bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating Atmospheric Responses to and Mechanisms Governing North Atlantic Sea Surface Temperatures over 10-Year Periods
Authors: Gu Qinxue , Gervais Melissa , Maroon Elizabeth , Kim Who M. , Danabasoglu Gokhan , Castruccio Frederic 
Published: October 2023

Abstract
North Atlantic sea surface temperature (SST) variability plays a critical role in modulating the climate system. However, characterizing patterns of North Atlantic SST variability and diagnosing the associated mechanisms is challenging because they involve coupled atmosphere–ocean interactions with complex spatiotemporal relationships. Here we address these challenges by applying a time-evolving self-organizing map approach to a long preindustrial coupled control simulation and identify a variety of 10-yr spatiotemporal evolutions of winter SST anomalies, including but not limited to those associated with the North Atlantic Oscillation–Atlantic multidecadal variability (NAO–AMV)-like interactions. To assess mechanisms and atmospheric responses associated with various SST spatiotemporal evolutions, composites of atmospheric and oceanic variables associated with these evolutions are investigated. Results show that transient-eddy activities and atmospheric circulation responses exist in almost all the evolutions that are closely correlated to the details of the SST pattern. In terms of the mechanisms responsible for generating various SST evolutions, composites of ocean heat budget terms demonstrate that contributions to upper-ocean temperature tendency from resolved ocean advection and surface heat fluxes rarely oppose each other over 10-yr periods in the subpolar North Atlantic. We further explore the potential for predictability for some of these 10-yr SST evolutions that start with similar states but end with different states. However, we find that these are associated with abrupt changes in atmospheric variability and are unlikely to be predictable. In summary, this study broadly investigates the atmospheric responses to and the mechanisms governing the North Atlantic SST evolutions over 10-yr periods.

Significance Statement
Climate variability in the North Atlantic Ocean has wide-ranging impacts on global and regional climate. However, the processes involved include interactions between the ocean and atmosphere that vary across both space and time, making it challenging to characterize and predict. Using a novel machine learning approach, this study identifies various time evolutions of North Atlantic sea surface temperature patterns over 10-yr periods. This includes evolutions with similar start states but different trajectories, which have important implications for predictability. Furthermore, we investigate the mechanisms responsible for these evolutions and how different sea surface temperature patterns affect atmospheric circulation through small-scale atmospheric disturbances. These new insights into the complex ocean–atmosphere interactions over time are critical for improving decadal prediction skill.
Mutual support between patients and family caregivers in palliative care: A qualitative study
Authors: McCauley Rachel , Ryan Karen , McQuillan Regina , Foley Geraldine 
Published: October 2023

Background: Patients in receipt of palliative care services are often viewed primarily as recipients of support from their family caregiver. There is a dearth of evidence in palliative care on what comprises mutual support between patients and their family caregivers in palliative care. Aim: To identify processes of mutual support between patients and family caregivers in palliative care. Design: Qualitative study comprising semi-structured interviews. Data were analysed using grounded theory procedures. Setting/participants: Fifteen patients with advanced illness (cancer n = 14, neurodegenerative n = 1) and 21 family caregivers recruited from a large regional-based hospice. Results: Mutual support between patients and family caregivers comprised two primary modes in which support was provided and received. Mutual support involved both patients and family caregivers providing similar types of support to each other, and which typically manifested as emotional support. However, mutual support also occurred when patients reciprocated by providing emotional support to their family caregivers to compensate for other forms of support which they felt no longer able to provide. Patients supported family caregivers by involving them in decision-making for care and both patient and family caregiver preferences were influenced by obligation to their respective other. Mutual support comprised both disclosure and concealment. Involving family caregivers in patient care decision-making was intended by patients to help family caregivers adjust to a caregiving role. Conclusions: The findings inform the development and delivery of psychosocial interventions for patients and family caregivers in palliative care aimed at facilitating supportive relations between them.
Design of a Miniature Observation Robot for Light Emitting Diode Irradiation and Indocyanine Green Fluorescence-emission Guided Lymph Node Monitoring in Operating Rooms
Authors: Seo Hyeon-Woong , Yoon Kicheol , Lee Sangyun , Lee Won-Suk , Kim Kwang Gi 
Published: October 2023

Motivation Typical surgical microscopes used for fluorescence-based lymph node detection experience limitations such as weight and restricted adjustability of the integrated light emitting diode (LED) and camera. This restricts the capture of detailed images of specific regions within the lesion. Research goal This study proposes a miniature observation robot design that offers adjustable working distance (WD) and rotational radius, along with zoom-in/zoom-out functionality. Methods A five-degree-of-freedom manipulator was designed, with the end effector incorporating an LED and concave lens to widen the beam width for comprehensive lesion illumination. Additionally, a long-pass filter was integrated into the camera system to enhance image resolution. Experimental results Experiments were conducted using a fluorescence-expressing phantom to evaluate the performance of the robot. Results demonstrated a captured image resolution of 9600 × 3240 pixels and a zoom-in/zoom-out capacity of up to 3.68 times. Conclusion The proposed robot design is cost-effective and highly adjustable, enabling suitability for rapid and accurate detection of fresh lymph nodes during surgeries. The robot’s capability to detect small lesions (<1 cm), as validated by phantom tests, holds promise for the detection of minute lymph nodes.
Machine learning approaches for predicting sleep arousal response based on heart rate variability, oxygen saturation, and body profiles
Authors: Kuo Chih-Fan , Tsai Cheng-Yu , Cheng Wun-Hao , Hs Wen-Hua , Majumdar Arnab , Stettler Marc , Lee Kang-Yun , Kuan Yi-Chun , Feng Po-Hao , Tseng Chien-Hua , Chen Kuan-Yuan , Kang Jiunn-Horng , Lee Hsin-Chien , Wu Cheng-Jung , Liu Wen-Te 
Published: October 2023

Objective Obstructive sleep apnea is a global health concern, and several tools have been developed to screen its severity. However, most tools focus on respiratory events instead of sleep arousal, which can also affect sleep efficiency. This study employed easy-to-measure parameters—namely heart rate variability, oxygen saturation, and body profiles—to predict arousal occurrence. Methods Body profiles and polysomnography recordings were collected from 659 patients. Continuous heart rate variability and oximetry measurements were performed and then labeled based on the presence of sleep arousal. The dataset, comprising five body profiles, mean heart rate, six heart rate variability, and five oximetry variables, was then split into 80% training/validation and 20% testing datasets. Eight machine learning approaches were employed. The model with the highest accuracy, area under the receiver operating characteristic curve, and area under the precision recall curve values in the training/validation dataset was applied to the testing dataset and to determine feature importance. Results InceptionTime, which exhibited superior performance in predicting sleep arousal in the training dataset, was used to classify the testing dataset and explore feature importance. In the testing dataset, InceptionTime achieved an accuracy of 76.21%, an area under the receiver operating characteristic curve of 84.33%, and an area under the precision recall curve of 86.28%. The standard deviations of time intervals between successive normal heartbeats and the square roots of the means of the squares of successive differences between normal heartbeats were predominant predictors of arousal occurrence. Conclusions The established models can be considered for screening sleep arousal occurrence or integrated in wearable devices for home-based sleep examination.
Top caregiver concerns in Rett syndrome and related disorders: data from the US natural history study
Authors: Neul Jeffrey L. , Benke Timothy A. , Marsh Eric D. , Suter Bernhard , Silveira Lori , Fu Cary , Peters Sarika U. , Percy Alan K. ,   for the Rett syndrome Natural History Study Group, Skinner Steven A. , Heydemann Peter T. , Ryther Robin C. , Haas Richard H. , Lieberman David N. , Beisang Art A. , Feyma Timothy , Standridge Shannon M. 
Published: October 2023

Abstract
Objective
Recent advances in the understanding of neurodevelopmental disorders such as Rett syndrome (RTT) have enabled the discovery of novel therapeutic approaches that require formal clinical evaluation of efficacy. Clinical trial success depends on outcome measures that assess clinical features that are most impactful for affected individuals. To determine the top concerns in RTT and RTT-related disorders we asked caregivers to list the top caregiver concerns to guide the development and selection of appropriate clinical trial outcome measures for these disorders.

Methods
Caregivers of participants enrolled in the US Natural History Study of RTT and RTT-related disorders (n = 925) were asked to identify the top 3 concerning problems impacting the affected participant. We generated a weighted list of top caregiver concerns for each of the diagnostic categories and compared results between the disorders. Further, for classic RTT, caregiver concerns were analyzed by age, clinical severity, and common RTT-causing mutations in MECP2.

Results
The top caregiver concerns for classic RTT were effective communication, seizures, walking/balance issues, lack of hand use, and constipation. The frequency of the top caregiver concerns for classic RTT varied by age, clinical severity, and specific mutations, consistent with known variation in the frequency of clinical features across these domains. Caregivers of participants with increased seizure severity often ranked seizures as the first concern, whereas caregivers of participants without active seizures often ranked hand use or communication as the top concern. Comparison across disorders found commonalities in the top caregiver concerns between classic RTT, atypical RTT, MECP2 duplication syndrome, CDKL5 deficiency disorder, and FOXG1 syndrome; however, distinct differences in caregiver concerns between these disorders are consistent with the relative prevalence and impact of specific clinical features.

Conclusion
The top caregiver concerns for individuals with RTT and RTT-related disorders reflect the impact of the primary clinical symptoms of these disorders. This work is critical in the development of meaningful therapies, as optimal therapy should address these concerns. Further, outcome measures to be utilized in clinical trials should assess these clinical issues identified as most concerning by caregivers.
lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
Authors: Africa Pasquale Claudio , Piersanti Roberto , Regazzoni Francesco , Bucelli Michele , Salvador Matteo , Fedele Marco , Pagani Stefano , Dede’ Luca , Quarteroni Alfio 
Published: October 2023

AbstractBackgroundSimulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors of various research teams, comprehensive and user-friendly software programs for cardiac simulations, capable of accurately replicating both normal and pathological conditions, are still in the process of achieving full maturity within the scientific community.ResultsThis work introduces$$\texttt {life}^{\text{x}}$$lifex, a publicly available software for numerical simulations of the electrophysiology activity of the cardiac muscle, under both normal and pathological conditions.$$\texttt {life}^{\text{x}}$$lifexemploys the monodomain equation to model the heart’s electrical activity. It incorporates both phenomenological and second-generation ionic models. These models are discretized using the Finite Element method on tetrahedral or hexahedral meshes. Additionally,$$\texttt {life}^{\text{x}}$$lifexintegrates the generation of myocardial fibers based on Laplace–Dirichlet Rule-Based Methods, previously released in Africa et al., 2023, within$$\texttt {life}^{\text{x}}$$lifex. As an alternative, users can also choose to import myofibers from a file. This paper provides a concise overview of the mathematical models and numerical methods underlying$$\texttt {life}^{\text{x}}$$lifex, along with comprehensive implementation details and instructions for users.$$\texttt {life}^{\text{x}}$$lifexfeatures exceptional parallel speedup, scaling efficiently when using up to thousands of cores, and its implementation has been verified against an established benchmark problem for computational electrophysiology. We showcase the key features of$$\texttt {life}^{\text{x}}$$lifexthrough various idealized and realistic simulations conducted in both normal and pathological scenarios. Furthermore, the software offers a user-friendly and flexible interface, simplifying the setup of simulations using self-documenting parameter files.Conclusions$$\texttt {life}^{\text{x}}$$lifexprovides easy access to cardiac electrophysiology simulations for a wide user community. It offers a computational tool that integrates models and accurate methods for simulating cardiac electrophysiology within a high-performance framework, while maintaining a user-friendly interface.$$\texttt {life}^{\text{x}}$$lifexrepresents a valuable tool for conducting in silico patient-specific simulations.
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)
Authors: Yang In Seok , Jang Insu , Yang Jin Ok , Choi Jinhyuk , Kim Min-Seo , Kim Ka-Kyung , Seung Byung-Joon , Cheong Jae-Ho , Sur Jung-Hyang , Nam Hojung , Lee Byungwook , Kim Junho , Kim Sangwoo 
Published: October 2023

Abstract
Background
The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete.

Results
We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns.

Conclusions
CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/.
Comparative transcriptome analysis of high- and low-embryogenic Hevea brasiliensis genotypes reveals involvement of phytohormones in somatic embryogenesis
Authors: Li Ling , Sun Xiaolong , Yu Wencai , Gui Mingchun , Qiu Yanfen , Tang Min , Tian Hai , Liang Guoping 
Published: October 2023

AbstractBackgroundRubber plant (Hevea brasiliensis) is one of the major sources of latex. Somatic embryogenesis (SE) is a promising alterative to its propagation by grafting and seed. Phytohormones have been shown to influence SE in different plant species. However, limited knowledge is available on the role of phytohormones in SE in Hevea. The anther cultures of two Hevea genotypes (Yunyan 73477-YT and Reken 628-RT) with contrasting SE rate were established and four stages i.e., anthers (h), anther induced callus (y), callus differentiation state (f), and somatic embryos (p) were studied. UPLC-ESI-MS/MS and transcriptome analyses were used to study phytohormone accumulation and related expression changes in biosynthesis and signaling genes.ResultsYT showed higher callus induction rate than RT. Of the two genotypes, only YT exhibited successful SE. Auxins, cytokinins (CKs), abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), gibberellins (GAs), and ethylene (ETH) were detected in the two genotypes. Indole-3-acetic acid (IAA), CKs, ABA, and ETH had notable differences in the studied stages of the two genotypes. The differentially expressed genes identified in treatment comparisons were majorly enriched in MAPK and phytohormone signaling, biosynthesis of secondary metabolites, and metabolic pathways. The expression changes in IAA, CK, ABA, and ETH biosynthesis and signaling genes confirmed the differential accumulation of respective phytohormones in the two genotypes.ConclusionThese results suggest potential roles of phytohormones in SE in Hevea.
Influencing factors of anthracycline-induced subclinical cardiotoxicity in acute leukemia patients
Authors: Zhou Xi , Weng Yue , Jiang Tiantian , Ou Wenxin , Zhang Nan , Dong Qian , Tang Xiaoqiong 
Published: October 2023

Abstract
Background
Current treatment of acute leukemia is based on anthracycline chemotherapy. Anthracyclines, despite improving patient survival, have serious cardiotoxicity and therefore cardiac monitoring should be a priority. The purpose of this study is to explore the possible early predictors of anthracycline-induced subclinical cardiotoxicity(AISC)in acute leukemia patients.

Methods
We conducted a prospective observational study involving 51 patients with acute leukemia treated with anthracycline. Demographic data, clinical variables, echocardiography variables and biochemical variables were collected at baseline and after 3 cycles of chemotherapy. Patients were divided into the AISC and No-AISC groups according to changes of global longitudinal peak systolic strain. Regression models and receiver operating characteristic curve analysis were used to explore the relationship between the variables and AISC.

Result
17 of the patients suffered subclinical cardiotoxicity after 3 cycles of anthracycline treatment. Multiple logistic regression analysis showed a significant association of DBil (OR 0.612, 95% CI 0.409–0.916, p = 0.017), TBil (OR 0.841, 95% CI 0.717–0.986, p = 0.033), PLT (OR 1.012, 95% CI 1.002–1.021, p = 0.016) and Glu (OR 1.873, 95% CI 1.009–3.475, p = 0.047) with the development of AISC. After 3 cycles of chemotherapy, there was a significant difference in PLT between the AISC and NO-AISC groups. Moreover, the dynamic changes in PLT from baseline to after 3 cycles of chemotherapy were each statistically significant in the AISC and NO-AISC groups. The combination of PLT and N-terminal pro–B-type natriuretic peptide (NT-proBNP) had the highest area under curves (AUC) for the diagnosis of AISC than PLT and NT-proBNP alone (AUC = 0.713, 95%CI: 0.56–0.87, P = 0.017).

Conclusion
Total bilirubin (TBil), direct bilirubin (DBil), platelets (PLT) and blood glucose (Glu) are independent influencing factors for AISC in acute leukemia patients receiving anthracycline therapy. Bilirubin may be a protective factor and PLT may be a contributing factor for AISC. The combination of baseline PLT and baseline NT-proBNP shows satisfactory predictive ability for AISC in acute leukemia cases treated with 3 cycles of chemotherapy.
Genomic analysis reveals limited hybridization among three giraffe species in Kenya
Authors: Coimbra Raphael T. F. , Winter Sven , Muneza Arthur , Fennessy Stephanie , Otiende Moses , Mijele Domnic , Masiaine Symon , Stacy-Dawes Jenna , Fennessy Julian , Janke Axel 
Published: October 2023

Abstract
Background
In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.

Results
We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.

Conclusions
Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.