bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thinking points for effective batch correction on biomedical data
Authors: Hui Harvard Wai Hann , Kong Weijia , Goh Wilson Wen Bin 
Published: October 2024

Abstract
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

ABSTRACT
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

Abstract

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

Abstract
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 &lt; 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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

Abstract

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

Abstract
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.