bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical Activity Moderates the Association Between Pain and Depressive Symptoms Among Persons with Multiple Sclerosis
Authors: Bradson Megan L , Riegler Kaitlin E , Thomas Garrett A , Sakamoto McKenna S , Arnett Peter A 
Published: January 2024

Abstract

Objective
The present study examined physical activity as a possible moderator in the relationship between pain and depressive symptoms among persons with multiple sclerosis (PwMS).

Method
Fifty-three PwMS completed a comprehensive neuropsychological test battery and psychosocial questionnaires. Pain was operationalized as a composite of measures from the Brief Pain Inventory. Metabolic equivalents (METs) of energy expended during self-reported vigorous activity (VA), moderate activity (MA), and walking, as well as global physical activity which combined the three, were derived from the International Physical Activity Questionnaire-Short Form. Self-reported physical activity was measured using the Cognitive Health Questionnaire Exercise Scale. Regressions on depressive symptoms (Beck Depression Inventory-Fast Screen) examining both conceptualizations of physical activity, pain, and their interactions were explored.

Results
Regression analyses revealed that interactions between pain and each measure of global physical activity were significant (p = .01). Simple effects tests revealed that pain only influenced depressive symptoms in PwMS with low global physical activity METs (p &lt; .001) and low overall self-reported physical activity (p &lt; .001). The separate interactions between pain and METs during self-reported VA, MA, and walking on depressive symptoms were not significant.

Conclusion
We found that global physical activity moderated the relationship between pain and depressive symptoms in MS. Specifically, pain influenced depressive symptoms in PwMS who engaged in less overall physical activity. These results highlight the importance of screening PwMS for pain and suggest that behavioral interventions aimed at increasing overall lifestyle physical activity may be useful in improving depressive outcomes in PwMS with pain.
Attention is all you need: utilizing attention in AI-enabled drug discovery
Authors: Zhang Yang , Liu Caiqi , Liu Mujiexin , Liu Tianyuan , Lin Hao , Huang Cheng-Bing , Ning Lin 
Published: January 2024

Abstract
Recently, attention mechanism and derived models have gained significant traction in drug development due to their outstanding performance and interpretability in handling complex data structures. This review offers an in-depth exploration of the principles underlying attention-based models and their advantages in drug discovery. We further elaborate on their applications in various aspects of drug development, from molecular screening and target binding to property prediction and molecule generation. Finally, we discuss the current challenges faced in the application of attention mechanisms and Artificial Intelligence technologies, including data quality, model interpretability and computational resource constraints, along with future directions for research. Given the accelerating pace of technological advancement, we believe that attention-based models will have an increasingly prominent role in future drug discovery. We anticipate that these models will usher in revolutionary breakthroughs in the pharmaceutical domain, significantly accelerating the pace of drug development.
NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing
Authors: Lin Yusen , Zhang Yongjun , Sun Hang , Jiang Hang , Zhao Xing , Teng Xiaojuan , Lin Jingxia , Shu Bowen , Sun Hao , Liao Yuhui , Zhou Jiajian 
Published: January 2024

Abstract
Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequencing. We present a deep learning framework, NanoDeep, to overcome these limitations by incorporating convolutional neural network and squeeze and excitation. We first showed that the raw squiggle derived from native DNA sequences determines the origin of microbial and human genomes. Then, we demonstrated that NanoDeep successfully classified bacterial reads from the pooled library with human sequence and showed enrichment for bacterial sequence compared with routine nanopore sequencing setting. Further, we showed that NanoDeep improves the sequencing efficiency and preserves the fidelity of bacterial genomes in the mock sample. In addition, NanoDeep performs well in the enrichment of metagenome sequences of gut samples, showing its potential applications in the enrichment of unknown microbiota. Our toolkit is available at https://github.com/lysovosyl/NanoDeep.
stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics
Authors: Fang Zhaoyu , Liu Teng , Zheng Ruiqing , A Jin , Yin Mingzhu , Li Min 
Published: January 2024

Abstract
With the development of spatially resolved transcriptomics technologies, it is now possible to explore the gene expression profiles of single cells while preserving their spatial context. Spatial clustering plays a key role in spatial transcriptome data analysis. In the past 2 years, several graph neural network-based methods have emerged, which significantly improved the accuracy of spatial clustering. However, accurately identifying the boundaries of spatial domains remains a challenging task. In this article, we propose stAA, an adversarial variational graph autoencoder, to identify spatial domain. stAA generates cell embedding by leveraging gene expression and spatial information using graph neural networks and enforces the distribution of cell embeddings to a prior distribution through Wasserstein distance. The adversarial training process can make cell embeddings better capture spatial domain information and more robust. Moreover, stAA incorporates global graph information into cell embeddings using labels generated by pre-clustering. Our experimental results show that stAA outperforms the state-of-the-art methods and achieves better clustering results across different profiling platforms and various resolutions. We also conducted numerous biological analyses and found that stAA can identify fine-grained structures in tissues, recognize different functional subtypes within tumors and accurately identify developmental trajectories.
Factors influencing the reliability of a CT angiography-based deep learning method for infarct volume estimation
Authors: Hokkinen Lasse , Mäkelä Teemu , Savolainen Sauli , Kangasniemi Marko 
Published: January 2024

Abstract

Objectives
CT angiography (CTA)-based machine learning methods for infarct volume estimation have shown a tendency to overestimate infarct core and final infarct volumes (FIV). Our aim was to assess factors influencing the reliability of these methods.

Methods
The effect of collateral circulation on the correlation between convolutional neural network (CNN) estimations and FIV was assessed based on the Miteff system and hypoperfusion intensity ratio (HIR) in 121 patients with anterior circulation acute ischaemic stroke using Pearson correlation coefficients and median volumes. Correlation was also assessed between successful and futile thrombectomies. The timing of individual CTAs in relation to CTP studies was analysed.

Results
The strength of correlation between CNN estimated volumes and FIV did not change significantly depending on collateral status as assessed with the Miteff system or HIR, being poor to moderate (r = 0.09-0.50). The strongest correlation was found in patients with futile thrombectomies (r = 0.61). Median CNN estimates showed a trend for overestimation compared to FIVs. CTA was acquired in the mid arterial phase in virtually all patients (120/121).

Conclusions
This study showed no effect of collateral status on the reliability of the CNN and best correlation was found in patients with futile thrombectomies. CTA timing in the mid arterial phase in virtually all patients can explain infarct volume overestimation.

Advances in knowledge
CTA timing seems to be the most important factor influencing the reliability of current CTA-based machine learning methods, emphasizing the need for CTA protocol optimization for infarct core estimation.
Prosopagnosia: face blindness and its association with neurological disorders
Authors: Josephs Kennedy A , Josephs Keith A 
Published: January 2024

Abstract
Loss of facial recognition or prosopagnosia has been well-recognized for over a century. It has been categorized as developmental or acquired depending on whether the onset is in early childhood or beyond, and acquired cases can have degenerative or non-degenerative aetiologies. Prosopagnosia has been linked to involvement of the fusiform gyri, mainly in the right hemisphere. The literature on prosopagnosia comprises case reports and small case series. We aim to assess demographic, clinical and imaging characteristics and neurological and neuropathological disorders associated with a diagnosis of prosopagnosia in a large cohort. Patients were categorized as developmental versus acquired; those with acquired prosopagnosia were further subdivided into degenerative versus non-degenerative, based on neurological aetiology. We assessed regional involvement on [18F] fluorodeoxyglucose-PET and MRI of the right and left frontal, temporal, parietal and occipital lobes. The Intake and Referral Center at the Mayo Clinic identified 487 patients with possible prosopagnosia, of which 336 met study criteria for probable or definite prosopagnosia. Ten patients, 80.0% male, had developmental prosopagnosia including one with Niemann–Pick type C and another with a forkhead box G1 gene mutation. Of the 326 with acquired prosopagnosia, 235 (72.1%) were categorized as degenerative, 91 (27.9%) as non-degenerative. The most common degenerative diagnoses were posterior cortical atrophy, primary prosopagnosia syndrome, Alzheimer’s disease dementia and semantic dementia, with each diagnosis accounting for &gt;10% of this group. The most common non-degenerative diagnoses were infarcts (ischaemic and haemorrhagic), epilepsy-related and primary brain tumours, each accounting for &gt;10%. We identified a group of patients with non-degenerative transient prosopagnosia in which facial recognition loss improved or resolved over time. These patients had migraine-related prosopagnosia, posterior reversible encephalopathy syndrome, delirium, hypoxic encephalopathy and ischaemic infarcts. On [18F] fluorodeoxyglucose-PET, the temporal lobes proved to be the most frequently affected regions in 117 patients with degenerative prosopagnosia, while in 82 patients with non-degenerative prosopagnosia, MRI revealed the right temporal and right occipital lobes as most affected by a focal lesion. The most common pathological findings in those with degenerative prosopagnosia were frontotemporal lobar degeneration with hippocampal sclerosis and mixed Alzheimer’s and Lewy body disease pathology. In this large case series of patients diagnosed with prosopagnosia, we observed that facial recognition loss occurs across a wide range of acquired degenerative and non-degenerative neurological disorders, most commonly in males with developmental prosopagnosia. The right temporal and occipital lobes, and connecting fusiform gyrus, are key areas. Multiple different pathologies cause degenerative prosopagnosia.
Cortical atrophy in early-stage patients with anti-NMDA receptor encephalitis: a machine-learning MRI study with various feature extraction
Authors: Shen Sisi , Wei Ran , Gao Yu , Yang Xinyuan , Zhang Guoning , Yan Bo , Xiao Zhuoling , Li Jinmei 
Published: January 2024

Abstract
Conventional brain magnetic resonance imaging (MRI) of anti-N-methyl-D-aspartate-receptor encephalitis (NMDARE) is non-specific, thus showing little differential diagnostic value, especially for MRI-negative patients. To characterize patterns of structural alterations and facilitate the diagnosis of MRI-negative NMDARE patients, we build two support vector machine models (NMDARE versus healthy controls [HC] model and NMDARE versus viral encephalitis [VE] model) based on radiomics features extracted from brain MRI. A total of 109 MRI-negative NMDARE patients in the acute phase, 108 HCs and 84 acute MRI-negative VE cases were included for training. Another 29 NMDARE patients, 28 HCs and 26 VE cases were included for validation. Eighty features discriminated NMDARE patients from HCs, with area under the receiver operating characteristic curve (AUC) of 0.963 in validation set. NMDARE patients presented with significantly lower thickness, area, and volume and higher mean curvature than HCs. Potential atrophy predominately presented in the frontal lobe (cumulative weight = 4.3725, contribution rate of 29.86%), and temporal lobe (cumulative weight = 2.573, contribution rate of 17.57%). The NMDARE versus VE model achieved certain diagnostic power, with AUC of 0.879 in validation set. Our research shows potential atrophy across the entire cerebral cortex in acute NMDARE patients, and MRI machine learning model has a potential to facilitate the diagnosis MRI-negative NMDARE.
On the survival of a flawed theory of capital: mainstream economics and the Cambridge capital controversies
Authors: Nunes-Pereira Francisco , Graça Moura Mário 
Published: January 2024

Abstract
The Cambridge controversies on capital theory opposed heterodox economists, mainly from the University of Cambridge, UK, to mainstream economists, mostly based at the Massachusetts Institute of Technology, Cambridge, USA. The controversies started in the 1950s and occupied the pages of some of the most influential journals. Their primary outcome was the broad acknowledgement of flaws, which we retrieve, in the concept of aggregate capital. Despite that acknowledgement, aggregate, homogeneous capital remains a staple of contemporary macroeconomics, as if the Cambridge controversies had never existed. To account for this apparent paradox is the aim of this article. We examine the arguments seeking to justify the enduring commitment to the aggregate capital approach and argue that they indicate an implicit commitment to instrumentalism. The indifference to the results of the Cambridge controversies is a consequence of methodological conformism and has shaky foundations.
Catheter-directed thrombolysis guided by pulmonary artery pressure registration in pulmonary embolism: a case report
Authors: Berenjkoub Ehssan , Kemper Charlotte , Lewandowski Nicole , Horlitz Marc , Rottländer Dennis 
Published: January 2024

Abstract

Background
Duration and dosage of thrombolysis for ultrasound-assisted catheter-directed thrombolysis (UACDT) in patients with intermediate high-risk pulmonary embolism remain controversial and treatment protocols vary.

Case summary
A 58-year-old female patient suffered from a right-sided urolithiasis. The clinical course was complicated by an intermediate high-risk pulmonary embolism [pulmonary embolism severity index (PESI) score 108 points and simplified PESI ≥1] with bilateral proximal thrombus and significant right heart dysfunction. The pulmonary embolism response team (PERT) made a decision towards UACDT. The standard duration of UACDT ranges between 6 and 15 h depending on clinical parameters. In this particular case, the clinical parameters such as heart rate (no tachycardia) or oxygen saturation (chronic obstructive pulmonary disease) might lead to premature termination of UACDT. Therefore, PERT decided to additionally monitor pulmonary artery pressure (PAP) continuously during the UACDT via a separate pigtail catheter in the pulmonary artery. Ultrasound-assisted catheter-directed thrombolysis was performed using 1 mg/h recombinant tissue plasminogen activator (rtPA) per catheter, while PAP was registered continuously. Heart rate and oxygen saturation remained unchanged during UACDT. However, after 6 h of UACDT, systolic PAP decreased slightly from 62 to 55 mmHg and therapy was prolonged to 15 h. Pulmonary artery pressure dropped to 46 mmHg after 15 h. The patient was discharged from hospital at Day 7, and echocardiography revealed no signs of right heart dysfunction.

Discussion
Dosage of the thrombolysis agent and duration of UACDT are still a matter of debate. Besides clinical parameters and transthoracic echocardiography, invasive real-time PAP monitoring during UACDT could facilitate important information for therapy guidance in selected cases.
Strategies for improving diversity, equity, and inclusion in cardiovascular research: a primer
Authors: Prichard Roslyn , Maneze Della , Straiton Nicola , Inglis Sally C , McDonagh Julee 
Published: January 2024

Abstract
This paper aims to empower cardiovascular (CV) researchers by promoting diversity, equity, and inclusion (DE&I) principles throughout the research cycle. It defines DE&I and introduces practical strategies for implementation in recruitment, retention, and team dynamics within CV research. Evidence-based approaches supporting underrepresented populations’ participation are outlined for each research phase. Emphasizing the significance of inclusive research environments, the paper offers guidance and resources. We invite CV researchers to actively embrace DE&I principles, enhancing research relevance and addressing longstanding CV health disparities.
A chromosome-scale assembly for ‘d’Anjou’ pear
Authors: Yocca Alan , Akinyuwa Mary , Bailey Nick , Cliver Brannan , Estes Harrison , Guillemette Abigail , Hasannin Omar , Hutchison Jennifer , Jenkins Wren , Kaur Ishveen , Khanna Risheek Rahul , Loftin Madelene , Lopes Lauren , Moore-Pollard Erika , Olofintila Oluwakemisola , Oyebode Gideon Oluwaseye , Patel Jinesh , Thapa Parbati , Waldinger Martin , Zhang Jie , Zhang Qiong , Goertzen Leslie , Carey Sarah B , Hargarten Heidi , Mattheis James , Zhang Huiting , Jones Teresa , Boston LoriBeth , Grimwood Jane , Ficklin Stephen , Honaas Loren , Harkess Alex 
Published: January 2024

Abstract
Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully phased chromosome-scale genome assembly of P. communis ‘d’Anjou.’ Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other and to the Malus domestica ‘Honeycrisp’ apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d’Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.
The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza
Authors: Harkess Alex , Bewick Adam J , Lu Zefu , Fourounjian Paul , Michael Todd P , Schmitz Robert J , Meyers Blake C 
Published: January 2024

Abstract
Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.
A Systematic Review of Red Blood Cells Biomarkers in Human Aging
Authors: Yadav Somu , Deepika  , Maurya Pawan Kumar 
Published: January 2024

Abstract
Red blood cells (RBCs) have emerged as biomarkers of the aging process as they undergo several changes in human aging and age-related diseases. The objectives of our study are to explore the effect of human aging on RBC indices, the strengths, therapeutic interventions, challenges, and future directions for using RBCs as a biomarker. Two online databases, PubMed and ScienceDirect, were used to search relevant studies using “RBCs as biomarkers of human aging,” “red blood cells [MeSH Terms] AND biomarkers [MeSH Terms] AND human aging [MeSH Terms],” and “erythrocytes and human aging” as keywords. A total of 474 studies were identified, and after the removal of duplicates, excluding studies based on title, abstract, or full text, 74 studies and 48 additional studies found through cross-referencing were included in this systematic review. Based on the evidence, we concluded that RBC indices such as hemoglobin concentration, mean corpuscular volume, RBC distribution width, RBC membrane, oxidative stress, and metabolism change with human aging. Several studies have applied therapeutic interventions to RBCs, including dietary supplementation, phytochemicals, nanoparticles, and physical activity, to mitigate aging and related outcomes. Hence, the quality of life for older people and healthy aging can be improved by further investigating the RBC parameters, molecular mechanisms, and their implications for age-related health consequences.
Prevention as a norm cluster? Mapping China's contestation on atrocity prevention
Authors: Zhang Qiaochu 
Published: January 2024

Abstract
This article argues that China's rhetorical support for prevention at the United Nations obscures its underlying contestation of atrocity prevention in both conception and practice. It introduces a novel conceptual framework, coined as the two-level norm cluster of prevention, which includes three conceptually aligned yet distinct parts: operational conflict prevention, direct atrocity prevention and root-cause prevention. Drawing on interviews and policy documents, this article finds that China conflates direct atrocity prevention with operational conflict prevention, with a preference for the agenda of conflict prevention, as seen in China's divergent commitments to preventing armed conflicts and peacetime atrocities. This conflation represents a deliberate political choice rather than a result of misunderstanding or lack of knowledge regarding their distinctions. China also endorses a strong linkage between direct atrocity prevention and development-focused root cause prevention. Despite China's growing assertiveness in shaping liberal norms and the favourable perception of its development-focused approaches among elite groups in host states, the Chinese government hesitates to officially promote the scholarly concept of developmental peace and present it as an alternative to the existing liberal principles. This reluctance reflects China's intention to avoid explicit confrontation with liberal norms and its concerns about the potential failure of norm entrepreneurship.