bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of psychological flexibility and resilience on psychopharmacological treatment response in patients with obsessive-compulsive disorder
Authors: Deveci Nisa , Uğurlu Mustafa , Karakaş Uğurlu Görkem , Kabadayi Şahin Esra , Erdoğan Ezgi Çisil , Çayköylü Ali
Published: August 2023

Obsessive-compulsive disorder (OCD) is a challenging psychiatric condition to treat. Previous research has explored various aspects of treatment response, but limited attention has been given to the significance of psychological flexibility and resilience. This study aimed to investigate the correlation between psychological flexibility, resilience, and different dimensions of OCD, as well as their role in treatment response specifically concerning OCD symptom sub-dimensions. The study involved 50 OCD patients and 42 healthy individuals as controls. Participants completed the Dimensional Obsessive-Compulsive Scale (DOCS), Acceptance and Action Questionnaire (AAQ-2), and Resilience Scale for Adults (RS). Initial scale scores were compared to post-treatment scores obtained after a 3-month follow-up using pharmacotherapy. The patient group exhibited significantly higher AAQ-2 scores and lower RS scores compared to the control group. During the post-treatment follow-up, a reduction in DOCS and AAQ-2 scores was observed, along with an increase in RS scores. The impact of differences in AAQ-2 and RS scores on the change in DOCS total scores was analyzed using mixed model linear regression analysis. The results showed a statistically significant effect of changes in AAQ-2 and RS sub-dimension scores on the change in DOCS total scores. The findings highlight the importance of flexibility and resilience in influencing treatment response among patients with OCD. When conventional pharmacotherapy and psychotherapy approaches prove insufficient, interventions focused on enhancing flexibility and resilience may contribute to improved treatment outcomes.
Possible genetic biomarker associated with antipsychotic-induced amenorrhea in female patients with schizophrenia
Authors: Moon Jung-Joon , Kim Ho-Sook , Shim Joo-Cheol , Ahn Jung-Mee , Jung Do-Un , Kim Dong-Jin , Jeong Hye-Eun , Kim Eun-Young , Jeon Dong-Wook , Kim Sung-Jin , Shin Jae-Gook
Published: August 2023

This study explored the association of pharmacogenomics with antipsychotic-induced amenorrhea in female patients with schizophrenia. A total of 89 female schizophrenia patients aged 18–40 receiving consistent antipsychotics at a consistent dose for more than 3 months were enrolled in this study. Amenorrhea was defined as the absence of menstrual period for 3 months or three periods in a row. Serum levels of prolactin, estradiol, follicle-stimulating hormone, luteinizing hormone, and thyroid-stimulating hormone were measured and Cytochrome P450 2D6, dopamine receptor D2 (DRD2) and estrogen receptor 1 were genotyped. Twenty-two patients with amenorrhea had higher prolactin levels and lower estradiol levels than those without amenorrhea (94.1 vs. 71.5 ng/ml for prolactin; P = 0.044 and 27.0 vs. 46.7 pg/ml for estradiol; P = 0.007, respectively). Multiple logistic regression analysis identified DRD2-141C deletion [odds ratio (OR) = 1.71, 95% confidence interval (CI) = 1.01–4.17; P = 0.049] and drugs increasing prolactin levels (OR = 6.17, 95% CI = 1.28–29.64; P = 0.023) as significant covariates for antipsychotic-induced amenorrhea. This study suggests that DRD2-141C deletion is associated with antipsychotic-induced amenorrhea although further studies are needed.
Stochastic models of ventilation driven by opposing wind and buoyancy
Authors: Andrian Veronica , Craske John
Published: August 2023

Stochastic versions of a classical model for natural ventilation are proposed and investigated to demonstrate the effect of random fluctuations on stability and predictability. In a stochastic context, the well-known deterministic result that ventilation driven by the competing effects of buoyancy and wind admits multiple steady states can be misleading. With fluctuations in the buoyancy exchanged with an external environment modelled as a Wiener process, such systems tend to reside in the vicinity of global minima of their potential, rather than states associated with metastable equilibria. For a heated space with a leeward low-level and windward high-level opening, sustained buoyancy-driven flow opposing the wind direction is unlikely for wind strengths exceeding a statistically critical value, which is slightly larger than the critical value of the wind strength at which bifurcation in the deterministic system occurs. When fluctuations in the applied wind strength are modelled as an Ornstein–Uhlenbeck process, the topology of the system’s potential is effectively modified due to the nonlinear role that wind strength has in the equation for buoyancy conservation. Consequently, large fluctuations in the wind of sufficient duration rule out the possibility of sustained ventilation opposing the wind direction at large base wind strengths.
Influenza Vaccination and Major Cardiovascular Risk: A Systematic Review and Meta-Analysis of Clinical Trials Studies
Authors: Omidi Fatemeh , Zangiabadian Moein , Shahidi Bonjar Amir Hasehm , Nasiri Mohammad Javad , Sarmastzadeh Tala
Published: August 2023

Background

Cardiovascular events remain a substantial global health concern, necessitating innovative strategies for prevention. This study aims to assess the potential impact of influenza vaccination on major cardiovascular events.

Methods

A search of the medical English literature was conducted using PubMed/MEDLINE, EMBASE, and the Cochrane CENTRAL up to 1 August 2023. Meta-analysis and stratified analyses were performed to investigate specific outcomes, including myocardial infarction (MI), cardiovascular death, and stroke. Pooled relative risks (RR) along with their 95% confidence intervals (CI) were calculated to evaluate the associations.

Results

A comprehensive analysis was conducted on a total of 9059 patients, with 4529 patients receiving the influenza vaccine and 4530 patients receiving a placebo. Among patients who received the influenza vaccine, a notable reduction in the occurrence of major cardiovascular events was observed, with 517 cases compared to 621 cases in the placebo group (RR, 0.70; 95%CI, 0.55-0.91). The stratified analysis revealed a decreased risk of MI in vaccinated patients (RR, 0.74; 95%CI, 0.56-0.97) and a significant reduction in cardiovascular death events (RR, 0.67; 95% CI 0.45–0.98).

Conclusion

This study provides compelling evidence that influenza vaccination is associated with a decreased risk of major cardiovascular events, particularly myocardial infarction, and cardiovascular death. These findings highlight the potential of influenza vaccination as an adjunctive strategy in cardiovascular disease prevention. Further research and exploration of underlying mechanisms are warranted to elucidate the observed beneficial effects.
Diagnostic test accuracy in longitudinal study settings: Theoretical approaches with use cases from clinical practice
Authors: Böhnke Julia , Zapf Antonia , Kramer Katharina , Weber Philipp ,   ELISE Study Group, Karch André , Rübsamen Nicole , Bode Louisa , Mast Marcel , Wulff Antje , Marschollek Michael , Schamer Sven , Rathert Henning , Jack Thomas , Beerbaum Philipp , Rübsamen Nicole , Böhnke Julia , Karch André , Das Pronaya Prosun , Wiese Lena , Groszweski-Anders Christian , Haller Andreas , Frank Torsten
Published: August 2023

In this study we evaluate how to estimate diagnostic test accuracy (DTA) correctly in the presence of longitudinal patient data (i.e., repeated test applications per patient). We used a nonparametric approach to estimate sensitivity and specificity of diagnostic tests for three use cases with different characteristics (i.e., episode length and intervals between episodes): 1) systemic inflammatory response syndrome, 2) depression, and 3) epilepsy. DTA was estimated on the levels ‘time’, ‘event’, and ‘patient-time’ for each diagnosis, representing different research questions. A comparison of DTA for these levels per and across use cases showed variations in the estimates, which resulted from the used level, the time unit (i.e., per minute/hour/day), the resulting number of observations per patient, and the diagnosis-specific characteristics. Researchers need to predefine their choices (i.e., estimation levels and time units) based on their individual research aims, including the estimand definitions, and give an appropriate rationale considering the diagnosis-specific characteristics of the target outcomes and the number of observations per patient to make sure that unbiased and clinically relevant measures are communicated. Nonetheless, researchers could report the DTA of the test using more than one estimation level and/or time unit if this still complies with the research aim.
Arbovirus surveillance in pregnant women in north-central Nigeria, 2019-2022
Authors: Ogwuche Jerry , Chang Charlotte Ajeong , Ige Olukemi , Sagay Atiene S. , Chaplin Beth , Kahansim Makshwar L. , Paul Michael , Elujoba Michael , Imade Godwin , Kweashi Georgenia , Dai Yu-Ching , Hsieh Szu-Chia , Wang Wei-Kung , Hamel Donald J. , Kanki Phyllis J.
Published: August 2023

The adverse impact of Zika (ZIKV), dengue (DENV), and chikungunya (CHIKV) virus infection in pregnancy has been recognized in Latin America and Asia but is not well studied in Africa.

In Nigeria, we screened 1006 pregnant women for ZIKV, DENV and CHIKV IgM/IgG by rapid test (2019-2022). Women with acute infection were recruited for prospective study and infants were examined for any abnormalities from delivery through six months. A subset of rapid test-reactive samples were confirmed using virus-specific ELISAs and neutralization assays.

Prevalence of acute infection (IgM+) was 3.8%, 9.9% and 11.8% for ZIKV, DENV and CHIKV, respectively; co-infections represented 24.5% of all infections. Prevalence in asymptomatic women was twice the level of symptomatic infection. We found a significant association between acute maternal ZIKV/DENV/CHIKV infection and any gross abnormal birth outcome (p=0.014).

Further prospective studies will contribute to our understanding of the clinical significance of these endemic arboviruses in Africa.
Large Language Models (LLMs) and Empathy – A Systematic Review
Authors: Sorin Vera , Brin Danna , Barash Yiftach , Konen Eli , Charney Alexander , Nadkarni Girish , Klang Eyal
Published: August 2023

Purpose

Empathy, a cornerstone of human interaction, is a unique quality to humans that Large Language Models (LLMs) are believed to lack. Our study aims to review the literature on the capacity of LLMs in demonstrating empathy

Methods

We conducted a literature search on MEDLINE up to July 2023. Seven publications ultimately met the inclusion criteria.

Results

All studies included in this review were published in 2023. All studies but one focused on ChatGPT-3.5 by OpenAI. Only one study evaluated empathy based on objective metrics, and all others used subjective human assessment. The studies reported LLMs to exhibits elements of empathy, including emotions recognition and providing emotionally supportive responses in diverse contexts, most of which were related to healthcare. In some cases, LLMs were observed to outperform humans in empathy-related tasks.

Conclusion

LLMs demonstrated some aspects of empathy in variable scenarios, mainly related to healthcare. The empathy may be considered “cognitive” empathy. Social skills are a fundamental aspect of intelligence, thus further research is imperative to enhance these skills in AI.
Exploring Quorum-Sensing-Based Bacterial GMOs for Addressing Bovine Mastitis: A Developmental Approach
Authors: Adhikary Adrija , Dutta Abeg , Ghosh Udit , Chatterjee Sourin , Borkar Shreyash , Das Shubhamay
Published: August 2023

Bovine mastitis, a prevalent and costly disease affecting dairy cows, severely impacts milk production, quality, and cow health and poses significant challenges to the dairy industry worldwide. Traditional treatment strategies relying on antibiotics face concerns of antibiotic resistance and residual antibiotic residues in dairy products. Therefore, there is an urgent need for innovative and sustainable approaches. Our study undertakes a preliminary investigation into the formulation and efficacy of a GMO-based antibiotic-free treatment in fighting Bovine mastitis. We propose to use the bioengineered defensin Nisin PV as the antimicrobial to specifically target the causative pathogenStaphylococcus aureus. To disrupt the biofilm formation, we have leveraged the potency of DNaseI. By hacking the quorum sensing technique ofStaphylococcus aureus, our proposed genetically modified bacteria would sense the presence of pathogens and initiate their eradication by producing Nisin PV and DNaseI. Results show the efficacy of DNase I against bacterial biofilm formation, in addition to the efficacy of our proposed sensor, which is based on the agr quorum sensing system ofStaphylococcus aureus, a major cause of bovine mastitis. Molecular dynamics and simulations show that our choice of the bacterial defensin, Nisin PV, is less susceptible to cleavage by bacterial strains resistant to the native bacteriocin Nisin A. Additionally, we theoretically propose a lysis-based kill switch to ensure the release of the therapeutic components. The solution proposed in this study has the potential to offer a sustainable and effective alternative to antibiotic-based treatments. Implementation of bioengineered defensins could reduce disease incidence, minimize economic losses, and promote responsible antimicrobial stewardship in the dairy industry.
AI in paleontology
Authors: Yu Congyu , Qin Fangbo , Watanabe Akinobu , Yao Weiqi , Li Ying , Qin Zichuan , Liu Yuming , Wang Haibing , Jiangzuo Qigao , Hsiang Allison Y. , Ma Chao , Rayfield Emily , Benton Michael J. , Xu Xing
Published: August 2023

Accumulating data have led to the emergence of data-driven paleontological studies, which reveal an unprecedented picture of evolutionary history. However, the fast-growing quantity and complication of data modalities make data processing laborious and inconsistent, while also lacking clear benchmarks to evaluate data collection and generation, and the performances of different methods on similar tasks. Recently, Artificial Intelligence (AI) is widely practiced across scientific disciplines, but has not become mainstream in paleontology where manual workflows are still typical. In this study, we review more than 70 paleontological AI studies since the 1980s, covering major tasks including micro-and macrofossil classification, image segmentation, and prediction. These studies feature a wide range of techniques such as Knowledge Based Systems (KBS), neural networks, transfer learning, and many other machine learning methods to automate a variety of paleontological research workflows. Here, we discuss their methods, datasets, and performance and compare them with more conventional AI studies. We attribute the recent increase in paleontological AI studies to the lowering bar in training and deployment of AI models rather than real progress. We also present recently developed AI implementations such as diffusion model content generation and Large Language Models (LLMs) to speculate how these approaches may interface with paleontological research. Even though AI has not yet flourished in paleontological research, successful implementation of AI is growing and show promise for transformative effect on the workflow in paleontological research in the years to come.

Highlights

First systematic review of AI applications in paleontology.

There is a 10 to 20-year gap between AI in paleontology and mainstream studies.

Recent progress in paleontological AI studies is likely a result of lowering bar in training and deployment.

Future direction discussed for interactions between paleontology and AI.
Novel Biomarkers and Distinct Transcriptomic Profile of Barrett’s Esophagus Epithelial Stem Cells
Authors: Alexander Katie L. , Smythies Lesley E. , Kyanam-Kabir-Baig Kondal R. , Poovey Emily , Crossman David K. , Smith Phillip D. , Peter Shajan
Published: August 2023

Barrett’s esophagus, a metaplastic condition that originates in the distal esophagus, is the only known precursor lesion for the development of esophageal adenocarcinoma, which has a devasting 5-year survival rate of <20%. The large number of subjects diagnosed with Barrett’s esophagus, and therefore at higher risk for esophageal adenocarcinoma, underscores the necessity for biomarkers that would benefit surveillance and potentially early treatment. To address this, we generated epithelial stem cell organoids from normal gastric cardia, non-dysplastic and dysplastic Barrett’s esophagus, and esophageal and gastric adenocarcinoma. Interestingly, non-dysplastic and dysplastic Barrett’s esophagus displayed higher expression of multiple archetypical cancer-associated genes compared with both esophageal and gastric adenocarcinoma in addition to expression of the novel biomarker CT83. ST6GAL1, a Golgi sialyltransferase upregulated in multiple epithelioid cancers, was strongly upregulated in dysplastic Barrett’s esophagus at both mRNA and protein levels. ST6GAL1 protein also was highly expressed in esophageal adenocarcinoma, suggesting that regulation of ST6GAL1 may play a role in Barrett’s esophagus progression to esophageal adenocarcinoma and serve as a potential biomarker of the development of esophageal cancer.
PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature
Authors: Rader Jonathan A. , Pivovarnik Madelyn A. , Vantilburg Matias E. , Whitehouse Logan S.
Published: August 2023

Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of two commonly used taxonomic databases to find associated synonyms with given target species names.

Availability and implementation

PhyloMatcher is easily installed as a Python package with pip, or as a standalone GUI application. PhyloMatcher source code and documentation are freely available athttps://github.com/Lswhiteh/PhyloMatcher, the GUI application can be downloaded from the Releases page.

Contact

Lswhiteh@unc.edu

Supplemental Information

We provide documentation for PhyloMatcher, including walkthrough instructions for the GUI application on the Releases page ofhttps://github.com/Lswhiteh/PhyloMatcher.
SonoPrint: Acoustically Assisted Volumetric 3D Printing for Composites
Authors: Agrawal Prajwal , Zhuang Shengyang , Dreher Simon , Mitter Sarthak , Ahmed Daniel
Published: August 2023

Advancements in additive manufacturing in composites have transformed various fields in aerospace, medical devices, tissue engineering, and electronics, enabling fine-tuning material properties by reinforcing internal particles and adjusting their type, orientation, and volume fraction. This capability opens new possibilities for tailoring materials to specific applications and optimizing the performance of 3D-printed objects. Existing reinforcement strategies are restricted to pattern types, alignment areas, and particle characteristics. Alternatively, acoustics provide versatility by controlling particles independent of their size, geometry, and charge and can create intricate pattern formations. Despite the potential of acoustics in most 3D printing, limitation arises from the scattering of the acoustic field between the polymerized hard layers and the unpolymerized resin, leading to undesirable patterning formation. However, this challenge can be addressed by adopting a novel approach that involves simultaneous reinforcement and printing the entire structure. Here, we present SonoPrint, an acoustically-assisted volumetric 3D printer that produces mechanically tunable composite geometries by patterning reinforcement microparticles within the fabricated structure. SonoPrint creates a standing wave field that produces a targeted particle motif in the photosensitive resin while simultaneously printing the object in just a few minutes. We have also demonstrated various patterning configurations such as lines, radial lines, circles, rhombuses, quadrilaterals, and hexagons using microscopic particles such as glass, metal, and polystyrene particles. Furthermore, we fabricated diverse composites using different resins, achieving 87 microns feature size. We have shown that the printed structure with patterned microparticles increased their tensile and compression strength by ∼38% and ∼75%, respectively.
Vascularized tumor on a microfluidic chip to study mechanisms promoting tumor neovascularization and vascular targeted therapies
Authors: Skubal Magdalena , Larney Benedict Mc , Phung Ngan Bao , Desmaras Juan Carlos , Dozic Abdul Vehab , Volpe Alessia , Ogirala Anuja , Machado Camila Longo , Djibankov Jakob , Ponomarev Vladimir , Grimm Jan
Published: August 2023

The cascade of events leading to tumor formation includes induction of a tumor supporting neovasculature as a primary hallmark of cancer. Developing vasculature is difficult to evaluatein vivobut can be captured using microfluidic chip technology and patient derived cells. Herein, we established anon chipapproach to investigate the mechanisms promoting tumor vascularization and vascular targeted therapies via co-culture of metastatic renal cell carcinoma spheroids and endothelial cells in a 3D environment. Our model permitted real-time, high-resolution observation and assessment of tumor-induced angiogenesis, where endothelial cells sprout towards the tumor and mimic a vascular network. Bevacizumab, an angiogenic inhibitor, disrupted interactions between vessels and tumors, destroying the vascular network. Theon chipapproach enabled assessment of endothelial cell biology, vessel’s functionality, drug delivery, and molecular expression of PSMA. Finally, observations in the vascularized tumoron chippermitted direct and conclusive quantification of this therapy in weeks as opposed to months in a comparable animal model.

Teaser

Vascularized tumor on microfluidic chip provides opportunity to study targeted therapies and improves preclinical drug discovery.
Insights into human outer kinetochore assembly and force transmission from a structure-function analysis of the KMN network
Authors: Polley Soumitra , Raisch Tobias , Koerner Marie , Terbeck Melina , Gräter Frauke , Raunser Stefan , Aponte-Santamaría Camilo , Vetter Ingrid R. , Musacchio Andrea
Published: August 2023

The biorientation of chromosomes during cell division is necessary for precise dispatching of a mother cell’s chromosomes into its two daughters. Kinetochores, large layered structures built on specialized chromosome loci named centromeres, promote biorientation by binding and sensing spindle microtubules. The kinetochore outer layer consists of a 10-subunit apparatus comprising Knl1C, Mis12C, and Ndc80C subcomplexes (KMN network). The KMN network is highly elongated and docks on kinetochores and microtubules using interfaces at its opposite extremes. Here, we combine cryo-EM reconstructions and AlphaFold2 predictions to generate a model of the KMN network that reveals all intra-KMN interfaces. We identify and functionally validate two interaction interfaces that link Mis12C to Ndc80C and Knl1C. Through targeted interference experiments and molecular dynamics simulations we demonstrate this mutual organization stabilizes the KMN network. Our work reports the first comprehensive structural and functional analysis of the microtubule binding machinery of kinetochores and elucidates a path of microtubule-generated force transmission
microRNA profile of endometrial cancer from Indian patients-Identification of potential biomarkers for prognosis
Authors: Hegde Shraddha , Wagh Kalpesh , Abikar Apoorva , Nambiar Sughosha , Ananthamurthy Shriraksha , Narayana Navyashree Hosahalli , Reddihalli Pallavi Venkateshaiah , Chandraiah Savitha , Narayana Suma Mysore , Ranganathan Prathibha
Published: August 2023

Endometrial cancer is one of the major cancers in women throughout the world. If diagnosed early, these cancers are treatable and the prognosis is usually good. However, one major problem in treating endometrial cancer is accurate diagnosis and staging. Till date, the choice method for diagnosis and staging is histopathology. Although there are few molecular markers identified, they are not always sufficient in making accurate diagnosis and deciding on therapeutic strategy. As a result, very often patients are under treated or over treated. In this study, our group has profiled microRNAs (miRNA) from Indian patients using NGS-based approach. We have identified differentially expressed microRNAs in endometrial cancer. These microRNAs have also been compared to data from TCGA (The Cancer Genome Atlas), which represent other populations and also correlated to relevance in overall survival. Usingin-silicoapproaches, mRNA targets of the miRNAs have been predicted. After comparing with TCGA, we have identified 16 miRNA-mRNA pairs which could be potential prognostic biomarkers for endometrial cancer. This is the first miRNA profiling report from Indian cohort and one of the very few studies which have identified potential biomarkers of prognosis in endometrial cancer.
Bloodmeal metabarcoding of the argasid tick (Ornithodoros turicataDugès) reveals extensive vector-host associations
Authors: Balasubramanian Sujata , Busselman Rachel E. , Fernandez-Santos Nadia , Grunwald Andy , Wolff Nicholas , Hathaway Nicholas , Hillhouse Andrew , Bailey Jeffrey A. , Teel Pete D. , Ferreira Francisco C. , Hamer Sarah A. , Hamer Gabriel L.
Published: August 2023

Molecular methods to understand host feeding patterns of arthropod vectors are critical to assess exposure risk to vector-borne disease and unveil complex ecological interactions. We build on our prior work discovering the utility of PCR-Sanger sequencing bloodmeal analysis that work remarkably well for soft ticks (Acari: Argasidae), unlike for hard ticks (Acari: Ixodidae), thanks to their unique physiology that retains vertebrate DNA from prior bloodmeals viable for years. Here, we capitalize on this feature and apply bloodmeal metabarcoding using amplicon deep sequencing to identify multiple host species in individualOrnithodoros turicatasoft ticks collected from two natural areas in Texas, United States. Of 788 collectedO. turicata, 394 were evaluated for bloodmeal source via metabarcoding, revealing 27 different vertebrate host species (17 mammals, 5 birds, 1 reptile, and 4 amphibians) fed upon by 274 soft ticks. Information on multiple hosts for individualO. turicatawas derived from 168 of these (61%). Metabarcoding revealed more mixed vertebrate bloodmeals inO. turicatapreviously processed using Sanger sequencing. These data reveal wide host range ofO. turicataand demonstrate the value of bloodmeal metabarcoding for understanding the ecology for known and potential tick-borne pathogens circulating among humans, domestic animals and wildlife such as relapsing fever caused byBorrelia turicatae. Our results also document, for the first time an off-host soft tick collected to have evidence of prior feeding on wild pig which is a critical observation in the context of the threat of enzootic transmission of African swine fever virus if it were introduced to the US. This research enhances our understanding of vector-host associations and offers a promising perspective for biodiversity monitoring and disease control strategies.
Discovery of an isoflavone oxidative catabolic pathway in legume root microbiota
Authors: Aoki Noritaka , Shimasaki Tomohisa , Yazaki Wataru , Sato Tomoaki , Nakayasu Masaru , Ando Akinori , Kishino Shigenobu , Ogawa Jun , Masuda Sachiko , Shibata Arisa , Shirasu Ken , Yazaki Kazufumi , Sugiyama Akifumi
Published: August 2023

Isoflavones are major specialized metabolites found in legume plants, where they contribute to environmental adaptation. Isoflavones also play a role human health as promising therapeutic agents. This metabolite group is involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. We previously reported that isoflavones enrich the Comamonadaceae, a predominant bacterial family in soybean roots, and that microorganisms in legume rhizosphere soil degrade isoflavones. However, the isoflavone catabolism pathway that underly the isoflavone-mediated legume–microbiota interactions have not yet been clarified. Here, we isolatedVariovoraxsp. strain V35, member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation namedifc. Strain V35 metabolizes isoflavones in a completely distinct oxidative manner from the reductive isoflavone metabolism pathway elucidated in the gut microbiota, in which resulting products enter the tricarboxylic acid cycle. The characterization ofifcmutants and heterologously expressed IFC enzymes revealed that isoflavones are catabolized via A-ring cleaving fission, which starts with hydroxylation at the 8-position of the A-ring. We further demonstrated thatifcgenes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an oxidative catabolism pathway of isoflavone in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume–microbiota interactions.

Significance

Isoflavones play pivotal roles in plant-environment interactions and in the maintenance and improvement of human health. Bacterial metabolism is a fundamental component of isoflavone-mediated interkingdom interactions. In the human gut, intestinal bacteria convert isoflavones into equol, a highly bioactive compound. However, the fate of isoflavones in the legume rhizosphere has not been elucidated, despite them being the key signaling molecules for nodule symbiosis and modulation of the legume root microbiota. Here, we discovered a novel isoflavone catabolism pathway in the soybean root microbiota and demonstrated the strong association between bacterial catabolic abilities and their interactions with host plants. Collectively, our findings provide new insights into bacterial isoflavone metabolism and a molecular understanding of legume-microbiota interactions.
The X-Linked Intellectual Disability gene,ZDHHC9, is important for oligodendrocyte subtype determination and myelination
Authors: Hollman Rocio B , Wild Angela R , O'Leary Timothy P , Thompson Andrew J , Flibotte Stephane , Poblete Tashana O , Peng Angie , Rogalski Jason C , Gill Gurmaan , Bamji Shernaz X
Published: August 2023

Two percent of patients with X-linked intellectual disability (XLID) exhibit loss-of-function mutations in the enzyme,ZDHHC9. One of the main anatomical deficits observed in these patients is a decrease in corpus callosum volume and a concurrent disruption in white matter integrity. In this study, we demonstrate that deletion ofZdhhc9in mice disrupts the balance of mature oligodendrocyte subtypes within the corpus callosum. While overall mature oligodendrocyte numbers are unchanged, there is a marked increase in MOL5/6 cells that are enriched in genes associated with cell adhesion and synapses, and a concomitant decrease in MOL2/3 cells that are enriched in genes associated with myelination. In line with this, we observed a decrease in the density of myelinated axons and disruptions in myelin compaction in the corpus callosum ofZdhhc9knockout mice. RNA sequencing and proteomic analysis further unveiled a reduction in genes and proteins essential for lipid metabolism, cholesterol synthesis, and myelin compaction. These findings reveal a previously under-appreciated and fundamental role forZDHHC9and protein palmitoylation in regulating oligodendrocyte subtype determination and myelinogenesis, offering mechanistic insights into the deficits observed in white matter volume in patients with mutations inZDHHC9.
Gene expression is the main driver of purifying selection in large penguin populations
Authors: Trucchi Emiliano , Massa Piergiorgio , Giannelli Francesco , Latrille Thibault , Fernandes Flavia A. N. , Ancona Lorena , Stenseth Nils Chr , Ferrer Obiol Joan , Paris Josephine , Bertorelle Giorgio , Le Bohec Céline
Published: August 2023

Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species’ lineages (known as E-R anticorrelation), pointing towards gene expression as an additional driver of purifying selection. However, estimates of the effect of gene expression on segregating deleterious variants in natural populations are scarce, as is an understanding of the relative contribution of population size and gene expression to purifying selection. Here, we analyse genomic and transcriptomic data from two natural populations of closely related sister species with different demographic histories, the Emperor penguin (Aptenodytes forsteri) and the King penguin (A. patagonicus), and show that purifying selection at the population-level depends on gene expression rate, resulting in very high selection coefficients at highly expressed genes. Leveraging realistic forward simulations, we estimate that the top 10% of the most highly expressed genes in a genome experience a selection pressure corresponding to an average selection coefficient of -0.1, which decreases to a selection coefficient of -0.01 for the top 50%. Gene expression rate can be regarded as a fundamental parameter of protein evolution in natural populations, maintaining selection effective even at small population size. We suggest it could be used as a proxy for gene selection coefficients, which are notoriously difficult to derive in non-model species under real-world conditions.
Cell type-specific role of CBX2 and its disordered region in spermatogenesis
Authors: Kim Jongmin J. , Steinson Emma R. , Lau Mei Sheng , de Rooij Dirk G. , Page David C. , Kingston Robert E.
Published: August 2023

Polycomb group (PcG) proteins maintain the repressed state of lineage-inappropriate genes and are therefore essential for embryonic development and adult tissue homeostasis. One critical function of PcG complexes is modulating chromatin structure. Canonical Polycomb repressive complex 1 (cPRC1), particularly its component CBX2, can compact chromatin and phase-separate in vitro. These activities are hypothesized to be critical for forming a repressed physical environment in cells. While much has been learned by studying these PcG activities in cell culture models, it is largely unexplored how cPRC1 regulates adult stem cells and their subsequent differentiation in living animals. Here, we show in vivo evidence of a critical nonenzymatic repressive function of cPRC1 component CBX2 in the male germline. CBX2 is up-regulated as spermatogonial stem cells differentiate and is required to repress genes that were active in stem cells. CBX2 forms condensates (similar to previously described Polycomb bodies) that colocalize with target genes bound by CBX2 in differentiating spermatogonia. Single-cell analyses of mosaicCbx2mutant testes show that CBX2 is specifically required to produce differentiating A1 spermatogonia. Furthermore, the region of CBX2 responsible for compaction and phase separation is needed for the long-term maintenance of male germ cells in the animal. These results emphasize that the regulation of chromatin structure by CBX2 at a specific stage of spermatogenesis is critical, which distinguishes this from a mechanism that is reliant on histone modification.
Black swan events and stock market behavior in Gulf countries: a comparative analysis of financial crisis (2008) and COVID-19 pandemic
Authors: Rehman Mohd Ziaur , Karimullah Karimullah
Published: August 2023

Purpose

The current study aims to examine the impact of two black swan events on the performance of six stock markets in Gulf Cooperation Council (GCC) economies (Abu Dhabi, Bahrain, Dubai, Oman, Qatar and Saudi Arabia). The two selected black swan events are the US Mortgage and credit crisis (Global Financial Crisis of 2008) and the COVID-19 pandemic.

Design/methodology/approach

The performance of all the six stock markets are represented by their return and price volatility behavior, which has been measured by applying ARCH/GARCH model. The comparative analysis is done by employing mean difference models. The data is collected from Bloomberg on a daily frequency.

Findings

The response of two black swan events on the GCC stock markets has been heterogenous in nature. During the financial crisis, the impact was heavily felt on most of the stock markets in the GCC countries. It is revealed that the financial crisis had a negative significant impact on four of the six countries. Whereas during the COVID-19 crisis, it is revealed that there is no significant impact on four of the six selected stock markets. The positive significant impact is felt on two stock markets, namely, the Abu Dhabi stock market and the Saudi stock market.

Originality/value

The present investigation attempts to fill the gap in the literature on the intended topic because it is evident from the literature on the chosen subject that no study has been undertaken to evaluate and contrast the impact of the GFC crisis and COVID-19 on the GCC stock markets.
Understanding organic food consumption in the European Union: the interaction between health and environmental consumer's goals
Authors: Valero-Gil Jesus , Escario José-Julián , Belanche Daniel , Casaló Luis V.
Published: August 2023

Purpose

Based on goal-directed behavior, this study explores the direct effects and the interaction between health and environmental concerns as the main drivers of organic food consumption. Consumer's economic problems are proposed as the main barrier for such behavior from a cost-benefit approach theoretically grounded on decision theory.

Design/methodology/approach

Data were collected using the 26,669 European 95.1 wave participants of the Eurobarometer survey. Logistic regression estimates are used to analyze the hypotheses postulated.

Findings

The results indicated the significant association of both health and environmental concerns with organic food consumption, as well as the existence of an interactive effect between both consumer goals. As a novel finding, health concern weakens the influence of environmental concern on organic food consumption. Consumer's economic problems harms the expansion of organic food consumption as well as other socio-demographic factors included as control variables.

Originality/value

For the first time, this research explores the interaction effect between health and environmental concerns as antecedents of organic food consumption. The study argues that these consumer goals present differential features in terms of individual importance, feasibility, abstractness and outcome demonstrability, resulting in a prevalence of health over environmental goals for some consumers. The research provides not only novel insights for understanding organic food consumption but also provides additional evidence for practitioners to develop sales strategies and policymakers to formulate policies to guide the promotion of this so desired example of sustainable consumption.
Measuring land lot shapes for property valuation
Authors: Lee Changro
Published: August 2023

Purpose

Unstructured data such as images have defied usage in property valuation for a long time. Instead, structured data in tabular format are commonly employed to estimate property prices. This study attempts to quantify the shape of land lots and uses the resultant output as an input variable for subsequent land valuation models.

Design/methodology/approach

Imagery data containing land lot shapes are fed into a convolutional neural network, and the shape of land lots is classified into two categories, regular and irregular-shaped. Then, the intermediate output (regularity score) is utilized in four downstream models to estimate land prices: random forest, gradient boosting, support vector machine and regression models.

Findings

Quantification of the land lot shapes and their exploitation in valuation led to an improvement in the predictive accuracy for all subsequent models.

Originality/value

The study findings are expected to promote the adoption of elusive price determinants such as the shape of a land lot, appearance of a house and the landscape of a neighborhood in property appraisal practices.
A robust study on fractional order HIV/AIDS model by using numerical methods
Authors: Roshan Tasmia , Ghosh Surath , Chauhan Ram P. , Kumar Sunil
Published: August 2023

Purpose

The fractional order HIV model has an important role in biological science. To study the HIV model in a better way, the model is presented with the help of Atangana- Baleanu operator which is in Caputo sense. Also, the characteristics of the solutions are described briefly with the help of the advance numerical techniques for the different values of fractional order derivatives. This paper aims to discuss the aforementioned objectives.

Design/methodology/approach

In this work, Adams-Bashforth method and Euler method are used to get the solution of the HIV model. These are the important numerical methods. The comparison results also are described with the physical meaning of the solutions of the model.

Findings

HIV model is analyzed under the view of fractional and AB derivative in Atangana-Baleanu-Caputo sense. The uniqueness of the solution is proved by using Banach Fixed point. The solution is derived with the help of Sumudu transform. Further, the authors employed fractional Adam-Bashforth method and Euler method to enumerate numerical results. The authors have used several values of fractional orders to present the outcomes graphically. The above calculations have been done with the help of MATLAB (R2016a). The numerical scheme used in the proposed study is valid and fruitful, and the same can be used to explore other real issues.

Research limitations/implications

This investigation can be done for the real data sets.

Practical implications

This paper aims to express the solution of the HIV model in a better way with the effect of non-locality, this work is very useful.

Originality/value

In this work, HIV model is developed with the help of Atangana- Baleanu operator in Caputo sense. By using Banach Fixed point, the authors proved that the solution is unique. Also, the solution is presented with the help of Sumudu transform. The behaviors of the solutions are checked for different values of fractional order derivatives with the physical meaning with help of the Adam-Bashforth method and the Euler method.
Data augmentation and data mining towards microstructure and property relationship for composites
Authors: Guo Ziyan , Liu Xuhao , Pan Zehua , Zhou Yexin , Zhong Zheng , Yan Zilin
Published: August 2023

Purpose

In recent years, the convolutional neural network (CNN) based deep learning approach has succeeded in data-mining the relationship between microstructures and macroscopic properties of materials. However, such CNN models usually rely heavily on a large set of labeled images to ensure the accuracy and generalization ability of the predictive models. Unfortunately, in many fields, acquiring image data is expensive and inconvenient. This study aims to propose a data augmentation technique to enhance the performance of the CNN models for linking microstructural images to the macroscopic properties of composites.

Design/methodology/approach

Microstructures of composites are synthesized using discrete element simulations and Potts kinetic Monte Carlo simulations. Macroscopic properties such as the elastic modulus, Poisson's ratio, shear modulus, coefficient of thermal expansion, and triple-phase boundary length density are extracted on representative volume elements. The CNN model is trained using the 3D microstructural images as inputs and corresponding macroscopic properties as the labels. The comparison of the predictive performance of the CNN models with and without data augmentation treatment are compared.

Findings

The comparison between the prediction performance of CNN models with and without data augmentation showed that the former reduced the weighted mean absolute percentage error (WMAPE) for the prediction from 5.1627% to 1.7014%. This significant reduction signifies that the proposed data augmentation method can effectively enhance the generalization ability and robustness of CNN models.

Originality/value

This study demonstrates that data augmentation is beneficial for solving the problems of model overfitting, data scarcity, and sample imbalance for CNN-based deep learning tasks at a low cost. By developing more and advanced data augmentation techniques, deep learning accelerated homogenization will boost the multi-scale computational mechanics and materials.
Nonlinear dynamic analysis of soil-pile interactions of nuclear power plants with nonlithological foundation
Authors: Sui Yi , Wang Yi , Yu Xiang
Published: August 2023

Purpose

The dynamic response of the nuclear power plants (NPPs) with pile foundation reinforcement have not yet been systemically investigated in detail. Thus, there is an urgent need to improve evaluation methods for nonlithological foundation reinforcements, as this issue is bound to become an unavoidable task.

Design/methodology/approach

A nonlinear seismic wave input method is adopted to consider both a nonlinear viscoelastic artificial boundary and the nonlinear properties of the overburden layer soil. Subsequently, the effects of certain vital parameters on the structural response are analyzed.

Findings

A suitable range for the size of the overburden foundation is suggested. Then, when piles are used to reinforce the overburden foundation, the peak frequencies in the floor response spectra (FRS) in the horizontal direction becomes higher (38%). Finally, the Poisson ratio of the foundation soil has a significant influence on the FRS peak frequency in the vertical direction (reduce 35%–48%).

Originality/value

The quantifiable results are performed to demonstrate the seismic responses with respect to key design parameters, including foundational dimensions, the Poisson Ratio of the soil and the depth of the foundation. The results can help guide the development of seismic safety requirements for NPPs.