Large Language Model ChatGPT. Considering the first small-scale reports and studies that have emerged, claiming that ChatGPT is politically biased towards progressive and libertarian points of view, this contribution is aimed at providing further clarity on this subject. Although the concept of political bias and affiliation is hard to define, lacking an agreed-upon measure for its quantification, this contribution attempts to examine this issue by having ChatGPT respond to questions on commonly used measures of political bias. In addition, further measures for personality traits that have previously been linked to political affiliations were examined. More specifically, ChatGPT was asked to answer the questions posed by the political compass test as well as similar questionnaires that are specific to the respective politics of the G7 member states. These eight tests were repeated ten times each and indicate that ChatGPT seems to hold a bias towards progressive views. The political compass test revealed a bias towards progressive and libertarian views, supporting the claims of prior research. The political questionnaires for the G7 member states indicated a bias towards progressive views but no significant bias between authoritarian and libertarian views, contradicting the findings of prior reports. In addition, ChatGPT’s Big Five personality traits were tested using the OCEAN test, and its personality type was queried using the Myers-Briggs Type Indicator (MBTI) test. Finally, the maliciousness of ChatGPT was evaluated using the Dark Factor test. These three tests were also repeated ten times each, revealing that ChatGPT perceives itself as highly open and agreeable, has the Myers-Briggs personality type ENFJ, and is among the test-takers with the least pronounced dark traits.
ASCF: Optimization of the Apriori Algorithm Using Spark-Based Cuckoo Filter Structure
Authors: Alrahwan Bana Ahmad , Farouk Mona
Published: January 2024

Data mining is the process used for extracting hidden patterns from large databases using a variety of techniques. For example, in supermarkets, we can discover the items that are often purchased together and that are hidden within the data. This helps make better decisions which improve the business outcomes. One of the techniques that are used to discover frequent patterns in large databases is frequent itemset mining (FIM) that is a part of association rule mining (ARM). There are different algorithms for mining frequent itemsets. One of the most common algorithms for this purpose is the Apriori algorithm that deduces association rules between different objects which describe how these objects are related together. It can be used in different application areas like market basket analysis, student’s courses selection process in the E-learning platforms, stock management, and medical applications. Nowadays, there is a great explosion of data that will increase the computational time in the Apriori algorithm. Therefore, there is a necessity to run the data-intensive algorithms in a parallel-distributed environment to achieve a convenient performance. In this paper, optimization of the Apriori algorithm using the Spark-based cuckoo filter structure (ASCF) is introduced. ASCF succeeds in removing the candidate generation step from the Apriori algorithm to reduce computational complexity and avoid costly comparisons. It uses the cuckoo filter structure to prune the transactions by reducing the number of items in each transaction. The proposed algorithm is implemented on the Spark in-memory processing distributed environment to reduce processing time. ASCF offers a great improvement in performance over the other candidate algorithms based on Apriori, where it achieves a time of only 5.8% of the state-of-the-art approach on the retail dataset with a minimum support of 0.75%.
Application of Constant Proportional Caputo Fractional Derivative to Thermodiffusion Flow of MHD Radiative Maxwell Fluid under Slip Effect over a Moving Flat Surface with Heat and Mass Diffusion
Authors: Ahmad Adnan , Nazar M. , Ahmad M. , Eldin Sayed M. , Nisa Zaib Un , Waqas Hassan , Imran M.
Published: January 2024

Thermal diffusion is a phenomenon where the concentration gradient or diffusive flux is created due to the temperature gradient. Thermal diffusion is induced because of the higher temperature and uneven distribution of the mixture. Formally, thermal diffusion is called the Soret effect, and it is a crucial factor in a number of natural occurrences like the separation of isotopes technique of purification. In this research paper, Maxwell fluid’s flow in the vicinage of a flat plate is discussed by considering the effect of the thermodiffusion subject to the first-order slip at the boundary with the application of a constant proportional Caputo (CPC) fractional derivative. The effect of heat generation and radiation is also taken into consideration, as well as the effect of a magnetic field of constant magnitude. The generalized heat and mass fluxes are considered, and this generalization of heat and mass fluxes is done by utilizing the CPC fractional derivative. After converting the current model’s governing equations into a dimensionless form, the temperature, concentration, and velocity fields’ analytical solutions are found. By drawing graphs of the temperature, concentration, and velocity fields for the parametric modifications, the results are graphically illustrated. It becomes clear from the results discussion that the outcomes produced by the constant proportional derivative are more decaying than those obtained with the classical differential operator of order one.
Clinical and Genomic Predictors of Adverse Events in Newly Diagnosed Glioblastoma
Authors: Lim-Fat Mary Jane , Iorgulescu J. Bryan , Rahman Rifaquat , Bhave Varun , Muzikansky Alona , Woodward Eleanor , Whorral Sydney , Allen Marie , Touat Mehdi , Li Xiaomei , Xy Gongwen , Patel Jay , Gerstner Elizabeth R. , Kalpathy-Cramer Jayashree , Youssef Gilbert , Chukwueke Ugonma , McFaline-Figueroa J. Ricardo , Nayak Lakshmi , Lee Eudocia Q. , Reardon David A. , Beroukhim Rameen , Huang Raymond Y. , Bi Wenya Linda , Ligon Keith L. , Wen Patrick Y.
Published: January 2024

Purpose:

Adverse clinical events cause significant morbidity in patients with GBM (GBM). We examined whether genomic alterations were associated with AE (AE) in patients with GBM.

Experimental Design:

We identified adults with histologically confirmed IDH-wild-type GBM with targeted next-generation sequencing (OncoPanel) at Dana Farber Cancer Institute from 2013 to 2019. Seizure at presentation, lymphopenia, thromboembolic events, pseudoprogression, and early progression (within 6 months of diagnosis) were identified as AE. The biologic function of genetic variants was categorized as loss-of-function (LoF), no change in function, or gain-of-function (GoF) using a somatic tumor mutation knowledge base (OncoKB) and consensus protein function predictions. Associations between functional genomic alterations and AE were examined using univariate logistic regressions and multivariable regressions adjusted for additional clinical predictors.

Results:

Our study included 470 patients diagnosed with GBM who met the study criteria. We focused on 105 genes that had sequencing data available for ≥ 90% of the patients and were altered in ≥10% of the cohort. Following false-discovery rate (FDR) correction and multivariable adjustment, the TP53, RB1, IGF1R, and DIS3 LoF alterations were associated with lower odds of seizures, while EGFR, SMARCA4, GNA11, BRD4, and TCF3 GoF and SETD2 LoF alterations were associated with higher odds of seizures. For all other AE of interest, no significant associations were found with genomic alterations following FDR correction.

Conclusions:

Genomic biomarkers based on functional variant analysis of a routine clinical panel may help identify AE in GBM, particularly seizures. Identifying these risk factors could improve the management of patients through better supportive care and consideration of prophylactic therapies.
Data from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas
Authors: Cheng Yingduan , Liang Pei , Geng Hua , Wang Zhaohui , Li Lili , Cheng Suk Hang , Ying Jianming , Su Xianwei , Ng Ka Man , Ng Margaret H.L. , Mok Tony S.K. , Chan Anthony T.C. , Tao Qian
Published: January 2024

Abstract
Epigenetic disruption of tumor suppressor genes is frequently involved in tumorigenesis. We identified a novel 19q13 KRAB domain-containing zinc finger protein, ZNF545/ZFP82, broadly expressed in normal tissues but downregulated in multiple tumor cell lines. The ZNF545 promoter contains a CpG island, which is frequently methylated in cell lines. The transcriptional silencing of ZNF545 could be reversed by pharmacologic or genetic demethylation, indicating direct epigenetic silencing. ZNF545 was also frequently methylated in multiple primary tumors of nasopharyngeal, esophageal, lung, gastric, colon, and breast, but rarely in normal epithelial tissues and paired normal tissues. ZNF545 is located in the nucleus and mainly sequestered in nucleoli, functioning as a repressor. ZNF545 is able to repress NF-κB and AP-1 signaling pathways, whereas ectopic expression of ZNF545 in silenced tumor cells significantly inhibited their growth and induced apoptosis. Functional studies showed that ZNF545 was involved in ribosome biogenesis through inhibiting the activity of rDNA promoter and decreasing cellular protein translation efficiency. Thus, we identified ZNF545 as a novel tumor suppressor inducing tumor cell apoptosis, repressing ribosome biogenesis and target gene transcription. The tumor-specific methylation of ZNF545 could be an epigenetic biomarker for cancer diagnosis. Mol Cancer Res; 10(7); 925–36. ©2012 AACR.
Data from miR-31 Is a Broad Regulator of β1-Integrin Expression and Function in Cancer Cells
Authors: Augoff Katarzyna , Das Mitali , Bialkowska Katarzyna , McCue Brian , Plow Edward F. , Sossey-Alaoui Khalid
Published: January 2024

Abstract
Integrins are adhesion receptors involved in bidirectional signaling that are crucial for various cellular responses during normal homeostasis and pathologic conditions such as cancer progression and metastasis. Aberrant expression of noncoding microRNAs (miRNA) has been implicated in the deregulation of integrin expression and activity, leading to the development and progression of cancer tumors, including their acquisition of the metastatic phenotype. miR-31 is a key regulator of several critical genes involved in the invasion-metastasis cascade in cancer. Using diverse cell-based, genetic, biochemical, flow cytometry, and functional analyses, we report that miR-31 is a master regulator of integrins as it targets multiple α subunit partners (α2, α5, and αV) of β1 integrins and also β3 integrins. We found that expression of miR-31 in cancer cells resulted in a significant repression of these integrin subunits both at the mRNA and protein levels. Loss of expression of α2, α5, αV, and β3 was a direct consequence of miR-31 targeting conserved seed sequences in the 3′ untranslated region of these integrin subunits leading to their posttranscriptional repression, which was reflected in their diminished surface expression in live cells. The biological consequence of decreased the cell surface of these integrins was a significant inhibition of cell spreading in a ligand-dependent manner. Although different reports have shown that a single integrin can be regulated by several miRNAs, here we show that a single miRNA, miR-31, is able to specifically target several integrin subunits to regulate key aspects of cancer cell invasion and metastasis. Mol Cancer Res; 9(11); 1500–8. ©2011 AACR.
Lung Fibroblasts Take up Breast Cancer Cell-derived Extracellular Vesicles Partially Through MEK2-dependent Macropinocytosis
Authors: Wan Yuhao , Zhao Yue , Cao Minghui , Wang Jingyi , Tran Sheila V. , Song Zhixuan , Hsueh Brent W. , Wang Shizhen Emily
Published: January 2024

Extracellular vesicles (EV) have emerged as critical effectors in the cross-talk between cancer and normal cells by transferring intracellular materials between adjacent or distant cells. Previous studies have begun to elucidate how cancer cells, by secreting EVs, adapt normal cells at a metastatic site to facilitate cancer cell metastasis. In this study, we utilized a high-content microscopic screening platform to investigate the mechanisms of EV uptake by primary lung fibroblasts. A selected library containing 90 FDA-approved anticancer drugs was screened for the effect on fibroblast uptake of EVs from MDA-MB-231 breast cancer cells. Among the drugs identified to inhibit EV uptake without exerting significant cytotoxicity, we validated the dose-dependent effect of Trametinib (a MEK1/2 inhibitor) and Copanlisib (a PI3K inhibitor). Trametinib suppressed macropinocytosis in lung fibroblasts and inhibited EV uptake with a higher potency comparing with Copanlisib. Gene knockdown and overexpression studies demonstrated that uptake of MDA-MB-231 EVs by lung fibroblasts required MEK2. These findings provide important insights into the mechanisms underlying lung fibroblast uptake of breast cancer cell-derived EVs, which could play a role in breast cancer metastasis to the lungs and suggest potential therapeutic targets for preventing or treating this deadly disease.

Significance:

Through a phenotypic screen, we found that MEK inhibitor Trametinib suppressed EV uptake and macropinocytosis in lung fibroblasts, and that EV uptake is mediated by MEK2 in these cells. Our results suggest that MEK2 inhibition could serve as a strategy to block cancer EV uptake by lung fibroblasts.
Immune Mechanisms Underpinning Long COVID: Collegium Internationale Allergologicum Update 2024
Authors: Untersmayr Eva , Venter Carina , Smith Peter , Rohrhofer Johanna , Ndwandwe Cebile , Schwarze Jurgen , Shannon Emer , Sokolowska Milena , Sadlier Corinna , O’Mahony Liam
Published: January 2024

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in a prolonged multisystem disorder termed long COVID, which may affect up to 10% of people following coronavirus disease 2019 (COVID-19). It is currently unclear why certain individuals do not fully recover following SARS-CoV-2 infection. Summary: In this review, we examine immunological mechanisms that may underpin the pathophysiology of long COVID. These mechanisms include an inappropriate immune response to acute SARS-CoV-2 infection, immune cell exhaustion, immune cell metabolic reprogramming, a persistent SARS-CoV-2 reservoir, reactivation of other viruses, inflammatory responses impacting the central nervous system, autoimmunity, microbiome dysbiosis, and dietary factors. Key Messages: Unfortunately, the currently available diagnostic and treatment options for long COVID are inadequate, and more clinical trials are needed that match experimental interventions to underlying immunological mechanisms.
The Role of Genetic Analysis in Distinguishing Multifocal and Multicentric Glioblastomas: An Illustrative Case
Authors: Karatsu Kosuke , Tamura Ryota , Yo Masahiro , Nogawa Hirotsugu , Hino Utaro , Kitamura Yohei , Ueda Ryo , Toda Masahiro
Published: January 2024

Introduction: Glioblastomas can manifest as multiple, simultaneous, noncontiguous lesions. We genetically analyzed multiple glioblastomas and discuss their etiological origins in this report. Case Presentation: We present the case of a 47-year-old woman who presented with memory impairment and left partial paralysis. Radiographic imaging revealed three apparently noncontiguous lesions in the right temporal and parietal lobes extending into the corpus callosum, leading to diagnosis of multicentric glioblastomas. All three lesions were excised. Genetic analysis of the lesions revealed a TERT promoter C228T mutation, a roughly equivalent amplification of EGFR, and homozygous deletion of CDKN2A/B exclusively in the two contrast-enhanced lesions. Additionally, the contrast-enhanced lesions exhibited the same two-base pair mutations of PTEN, whereas the non-enhanced lesion showed a partially distinct 13-base pair mutation. The other genetic characteristics were consistent. Rather than each having arisen de novo, we believe that they had developed by infiltration and are therefore best classified as multifocal glioblastomas. Conclusion: Our findings underscore anew the possibility of infiltration by glioblastomas, even within regions devoid of signal alterations on T2-weighted images or fluid-attenuated inversion recovery images. Genetic analysis can play a crucial role in differentiating whether multiple glioblastomas are multifocal or multicentric.
Endovascular Treatment of Anterior Inferior Cerebellar Artery Aneurysms: A Single-Center Experience and Review of 33 Patients
Authors: Li Junrao , Wang Xing , Wang Ting , Lin Sen , Zhang Changwei , Xie Xiaodong , Ma Lu , Wang Chaohua
Published: January 2024

Objective: The aim of the present article was the demonstration of the institutional experience with the endovascular management of the anterior inferior cerebellar artery (AICA) aneurysms in order to propose a treatment algorithm. Methods: Clinical data were obtained from 33 patients with 37 AICA aneurysms who had been surgically treated at the authors’ hospital between 2010 and 2022. The patients’ medical records, imaging data, and follow-up outcomes were retrospectively analyzed. Results: All 33 patients (10 males, 23 females; mean age 54.88 ± 12.49 years) underwent endovascular therapy for AICA aneurysms. The most common chief complaints were headache (87.9%), nausea and vomiting (57.6%), and alteration of consciousness (27.3%). Thirty-one patients experienced subarachnoid hemorrhage. Regarding the AICA aneurysm location, 23 aneurysms were found at the right side of AICA in digital subtraction angiography images, and there were 6, 9, 16, 6 aneurysms in segments A1-A4, respectively. Coiling (59.5%), Onyx embolization (29.7%), coiling-combined Onyx embolization (5.4%), nonintervention (5.4%) were chosen in the surgical strategy. The length of follow-up was 8.09 ± 5.05 months, and 84.8% of the patients had favorable modified Rankin Scale (mRS) scores. The complete occlusion rates were 94.6%. Postoperative complications occurred in 4 cases (12.1%), including new neurological deficit in 3 cases and cerebral infarction in 1 case. One patient died after follow-up because of the severe pneumonia. Poor initial Hunt and Hess grade (HHG) (p = 0.007) was the risk factor for unfavorable clinical outcome. The rupture status (p = 0.025) and the location (p = 0.021) of the AICA aneurysms are statistically significant in determining which operation strategy to be chosen. Coiling had an advantage over Onyx embolization (p = 0.001) in parent artery preservation. Conclusions: In this study, an algorithm for the treatment of AICA aneurysms was proposed based on the clinical status of the patients before treatment, the anatomical factors of AICA, and the technical conditions of endovascular treatment (EVT). To our knowledge, this is the first study to report more than 30 cases of AICA aneurysms that had been treated by EVT and to advocate a treatment algorithm. EVT of AICA aneurysms is an optional strategy, but decisions are made based on the specific condition, anatomical location, and other factors.