bluuebunny/crossref_metadata_2025 huggingface dataset:
One-step solution processing of printable Sb2S3 nano-rods for high-performance photoconductors
Authors: Hasan Md Rezaul , Sohel Ikramul Hasan , Rao Mulpuri V
Published: October 2024

Achieving large-scale, affordable, and highly dependable production of antimony sulfide is crucial for unlocking its potential in various applications, including photoconductors, solid-state batteries, thermoelectrics, and solar cells. In our study, we introduce a straightforward, economical, and catalyst-free single-step solution process for fabricating one-dimensional Sb2S3 nanostructures on flexible polyimide substrates, and we explore their use as photoconductors in the ultraviolet (UV) and visible light spectrum. The precursor solution for creating the Sb2S3 films is prepared by dissolving specified quantities of elemental Sb and S in a solution mixture of ethylenediamine and 2-mercaptoethanol. This solution is then spin-coated onto a polyimide substrate and subsequently annealed at 300 °C for several minutes. Utilizing field emission scanning electron microscopy, grazing incidence x-ray diffraction, Raman spectroscopy, and transmission electron microscopy, we demonstrate that the Sb2S3 films possess high crystallinity, uniform morphology, and a composition that is nearly stoichiometric. Additionally, through Tauc plot analysis, we determine that the films exhibit a direct bandgap of approximately 1.67 eV, which is in close agreement with the bandgap predicted by Heyd–Scuseria–Ernzerhof (HSE06) density-functional theory simulations. The metal-semiconductor–metal photoconductors fabricated with these films display a significant photoresponse to both UV and visible light. These devices achieve a UV on/off ratio of up to 160 at a light intensity of 30 mW cm−2, with brief rise and fall times of 44 ms and 28 ms, respectively.
Dye wastewater treatment using nonthermal plasma-treated copper oxide nanoparticles produced through electrolysis technique
Authors: Shukrullah Shazia , Sarwar Tahreem , Shoaib Muhammad , Khan Yasin , Ibrahim Ahmed Ahmed
Published: October 2024

Copper oxide nanoparticles (CuO-NPs) were produced by implementing an electrolysis technique. The prepared CuO-NPs were processed with nonthermal microwave plasma to check the effect of plasma treatment on their morphology and photocatalytic response. The plasma processed and blank CuO-NPs samples were used in dye degradation and water splitting applications under simulated sunlight. The blank sample posed undefined morphology, which turned to spherical particles on plasma processing. The particle size grows slightly with processing time. The blank samples showed a crystallite size of 4.512 nm, which grew to 5.34 nm, 5.40 nm, and 5.49 nm after plasma processing for 10, 20, and 30 min, respectively. The lattice parameter UT sample was measured to be 2.4308 Å, with turned to 3.1091, 3.2112, and 3.3099 after 10, 20, and 30 min of plasma treatment, respectively. Similarly, band gap of CuO-NPs reduced from 2.4 eV to 2.24 eV after plasma processing for 30 min. The porosity of the nanoparticles also showed a similar trend. The plasma processing of CuO-NPs for 30 min produced the best results for photocatalytic water splitting and dye degradation applications. The photocatalytic activity revealed hydrogen evolution of 38.05 mmol.g−1.h−1 and dye removal efficiency of 91%.
Assessing the influence of visual stimulus properties on steady-state visually evoked potentials and pupil diameter
Authors: Eisma Y B , van Vliet S T , Nederveen A J , de Winter J C F
Published: October 2024

Steady-State Visual Evoked Potentials (SSVEPs) are brain responses measurable via electroencephalography (EEG) in response to continuous visual stimulation at a constant frequency. SSVEPs have been instrumental in advancing our understanding of human vision and attention, as well as in the development of brain-computer interfaces (BCIs). Ongoing questions remain about which type of visual stimulus causes the most potent SSVEP response. The current study investigated the effects of color, size, and flicker frequency on the signal-to-noise ratio of SSVEPs, complemented by pupillary light reflex measurements obtained through an eye-tracker. Six participants were presented with visual stimuli that differed in terms of color (white, red, green), shape (circles, squares, triangles), size (10,000 to 30,000 pixels), flicker frequency (8 to 25 Hz), and grouping (one stimulus at a time versus four stimuli presented in a 2 × 2 matrix to simulate a BCI). The results indicated that larger stimuli elicited stronger SSVEP responses and more pronounced pupil constriction. Additionally, the results revealed an interaction between stimulus color and flicker frequency, with red being more effective at lower frequencies and white at higher frequencies. Future SSVEP research could focus on the recommended waveform, interactions between SSVEP and power grid frequency, a wider range of flicker frequencies, a larger sample of participants, and a systematic comparison of the information transfer obtained through SSVEPs, pupil diameter, and eye movements.
Crime and Civilization
Authors: Kivivuori Janne
Published: October 2024

Crime and Civilization presents a history of the rise of criminology in the first part of the nineteenth century. The story begins in 1827, in Paris, when the first modern national crime statistic was published. The Compte général de l’administration de la justice criminelle en France was a paradigmatic game changer, sending shock waves across European intellectual circles interested in the analysis of crime. The new concept of national crime statistics made it possible to test theories and hypotheses about crime using a shared data instrument. Much of the initial research and reception triggered by the new instrument reflected a core theme of the Enlightenment tradition—the question of how the civilizing process impacted human morality. This cultural context had several variations: British parliamentarians struggling to civilize their ‘bloody code’, French liberals supporting technical progress against royalist and religious backlash, and German lawyers raising the flag of their religious and moral Kultur against secular civilization. Yet they all embraced the concept of national crime statistics as research-enabling innovation. While the French ignited the flame, the story of the first criminology is a European affair transcending national borders. Crime and Civilization argues that the history of criminology should be approached from the perspective of data and instruments, complementing the traditional story based on theories and explanatory shifts from ‘classicism’ to ‘positivism’ and beyond. The book is a prequel to Discovery of Hidden Crime (2011), which inspected the rise of the crime survey in the twentieth century.
Thinking about crime before criminology
Authors: Kivivuori Janne
Published: October 2024

This chapter describes selected key themes of thinking about crime before criminology, that is, during the eighteenth-century Enlightenment period. This backdrop is needed because the standard narrative of the history of criminology usually starts from the ‘classical school’ after the mid-eighteenth century (Montesquieu, Beccaria), and because the Enlightenment tradition forms the cultural context of discovery for the first data-driven criminology generation. The relevant Enlightenment themes include criminal justice reform, labelling perspectives, ‘luxury of the poor’, and the moral consequences of the civilizing process. The chapter ends by examining the evidentiary bases in thinking about crime before criminology: rational philosophy, sources from classical antiquity, fact-finding visits, travellers’ narratives, and participant observation by magistrates. These standard methods, while not completely non-empirical, were largely replaced in the rise of data-driven criminology during the 1820s.
Civilization debate
Authors: Kivivuori Janne
Published: October 2024

This chapter describes the immediate cultural and societal context of discovery in the foreground of the publication of the first modern crime statistical report in France (1827). Drawing on De Graaf’s study on ‘European Security Order’, the chapter discusses the post-Napoleonic settlement not as period of stagnation, but rather as an era of innovation and optimism. Many of the key participants in the emergence of data-driven criminology saw a crime drop linked to the civilizing process. The century-long debate on the moral consequences of civilization forced the moment to its crisis, climaxing in Charles Dupin’s coropleth map (1826) and the first national crime statistic (1827). These innovations aimed at settling the morality–civilization debate with an empirical social science basis.
First criminology
Authors: Kivivuori Janne
Published: October 2024

This chapter describes the impact of the new national crime report concept on research. The emergence of the new data instrument constituted the first field of criminology by the original scholars using it. The most prominent of them were Charles Lucas (1803–89), Adolphe Quetelet (1796–1874), and André-Miche Guerry (1802–66), but there were others who are today less well known. When themes such as the civilizing process collided with data, they were transformed into the nuclei of criminological theories. The chapter descriptively points out the similarities between the early studies and later perspectives, without postulating causation or direct influence. Prominent similarities point towards routine activities perspectives and strain theoretical approaches.
French civilization and German Kultur
Authors: Kivivuori Janne
Published: October 2024

This chapter focuses on the German reception of the concept of national crime statistics after 1827. Three core interpreters are discussed: Nikolaus H. Julius (1783–1862), Carl J. A. Mittermaier (1787–1867), and Karl S. Zachariä (1769–1843). The Germans contrasted their religious–moral culture with the Anglo-French secular and technical concept of civilization. They saw the effect of education on crime as depending on the moral content of the curriculum. In interpreting the new data, they exemplified the core arguments which are still used in criminal justice policy debates. Drawing on Albert Hirschman’s classical trichotomy of rhetoric of reaction, this chapter describes the futility (criminal law has weak or no effects on behaviour), mismatch (criminal law is ineffective without correspondence to popular feelings), and perversity (criminal law yields counterproductive results) arguments.
Predicting frailty domain impairments and mortality with the Hospital Frailty Risk Score among older adults with cancer: the ELCAPA-EDS cohort study
Authors: Jean Charline , Paillaud Elena , Boudou-Rouquette Pascaline , Martinez-Tapia Claudia , Pamoukdjian Frédéric , Hagège Meoïn , Bréant Stéphane , Hassen-Khodja Claire , Natella Pierre-André , Cudennec Tristan , Laurent Marie , Caillet Philippe , Canouï-Poitrine Florence , Audureau Etienne
Published: October 2024

Background

Automated frailty screening tools like the Hospital Frailty Risk Score (HFRS) are primarily validated for care consumption outcomes. We assessed the predictive ability of the HFRS regarding care consumption outcomes, frailty domain impairments and mortality among older adults with cancer, using the Geriatric 8 (G8) screening tool as a clinical benchmark.

Methods

This retrospective, linkage-based study included patients aged ≥70 years with solid tumor, enrolled in the Elderly Cancer Patients (ELCAPA) multicentre cohort study (2016–2020) and hospitalized in acute care within the Greater Paris University Hospitals. HFRS scores, which encompass hospital-acquired problems and frailty-related syndromes, were calculated using data from the index admission and the preceding 6 months. A multidomain geriatric assessment (GA), including cognition, nutrition, mood, functional status, mobility, comorbidities, polypharmacy, incontinence, and social environment, was conducted at ELCAPA inclusion, with computation of the G8 score. Logistic and Cox regressions measured associations between the G8, HFRS, altered GA domains, length of stay exceeding 10 days, 30-day readmission, and mortality.

Results

Among 587 patients included (median age 82 years, metastatic cancer 47.0%), 237 (40.4%) were at increased frailty risk by the HFRS (HFRS>5) and 261 (47.5%) by the G8 (G8≤10). Both HFRS and G8 were significantly associated with cognitive and functional impairments, incontinence, comorbidities, prolonged length of stay, and 30-day mortality. The G8 was associated with polypharmacy, nutritional and mood impairment.

Discussion

Although showing significant associations with short-term care consumption, the HFRS could not identify polypharmacy, nutritional, mood and social environment impairments and showed low discriminatory ability across all GA domains.
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review
Authors: Nguyen Quang-Huy , Nguyen Ha , Oh Edwin C , Nguyen Tin
Published: October 2024

Metabolite profiling is a powerful approach for the clinical diagnosis of complex diseases, ranging from cardiometabolic diseases, cancer, and cognitive disorders to respiratory pathologies and conditions that involve dysregulated metabolism. Because of the importance of systems-level interpretation, many methods have been developed to identify biologically significant pathways using metabolomics data. In this review, we first describe a complete metabolomics workflow (sample preparation, data acquisition, pre-processing, downstream analysis, etc.). We then comprehensively review 24 approaches capable of performing functional analysis, including those that combine metabolomics data with other types of data to investigate the disease-relevant changes at multiple omics layers. We discuss their availability, implementation, capability for pre-processing and quality control, supported omics types, embedded databases, pathway analysis methodologies, and integration techniques. We also provide a rating and evaluation of each software, focusing on their key technique, software accessibility, documentation, and user-friendliness. Following our guideline, life scientists can easily choose a suitable method depending on method rating, available data, input format, and method category. More importantly, we highlight outstanding challenges and potential solutions that need to be addressed by future research. To further assist users in executing the reviewed methods, we provide wrappers of the software packages at https://github.com/tinnlab/metabolite-pathway-review-docker.
Digital PCR threshold robustness analysis and optimization using dipcensR
Authors: Vynck Matthijs , Trypsteen Wim , Thas Olivier , Vandesompele Jo , De Spiegelaere Ward
Published: October 2024

Digital polymerase chain reaction (dPCR) is a best-in-class molecular biology technique for the accurate and precise quantification of nucleic acids. The recent maturation of dPCR technology allows the quantification of up to thousands of targeted nucleic acids per instrument per day. A key step in the dPCR data analysis workflow is the classification of partitions into two classes based on their partition intensities: partitions either containing or lacking target nucleic acids of interest. Much effort has been invested in the design and tailoring of automated dPCR partition classification procedures, and such procedures will be increasingly important as the technology ventures into high-throughput applications. However, automated partition classification is not fail-safe, and evaluation of its accuracy is highly advised. This accuracy evaluation is a manual endeavor and is becoming a bottleneck for high-throughput dPCR applications. Here, we introduce dipcensR, the first data-analysis procedure that automates the assessment of any linear partition classifier’s partition classification accuracy, offering potentially substantial efficiency gains. dipcensR is based on a robustness evaluation of said partition classification and flags classifications with low robustness as needing review. Additionally, dipcensR’s robustness analysis underpins (optional) automatic optimization of partition classification to achieve maximal robustness. A freely available R implementation supports dipcensR’s use.
Robust variable selection methods with Cox model—a selective practical benchmark study
Authors: Zhang Yunwei , Muller Samuel
Published: October 2024

With the advancement of biological and medical techniques, we can now obtain large amounts of high-dimensional omics data with censored survival information. This presents challenges in method development across various domains, particularly in variable selection. Given the inherently skewed distribution of the survival time outcome variable, robust variable selection methods offer potential solutions. Recently, there has been a focus on extending robust variable selection methods from linear regression models to survival models. However, despite these developments, robust methods are currently rarely used in practical applications, possibly due to a limited appreciation of their overall good performance. To address this gap, we conduct a selective review comparing the variable selection performance of twelve robust and non-robust penalised Cox models. Our study reveals the intricate relationship among covariates, survival outcomes, and modeling approaches, demonstrating how subtle variations can significantly impact the performance of methods considered. Based on our empirical research, we recommend the use of robust Cox models for variable selection in practice based on their superior performance in presence of outliers while maintaining good efficiency and accuracy when there are no outliers. This study provides valuable insights for method development and application, contributing to a better understanding of the relationship between correlated covariates and censored outcomes.
Thinking points for effective batch correction on biomedical data
Authors: Hui Harvard Wai Hann , Kong Weijia , Goh Wilson Wen Bin
Published: October 2024

Batch effects introduce significant variability into high-dimensional data, complicating accurate analysis and leading to potentially misleading conclusions if not adequately addressed. Despite technological and algorithmic advancements in biomedical research, effectively managing batch effects remains a complex challenge requiring comprehensive considerations. This paper underscores the necessity of a flexible and holistic approach for selecting batch effect correction algorithms (BECAs), advocating for proper BECA evaluations and consideration of artificial intelligence–based strategies. We also discuss key challenges in batch effect correction, including the importance of uncovering hidden batch factors and understanding the impact of design imbalance, missing values, and aggressive correction. Our aim is to provide researchers with a robust framework for effective batch effects management and enhancing the reliability of high-dimensional data analyses.
Temporal generative models for learning heterogeneous group dynamics of ecological momentary assessment data
Authors: Kim Soohyun , Kim Young-geun , Wang Yuanjia
Published: October 2024

One of the goals of precision psychiatry is to characterize mental disorders in an individualized manner, taking into account the underlying dynamic processes. Recent advances in mobile technologies have enabled the collection of ecological momentary assessments that capture multiple responses in real-time at high frequency. However, ecological momentary assessment data are often multi-dimensional, correlated, and hierarchical. Mixed-effect models are commonly used but may require restrictive assumptions about the fixed and random effects and the correlation structure. The recurrent temporal restricted Boltzmann machine (RTRBM) is a generative neural network that can be used to model temporal data, but most existing RTRBM approaches do not account for the potential heterogeneity of group dynamics within a population based on available covariates. In this paper, we propose a new temporal generative model, the HDRBM, to learn the heterogeneous group dynamics and demonstrate the effectiveness of this approach on simulated and real-world ecological momentary assessment datasets. We show that by incorporating covariates, HDRBM can improve accuracy and interpretability, explore the underlying drivers of the group dynamics of participants, and serve as a generative model for ecological momentary assessment studies.
Comparative diagnostic efficacy of abbreviated and full protocol breast MRI: a systematic review and a meta-analysis
Authors: Pesapane Filippo , Battaglia Ottavia , Rotili Anna , Gnocchi Giulia , D’Ecclesiis Oriana , Bellerba Federica , Penco Silvia , Signorelli Giulia , Nicosia Luca , Trentin Chiara , Dominelli Valeria , Priolo Francesca , Bozzini Anna , Gandini Sara , Cassano Enrico
Published: October 2024

Objectives

This meta-analysis compares the efficacy, limitations, and clinical implications of abbreviated breast MRI (AB-MRI) and full protocol MRI (FP-MRI), focusing on diagnostic accuracy across diverse populations. It extends previous analyses by including studies conducted after 2019 in both screening and diagnostic contexts.

Methods

We conducted a systematic review (November 2019 to December 2022), using a bivariate model to calculate summary estimates of sensitivity and specificity. Random effect models were applied for summary area under the curve (AUC), and probability distributions for negative and positive predictive values were obtained. Subgroup analyses explored differences in sensitivity, specificity, and AUC between AB-MRI and FP-MRI.

Results

From 11 eligible studies (1 prospective, 10 retrospective), statistical analysis revealed a significant difference in sensitivity between FP-MRI (95%) and AB-MRI (86%, P = .005), with no significant difference in specificity (P = .50). AB-MRI’s shorter acquisition time suggests potential for higher patient throughput, but challenges remain in detecting small lesions and nonmass enhancements. Some studies recommend additional sequences, like diffusion-weighted imaging, to improve diagnostic performance.

Conclusions

While FP-MRI remains the gold standard in breast cancer detection, AB-MRI offers a quicker alternative, especially in high-risk screening. However, its lower sensitivity limits its use as a standalone diagnostic tool. Future research should optimize AB-MRI protocols and consider patient-specific factors to enhance breast cancer screening and diagnostic strategies.

Advances in knowledge

This meta-analysis expands understanding of AB-MRI's role in breast cancer detection, highlighting its benefits and limitations compared to FP-MRI, particularly in terms of sensitivity and screening efficiency.
Simulated resections and responsive neurostimulator placement can optimize postoperative seizure outcomes when guided by fast ripple networks
Authors: Weiss Shennan Aibel , Sperling Michael R , Engel Jerome , Liu Anli , Fried Itzhak , Wu Chengyuan , Doyle Werner , Mikell Charles , Mofakham Sima , Salamon Noriko , Sim Myung Shin , Bragin Anatol , Staba Richard
Published: October 2024

In medication-resistant epilepsy, the goal of epilepsy surgery is to make a patient seizure free with a resection/ablation that is as small as possible to minimize morbidity. The standard of care in planning the margins of epilepsy surgery involves electroclinical delineation of the seizure-onset zone and incorporation of neuroimaging findings from MRI, PET, single-photon emission CT and magnetoencephalography modalities. Resecting cortical tissue generating high-frequency oscillations has been investigated as a more efficacious alternative to targeting the seizure-onset zone. In this study, we used a support vector machine (SVM), with four distinct fast ripple (FR: 350–600 Hz on oscillations, 200–600 Hz on spikes) metrics as factors. These metrics included the FR resection ratio, a spatial FR network measure and two temporal FR network measures. The SVM was trained by the value of these four factors with respect to the actual resection boundaries and actual seizure-free labels of 18 patients with medically refractory focal epilepsy. Leave-one-out cross-validation of the trained SVM in this training set had an accuracy of 0.78. We next used a simulated iterative virtual resection targeting the FR sites that were of highest rate and showed most temporal autonomy. The trained SVM utilized the four virtual FR metrics to predict virtual seizure freedom. In all but one of the nine patients who were seizure free after surgery, we found that the virtual resections sufficient for virtual seizure freedom were larger in volume (P < 0.05). In nine patients who were not seizure free, a larger virtual resection made five virtually seizure free. We also examined 10 medically refractory focal epilepsy patients implanted with the responsive neurostimulator system and virtually targeted the responsive neurostimulator system stimulation contacts proximal to sites generating FR at highest rates to determine if the simulated value of the stimulated seizure-onset zone and stimulated FR metrics would trend towards those patients with a better seizure outcome. Our results suggest the following: (i) FR measures can accurately predict whether a resection, defined by the standard of care, will result in seizure freedom; (ii) utilizing FR alone for planning an efficacious surgery can be associated with larger resections; (iii) when FR metrics predict the standard-of-care resection will fail, amending the boundaries of the planned resection with certain FR-generating sites may improve outcome and (iv) more work is required to determine whether targeting responsive neurostimulator system stimulation contact proximal to FR generating sites will improve seizure outcome.
Silk fibroin–gelatine haemostatic sponge loaded with thrombin for wound haemostasis and tissue regeneration
Authors: Zhang Yajun , Li Ming , Chang Jing , Li Chang , Hui Yuwen , Wang Yanhua , Xu Weiguo
Published: October 2024

Background

Wound haemostasis is an important part of clinical treatments, especially treatments for patients with avulsion injury, destructive injury and large-scale soft tissue injury. Therefore, developing fast and effective haemostatic materials is critical. This study aimed to design a novel and efficient silk fibroin–gelatine composite haemostatic sponge loaded with thrombin (SFG@TB) to assist in wound haemostasis.

Methods

The SFG@TB composite haemostatic sponge was formed with gelatine, silk fibroin and thrombin through a freeze-drying technique. First, the material characteristics of SFG@TB were measured, including the elastic modulus, swelling rate and porosity. Second, in vitro cell coculture experiments, in vivo embedding experiments and haemolytic analyses were performed to evaluate the biocompatibility of SFG@TB. Then, coagulation experiments and femoral artery and liver bleeding models were used to evaluate the haemostatic performance of SFG@TB. Finally, the ability of SFG@TB to promote tissue healing was evaluated through experiments with Sprague–Dawley rat models of injury.

Results

Compared with gelatine sponges, SFG@TB exhibited outstanding mechanical properties and water absorption properties. In addition, the excellent biosafety of the composite haemostatic sponge was confirmed by cell experiments, subcutaneous embedding experiments and haemolytic analysis. Based on the in vitro coagulation test results, SFG@TB exhibited greater adhesion of red blood cells and platelets and a shorter dynamic coagulation time. Compared to the use of silk fibroin–gelatine composite haemostatic sponges or gelatine sponges, the introduction of thrombin resulted in a shorter haemostasis time and a smaller bleeding volume, as revealed by in vivo coagulation tests. The experiments with Sprague–Dawley rat models of injury indicated that SFG@TB accelerated the wound healing process and reduced scar width, which was accompanied by thicker granulation tissue.

Conclusions

Overall, the SFG@TB composite haemostatic sponge, which exhibits outstanding mechanical properties, good haemostatic performance and high biosafety, promoted wound haemostasis and tissue repair. Therefore, the SFG@TB composite haemostatic sponge could be a promising material for wound haemostasis.
Structure determination of tweezer-shaped π-extended tetraphenylenes by microcrystal electron diffraction
Authors: Sugiyama Haruki , Watanabe Kosuke , Song Chihong , Murata Kazuyoshi , Segawa Yasutomo
Published: October 2024

The structure determination of large π-conjugated molecules using microcrystal electron diffraction (MicroED) was demonstrated. The poorly soluble solids of the tweezer-shaped molecules were subjected directly from the reaction vessel to MicroED to determine their structures and packing modes. This work validated the efficiency of MicroED in determining the structures of such compounds.
A comparison of reserved graph grammar and edge-based graph grammar
Authors: Zou Yang
Published: October 2024

Context-sensitive graph grammars are natural formalisms for the generation and parsing of visual programming languages. Being intuitive, rigorous, and expressive tools, they have been frequently employed in a wide range of research fields. Nevertheless, the expressive powers of the existing context-sensitive formalisms have not been investigated yet. To this end, this paper is dedicated to the comparison of expressive powers of the two prevalent graph grammar formalisms, Reserved Graph Grammar (RGG) and Edge-based Graph Grammar (EGG). By introducing a special variant of RGG as an intermediary, the relation between them concerning the expressive power is revealed that the set of graph languages of EGG is a proper subset of that of RGG. Moreover, bidirectional transformations between EGG and the variant of RGG are accordingly established, allowing them to take the advantages of each other in applications.
A clustering ensemble algorithm for handling deep embeddings using cluster confidence
Authors: Zeng Lingbin , Yao Shixin , Liu Xinwang , Xiao Liquan , Qian Yue
Published: October 2024

Clustering ensemble, which aims to learn a robust consensus clustering from multiple weak base clusterings, has achieved promising performance on various applications. With the development of big data, the scale and complexity of data is constantly increasing. However, most existing clustering ensemble methods typically employ shallow clustering algorithms to generate base clusterings. When confronted with high-dimensional complex data, these shallow algorithms fail to fully utilize the intricate features present in the latent data space. As a result, the quality and diversity of the generated base clusterings are insufficient, thus affecting the subsequent ensemble performance. To address this issue, we propose a novel clustering ensemble algorithm for handling deep embeddings using cluster confidence (CEDECC) to improve the robustness and performance. Instead of simply combining deep clustering with clustering ensembles, we take into consideration that the performance of existing deep clustering methods heavily relies on the quality of low-dimensional embeddings generated during the pre-training stage. The quality of embeddings is unstable due to the influence of different initialization parameters. In CEDECC, specifically, we first construct a cluster confidence measure to evaluate the quality of low-dimensional embeddings. Typically, high-quality low-dimensional embeddings yield accurate clustering results with the same model parameters. Then, we utilize multiple high-quality embeddings to generate the base partitions. In the ensemble strategy phase, we consider the cluster-wise diversity and propose a novel ensemble cluster estimation to improve the overall consensus performance of the model. Extensive experiments on three benchmark datasets and four real-world biological datasets have demonstrated that the proposed CEDECC consistently outperforms the state-of-the-art clustering ensemble methods.
Sparrowhawk imitation or convergent alarm signal? A new hypothesis for bubbling call of cuckoos with empirical testing
Authors: Wang Huisheng , Chen Xiangyang , Wang Jiaojiao , Ma Laikun , Yang Canchao
Published: October 2024

Alarm calls in bird vocalizations serve as acoustic signals announcing danger. Owing to the convergent evolution of alarm calls, some bird species can benefit from eavesdropping on certain parameters of alarm calls of other species. Vocal mimicry, displayed by many bird species, aids defense against predators and may help brood parasites during parasitism. In the coevolutionary dynamics between brood parasites, such as the common cuckoo (Cuculus canorus), and their hosts, female cuckoo vocalizations can induce hosts to leave the nest, increasing the probability of successful parasitism and reducing the risk of host attacks. Such cuckoo calls were thought to mimic those of the sparrowhawk. However, owing to their similarity to alarm calls, we propose a new hypothesis: Female cuckoos cheat their hosts by mimicking the parameters of the host alarm call. In this study, we tested this new hypothesis and the sparrowhawk mimicry hypothesis simultaneously by manipulating the syllable rate in male and female common cuckoo vocalizations and playing them in front of the host Oriental reed warbler (Acrocephalus orientalis) for examination. The results indicate that similar to a normal female cuckoo call, a female call with a reduced syllable rate prompted the hosts to leave their nests more frequently and rapidly than male cuckoo calls. Additionally, the male cuckoo calls with increased syllable rate did not prompt the host to leave their nests more frequently or quickly compared with the male cuckoo calls with a normal syllable rate. Our results further confirm that female common cuckoos mimic the vocalizations of Eurasian sparrowhawks (Accipiter nisus), reveal the function mechanisms underlying such mimicry, and support the theory of imperfect mimicry.
A case report of an unprovoked neonatal pulmonary embolism: management strategies and cardiopulmonary complications
Authors: Cowan Aashana Dhruva , Emelue Ezinwanne Rosemary , Spyropoulos George , Thakkar Mehul , Di Paola Jorge , Glatz Andrew , Rabinowitz Edon J
Published: October 2024

Background

Neonatal pulmonary embolism is a rare occurrence, especially when idiopathic, instead occurring in patients with identifiable risk factors including severe dehydration, presence or history of a central venous line, or identifiable genetic causes. Given the rarity of paediatric and neonatal pulmonary emboli, few guidelines exist to support the clinician in both the initial resuscitation and ongoing management of the critically ill patient with pulmonary emboli.

Case summary

We present a 5-day-old female with unprovoked massive pulmonary embolism and associated haemodynamic compromise. She presented with central cyanosis and weak respiratory effort with hypoxaemia, persistent tachycardia, and hypotension despite initial fluid resuscitation, intubation, and administration of 100% FiO2 with inhaled nitric oxide. She was ultimately diagnosed with a massive pulmonary embolism involving the right pulmonary artery by both echocardiography and computed chest tomography, initiated on inotropic support and systemic anticoagulation, after which she underwent mechanical thrombectomy. She was successfully extubated soon thereafter, with subsequent resolution of her emboli. No provoking factors were able to be identified for this patient.

Discussion

This case highlights the cumulative burden of pulmonary obstruction and inter-ventricular interactions that lead to haemodynamic compromise in the event of massive pulmonary embolism, with resultant considerations of key management strategies. These include the risks of fluid resuscitation and introduction of positive pressure ventilation, as well as the need for early consideration of inotropic support and an institutional pathway for anticoagulation, ultimately proposing a multidisciplinary algorithm for the clinician to deploy when faced with impending cardiovascular collapse from massive pulmonary embolism.
Atrioventricular node ablation for atrial fibrillation in the era of conduction system pacing
Authors: Joza Jacqueline , Burri Haran , Andrade Jason G , Linz Dominik , Ellenbogen Kenneth A , Vernooy Kevin
Published: October 2024

Despite key advances in catheter-based treatments, the management of persistent atrial fibrillation (AF) remains a therapeutic challenge in a significant subset of patients. While success rates have improved with repeat AF ablation procedures and the concurrent use of antiarrhythmic drugs, the likelihood of maintaining sinus rhythm during long-term follow-up is still limited. Atrioventricular node ablation (AVNA) has returned as a valuable treatment option given the recent developments in cardiac pacing. With the advent of conduction system pacing, AVNA has seen a revival where pacing-induced cardiomyopathy after AVNA is felt to be overcome. This review will discuss the role of permanent pacemaker implantation and AVNA for AF management in this new era of conduction system pacing. Specifically, this review will discuss the haemodynamic consequences of AF and the mechanisms through which ‘pace-and-ablate therapy’ enhances outcomes, analyse historical and more recent literature across various pacing methods, and work to identify patient groups that may benefit from earlier implementation of this approach.
Plasma proteome and incident myocardial infarction: sex-specific differences
Authors: Titova Olga E , Yuan Shuai , Byberg Liisa , Baron John A , Lind Lars , Michaëlsson Karl , Larsson Susanna C
Published: October 2024

Background and aims

Few population-based cohort studies, including both men and women, have explored circulating proteins associated with incident myocardial infarction (MI). This study investigated the relationships between circulating cardiometabolic-related proteins and MI risk using cohort-based and Mendelian randomization (MR) analyses and explored potential sex-specific differences.

Methods

The discovery cohort included 11 751 Swedish adults (55–93 years). Data on 259 proteins assessed with Olink proximity extension assays, biochemical, and questionnaire-based information were used. Participants were followed up for incident MI and death over 8 years through linkage to Swedish registers. Replication analyses were conducted on the UK Biobank sample (n = 51 613). In MR analyses, index cis-genetic variants strongly related to the proteins were used as instrumental variables. Genetic association summary statistic data for MI were obtained from the CARDIoGRAMplusC4D consortium and FinnGen.

Results

Forty-five proteins were associated with incident MI in discovery and replication samples following adjustment for potential confounders and multiple testing. In the secondary analysis, 13 of the protein associations were sex-specific, with most associations identified among women. In MR analysis, genetically predicted higher levels of renin, follistatin, and retinoic acid receptor responder protein 2 were linked to an increased risk of MI. Tissue factor pathway inhibitor, tumor necrosis factor receptors 1 and 2, placenta growth factor had an inverse association with MI.

Conclusions

This study identified both new and confirmed previously established associations between circulating proteins and incident MI and, for the first time, suggested sex-specific patterns in multiple protein-MI associations.
Subalpine fir response to drought in northern British Columbia, Canada
Authors: Haghshenas Malek , Wood Lisa J
Published: October 2024

As global warming continues, drought severity and duration are expected to increase in many areas of the world, necessitating a thorough understanding of how trees react to severe drought periods. In this study, we used dendrochronological analyses to determine the response of subalpine fir [Abies lasiocarpa (Hook.) Nutt.] to historical drought events on sites along a latitudinal interval of 500 km in the Rocky Mountains in northern British Columbia, Canada. We used the ClimateBC Climate Moisture Deficit index to approximate drought conditions at the sites and to identify common drought years across sites. We then compared wood densities across the time series to temperature, precipitation, and climate moisture indices for the locations studied to determine relationships between subalpine fir wood densities and climate in this region. We demonstrated that subalpine fir wood density was often negatively correlated to spring and summer temperatures and that these stands are responsive to drought events in the short term. We found that the latitudinal difference between stands was not as pronounced as expected; however, northern sites had a stronger climate response and more frequent drought years than southern sites. This cautiously suggests that the impacts of climate change may be more intensely felt in forests at more northern latitudes. If droughts continue to become more frequent in northern British Columbia, as is predicted with changing climates, we might expect less carbon sequestration and lower wood strength in subalpine fir trees from this region.
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug
Authors: Du Zhenyong , Wang Xuan , Duan Yuange , Liu Shanlin , Tian Li , Song Fan , Cai Wanzhi , Li Hu
Published: October 2024

Invasive species cause massive economic and ecological damage. Climate change has resulted in an unprecedented increase in the number and impact of invasive species; however, the mechanisms underlying these invasions are unclear. The sycamore lace bug, Corythucha ciliata, is a highly invasive species originating from North America and has expanded across the Northern Hemisphere since the 1960s. In this study, we assembled the C. ciliata genome using high-coverage Pacific Biosciences (PacBio), Illumina, and high-throughput chromosome conformation capture (Hi-C) sequencing. A total of 15,278 protein-coding genes were identified, and expansions of gene families with oxidoreductase and metabolic activities were observed. In-depth resequencing of 402 samples from native and nine invaded countries across three continents revealed 2.74 million single nucleotide polymorphisms. Two major invasion routes of C. ciliata were identified from North America to Europe and Japan, with a contact zone forming in East Asia. Genomic signatures of selection associated with invasion and long-term balancing selection in native ranges were identified. These genomic signatures overlapped with expanded genes, suggesting improvements in the oxidative stress and thermal tolerance of C. ciliata. These findings offer valuable insights into the genomic architecture and adaptive evolution underlying the invasive capabilities of species during rapid environmental changes.
Community voices in health literacy: a qualitative exploration into perceptions of a health literacy mediator
Authors: Spencer Madeline , Cruickshank Vaughan , Kemp Nenagh , Nash Rosie
Published: October 2024

Health literacy is a vital asset needed to empower individuals to take control of their health. An individual’s health literacy is the ability to find, use and apply health information and services to manage their health. They interact with the health services and members of their community who can offer additional support. Creating the role of a health literacy mediator (HLM) may help to improve health literacy outcomes for all. For this role to be accepted by individuals within a community, the community itself should be involved in the development of the roles and associated responsibilities. The aim of this study was to engage with community members to acquire their perspectives on the potential of this role. Qualitative semi-structured online interviews were used to engage in discussions with local community members. This study implemented a constructivist epistemology with qualitative research design. Data were thematically analysed to identify evolving themes that were important to the HLM role. The analysis identified three main themes that need to be considered when adopting an HLM role: (i) health empowerment of individuals, organizations and communities, (ii) meeting the needs of the community and (iii) addressing the existing barriers in navigating and accessing the healthcare system. Those working in the health promotion space must adopt novel and innovative ways to improve HL on both a local and an international scale. This study concluded that for the role of a HLM to be accepted, it would need to encompass these attributes.
CHH hypermethylation contributes to the early ripening of grapes revealed by DNA methylome landscape of ‘Kyoho’ and its bud mutant
Authors: Wei Tong-Lu , Wan Yu-Tong , Liu Hai-Nan , Pei Mao-Song , He Guang-Qi , Guo Da-Long
Published: October 2024

DNA methylation is a stable epigenetic mark that plays a crucial role in plant life processes. However, the specific functions of DNA methylation in grape berry development remain largely unknown. In this study, we performed whole-genome bisulfite sequencing on ‘Kyoho’ grape and its early-ripening bud mutant ‘Fengzao’ at different developmental stages. Our results revealed that transposons (TEs) and gene flanking regions exhibited high levels of methylation, particularly in ‘Fengzao’, attributed to CHH site methylation. Interestingly, the methylation patterns in these two cultivars showed distinct dynamics during berry development. While methylation levels of genes and TEs increased gradually in ‘Kyoho’ throughout berry development, ‘Fengzao’ did not display consistent changes. Notably, ‘Fengzao’ exhibited higher methylation levels in promoters compared to ‘Kyoho’, suggesting that hypermethylation of promoters may contribute to its early ripening phenotype. Integration of methylome and transcriptome data highlighted differentially methylated genes (DMGs) and expressed genes (DEGs) associated with secondary metabolite biosynthesis, with 38 genes identified as potential candidates involved in grape berry development. Furthermore, the study identified a jasmonate-induced oxygenase gene (JOX1) as a negative regulator of ripening in Arabidopsis and grapes, indicating that hypermethylation of JOX1 may play a role in the early ripening of ‘Fengzao’. Overall, our findings provide insights into the distinct DNA methylation patterns during grape berry development, shedding light on the epigenetic regulatory mechanisms underlying the early-ripening bud mutant.