bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilayer Exponential Family Factor models for integrative analysis and learning disease progression
Authors: Wang Qinxia , Wang Yuanjia 
Published: September 2022

Summary
Current diagnosis of neurological disorders often relies on late-stage clinical symptoms, which poses barriers to developing effective interventions at the premanifest stage. Recent research suggests that biomarkers and subtle changes in clinical markers may occur in a time-ordered fashion and can be used as indicators of early disease. In this article, we tackle the challenges to leverage multidomain markers to learn early disease progression of neurological disorders. We propose to integrate heterogeneous types of measures from multiple domains (e.g., discrete clinical symptoms, ordinal cognitive markers, continuous neuroimaging, and blood biomarkers) using a hierarchical Multilayer Exponential Family Factor (MEFF) model, where the observations follow exponential family distributions with lower-dimensional latent factors. The latent factors are decomposed into shared factors across multiple domains and domain-specific factors, where the shared factors provide robust information to perform extensive phenotyping and partition patients into clinically meaningful and biologically homogeneous subgroups. Domain-specific factors capture remaining unique variations for each domain. The MEFF model also captures nonlinear trajectory of disease progression and orders critical events of neurodegeneration measured by each marker. To overcome computational challenges, we fit our model by approximate inference techniques for large-scale data. We apply the developed method to Parkinson’s Progression Markers Initiative data to integrate biological, clinical, and cognitive markers arising from heterogeneous distributions. The model learns lower-dimensional representations of Parkinson’s disease (PD) and the temporal ordering of the neurodegeneration of PD.
Age-dependent increased sag amplitude in human pyramidal neurons dampens baseline cortical activity
Authors: Guet-McCreight Alexandre , Chameh Homeira Moradi , Mahallati Sara , Wishart Margaret , Tripathy Shreejoy J , Valiante Taufik A , Hay Etay 
Published: September 2022

AbstractAging involves various neurobiological changes, although their effect on brain function in humans remains poorly understood. The growing availability of human neuronal and circuit data provides opportunities for uncovering age-dependent changes of brain networks and for constraining models to predict consequences on brain activity. Here we found increased sag voltage amplitude in human middle temporal gyrus layer 5 pyramidal neurons from older subjects and captured this effect in biophysical models of younger and older pyramidal neurons. We used these models to simulate detailed layer 5 microcircuits and found lower baseline firing in older pyramidal neuron microcircuits, with minimal effect on response. We then validated the predicted reduced baseline firing using extracellular multielectrode recordings from human brain slices of different ages. Our results thus report changes in human pyramidal neuron input integration properties and provide fundamental insights into the neuronal mechanisms of altered cortical excitability and resting-state activity in human aging.
Effects of emotional valence and intensity on cognitive and affective empathy after insula lesions
Authors: Holtmann Olga , Schloßmacher Insa , Franz Marcel , Moenig Constanze , Tenberge Jan-Gerd , Preul Christoph , Schwindt Wolfram , Bruchmann Maximilian , Melzer Nico , Miltner Wolfgang H R , Straube Thomas 
Published: September 2022

AbstractThe insula plays a central role in empathy. However, the complex structure of cognitive (CE) and affective empathy (AE) deficits following insular damage is not fully understood. In the present study, patients with insular lesions (n = 20) and demographically matched healthy controls (n = 24) viewed ecologically valid videos that varied in terms of valence and emotional intensity. The videos showed a person (target) narrating a personal life event. In CE conditions, subjects continuously rated the affective state of the target, while in AE conditions, they continuously rated their own affect. Mean squared error (MSE) assessed deviations between subject and target ratings. Patients differed from controls only in negative, low-intensity AE, rating their own affective state less negative than the target. This deficit was not related to trait empathy, neuropsychological or clinical parameters, or laterality of lesion. Empathic functions may be widely spared after insular damage in a naturalistic, dynamic setting, potentially due to the intact interpretation of social context by residual networks outside the lesion. The particular role of the insula in AE for negative states may evolve specifically in situations that bear higher uncertainty pointing to a threshold role of the insula in online ratings of AE.
CCESHP: Causal Consistency Model of Edge Storage Based on Hash Ring and Partial Geo-Replication
Authors: Tian Junfeng , Jia Haoyi , Bai Wenqing 
Published: September 2022

Abstract
At present, most of the causal consistency models that rely on cloud storage have problems such as high operation delays and large metadata overhead. To solve these problems, this paper proposes a causal consistency model for edge storage based on hash rings, CCESHP. The proposed model uses two hashes to map the keys and servers on the hash ring for grouping and stores a subset of the complete data set in a replica node located at the edge of the network, thereby realizing a partial geographic replication strategy in the edge storage environment. Operation latency will be reduced since the edge replica is closer to the client. At the same time, it also generates and maintains a combined timestamp to capture causality according to the update type, which can keep the amount of managed metadata in a relatively stable and low state, reduce the overhead of system management metadata, and improve system throughput. The experimental evaluation results under different workloads show that the model has better performance in throughput and operation delay when compared with the existing causal consistency model.
Single-center experience in implementation of endoscopic surveillance protocol after esophagectomy
Authors: Kamaludin Ahmad , Donlon Noel E , Kavanagh Matthew , Reynolds John V , Donohoe Claire L 
Published: September 2022

AbstractEsophageal cancer has a notably high recurrence rate with a paucity of robust evidence in defining the optimal surveillance strategy. The surveillance protocol at our institution comprises of annual esophagogastroduodenoscopy (OGD) from years 1 to 5 postoperatively. This study aims to evaluate the implementation of the endoscopic surveillance at our center and ascertain the value of endoscopy in detecting local recurrence after esophagectomy. A retrospective cohort review of all patients (320 patients) who underwent esophagectomy between 2013 and 2018 was conducted. The local esophageal cancer database and corresponding OGD reports were accessed to obtain data on demographics, operation details, local recurrence, and endoscopy performed. 1086 OGDs were performed between 2014 and 2020, broadly categorized to surveillance and symptomatic OGDs; 555 and 531, respectively. Surveillance OGDs detected four asymptomatic local recurrences, of which only one was treated with curative intent. Symptomatic OGDs resulted in a higher yield for the detection of local recurrence compared with surveillance endoscopy; 5% versus 0.7%, with overall median time-to-recurrence of 11.5 months (95% confidence interval 9–17). Of local recurrences, 85.7% occurred within the first 2 years postoperatively. The proportion of endoscopic findings differed between intensive and ad hoc surveillance cohorts for strictures, esophagitis, Barrett’s esophagus, and sloughing. Thirteen patients were diagnosed with histologically confirmed Barrett’s with no subsequent local recurrences. Surveillance endoscopy had a low positive yield rate with subsequent minimal survival benefits. Therefore, it is prudent to consider an alternative protocol that focuses on the period with the highest risk of recurrence and symptom presentation.
Disease Activity Patterns of Inflammatory Bowel Disease—A Danish Nationwide Cohort Study 1995–2018
Authors: Wewer Mads Damsgaard , Langholz Ebbe , Munkholm Pia , Bendtsen Flemming , Benedict Seidelin Jakob , Burisch Johan 
Published: September 2022

AbstractBackground and AimsFew studies have assessed the contemporary patterns of disease activity in patients with inflammatory bowel disease [IBD]. We aimed to describe the disease patterns and their long-term outcomes.MethodsAll Danish individuals with IBD between 1995 and 2018 were identified using information about IBD-related hospitalizations, surgeries and redeemed prescriptions. The disease activity patterns for 5- and 10-year periods were assessed.ResultsIn incident patients with Crohn’s disease [CD], severe disease activity occurred in the year of diagnosis in 80% of patients; for ulcerative colitis [UC] this figure was 75%, in addition to 3.4% of UC patients who underwent a colectomy within the first year. After 20 years of disease, the proportion of CD and UC patients in remission increased to 89% and 72%, respectively. The proportion of prevalent patients in remission each year was stable, despite the introduction of biological therapies. A decreasing activity pattern was the most common in both CD and UC patients [both 45%]. The distribution of the disease activity patterns was seen to be stable over time. A quiescent disease pattern was accompanied by a significantly higher risk of intestinal cancer [HR: 3.37, 95% CI: 1.23–9.19] for CD patients, according to a Cox proportional hazards model. In UC patients, increasing disease activity [HR: 0.67, 95% CI: 0.31–1.48] was associated with an increased risk of intestinal cancer.ConclusionsWe report the distribution of disease patterns among IBD patients. Patients with quiescent CD, as well as UC patients with chronic continuous or increasing activity, were at increased risk of developing intestinal cancer.
Excess demand amid quality misperceptions: the case for low-cost seed quality signalling strategies
Authors: Maredia Mywish K , Bartle Brian 
Published: September 2022

Abstract
Planting quality seed is essential for increasing crop productivity. We study the potato seed market in Kenya and estimate farmers’ willingness to pay for certified, clean and ware potato seeds that use reputation and certification strategies at varying costs to provide quality signal. We find that farmers are prone to quality misperceptions and adjust their bids for high (low) quality seed upward (downward) in response to positive (negative) quality signals. Effective demand for quality seeds exceeds supply 286 per cent after correcting quality misperceptions. We make a strong case for the need of low-cost alternatives to meet this excess demand for quality seeds.
Self-reported health and adverse outcomes among women living with symptoms of angina or unspecific chest pain but no diagnosis of obstructive coronary artery disease—findings from the DenHeart study
Authors: Dalsgaard Jane Lange , Hansen Michael Skov , Thrysoee Lars , Ekholm Ola , Thorup Charlotte Brun , Mols Rikke Elmose , Rasmussen Trine Bernholdt , Christensen Anne Vinggaard , Berg Selina Kikkenborg , Pedersen Andreas Kristian , Jensen Lisette Okkels , Mogensen Christian Backer , Borregaard Britt 
Published: September 2022

Abstract

Aims
The objectives were to describe differences in self-reported health at discharge between women diagnosed with angina or unspecific chest pain and investigate the association between self-reported health and adverse outcomes within 3 years.

Methods and results
Data from a national cohort study were used, including data from the DenHeart survey combined with 3 years of register-based follow-up. The population included two groups of women with symptoms of angina but no diagnosis of obstructive coronary artery disease at discharge (women with angina and women with unspecific chest pain). Self-reported health measured with validated instruments was combined with register-based follow-up on adverse outcomes (a composite of unplanned cardiac readmissions, revascularization, or all-cause mortality). Associations between self-reported health and time to first adverse outcomes were investigated with Cox proportional hazard models, reported as hazards ratios with 95% confidence intervals. In total, 1770 women completed the questionnaire (49%). Women with angina (n = 931) reported significantly worse self-reported health on several outcomes compared to women with unspecific chest pain (n = 839). Within the 3 years follow-up, women with angina were more often readmitted (29 vs. 23%, P = 0.011) and more underwent revascularization (10 vs. 1%, P &lt; 0.001), whereas mortality rates were similar (4 vs. 4%, P = 0.750). Self-reported health (physical and mental) was associated with adverse outcomes between both groups (on most instruments).

Conclusion
Women with angina reported significantly worse self-reported health on most instruments compared to women with unspecific chest pain. Adverse outcomes varied between groups, with women diagnosed with angina experiencing more events.

Registration
ClinicalTrials.gov (NCT01926145).
Transvenous phrenic nerve stimulation to treat central sleep apnoea in patients with heart failure may improve sleep, quality of life, and symptoms
Authors: Hill Loreena , Meyer Timothy , McKane Scott , Lainscak Mitja , Ahmed Qanta A 
Published: September 2022

Abstract

Aims
Sleep disorder breathing is an important non-cardiovascular comorbidity in patients with heart failure (HF). However, central sleep apnoea (CSA) remains poorly diagnosed and treated. This post hoc analysis examined symptoms and quality of life in patients with CSA and HF following 12 months of transvenous phrenic nerve stimulation (TPNS) therapy.

Methods and results
Patients enrolled in the remedē System Pivotal trial were invited to complete self-reported questionnaires. Symptoms and responses to three validated questionnaires were examined. Percentage of patients noting an impairment was calculated at baseline. At 12 months, % of patients experiencing improvement, no change, or worsening was calculated. Shifts from symptom presence at baseline to absence at 12 months were assessed for those symptoms experienced by ≥50% of patients at baseline. Seventy-five patients were included. Most frequently reported symptoms were fatigue and daytime sleepiness. Following 12 months of TPNS, a variety of subjective improvements were observed; 45% of patients indicating cessation of daytime sleepiness, 44% cessation of fatigue/weakness, and 52% no longer having difficulty falling/staying asleep. Specific questions related to tiredness/fatigue, motivation, and chance of dozing provided an insight into potential areas of improvement. Furthermore, at least 60% of patients reported resolution of insomnia/fragmented sleep and snoring on therapy.

Conclusion
Adult patients with CSA and HF experience distressing symptoms and limitations. Transvenous phrenic nerve stimulation was found to improve many of these. Awareness of key symptoms or limitations patients experience can be used to inform the development of a CSA-specific patient questionnaire to identify CSA sooner and aid treatment decisions.
Risk of ionizing radiation in pregnancy: just a myth or a real concern?
Authors: Saada Majdi , Sanchez-Jimenez Erick , Roguin Ariel 
Published: September 2022

Abstract
There are natural concerns regarding the risks posed to the foetus by ionizing radiation exposure during pregnancy. Therefore, many female physicians select to avoid working in an environment associated with ionizing radiation exposure like the catheterization laboratory and even exclude training as electrophysiology, interventional cardiologists, or radiologists. For those already working in this field, pregnancy involves usually a 1-year interruption (pregnancy and maternity leave) to their careers, leading at times to delays in the decision to become pregnant. This review describes the low added risk of malformation/cancer in the offspring, highlight gaps in our understanding, discuss several common wrong beliefs, and recommend how to further decrease radiation dose, especially during pregnancy.
Non-invasive assessment of pulmonary vein isolation durability using late gadolinium enhancement magnetic resonance imaging
Authors: Padilla-Cueto David , Ferro Elisenda , Garre Paz , Prat Susanna , Guichard Jean-Baptiste , Perea Rosario J , Tolosana Jose Maria , Guasch Eduard , Arbelo Elena , Porta-Sanchéz Andreu , Roca-Luque Ivo , Sitges Marta , Brugada Josep , Mont Lluís , Althoff Till F 
Published: September 2022

AbstractAimsElectrical reconnection of pulmonary veins (PVs) is considered an important determinant of recurrent atrial fibrillation (AF) after pulmonary vein isolation (PVI). To date, AF recurrences almost automatically trigger invasive repeat procedures, required to assess PVI durability. With recent technical advances, it is becoming increasingly common to find all PVs isolated in those repeat procedures. Thus, as ablation of extra-PV targets has failed to show benefit in randomized trials, more and more often these highly invasive procedures are performed only to rule out PV reconnection. Here we aim to define the ability of late gadolinium enhancement (LGE)-magnetic resonance imaging (MRI) to rule out PV reconnection non-invasively.Methods and resultsThis study is based on a prospective registry in which all patients receive an LGE-MRI after AF ablation. Included were all patients that—after an initial PVI and post-ablation LGE-MRI—underwent an invasive repeat procedure, which served as a reference to determine the predictive value of non-invasive lesion assessment by LGE-MRI.: 152 patients and 304 PV pairs were analysed. LGE-MRI predicted electrical PV reconnection with high sensitivity (98.9%) but rather low specificity (55.6%). Of note, LGE lesions without discontinuation ruled out reconnection of the respective PV pair with a negative predictive value of 96.9%, and patients with complete LGE lesion sets encircling all PVs were highly unlikely to show any PV reconnection (negative predictive value: 94.4%).ConclusionLGE-MRI has the potential to guide selection of appropriate candidates and planning of the ablation strategy for repeat procedures and may help to identify patients that will not benefit from a redo-procedure if no ablation of extra-PV targets is intended.
d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes
Authors: Gress Alexander , Srikakulam Sanjay K , Keller Sebastian , Ramensky Vasily , Kalinina Olga V 
Published: September 2022

Abstract

Background
Structural annotation of genetic variants in the context of intermolecular interactions and protein stability can shed light onto mechanisms of disease-related phenotypes. Three-dimensional structures of related proteins in complexes with other proteins, nucleic acids, or ligands enrich such functional interpretation, since intermolecular interactions are well conserved in evolution.

Results
We present d-StructMAn, a novel computational method that enables structural annotation of local genetic variants, such as single-nucleotide variants and in-frame indels, and implements it in a highly efficient and user-friendly tool provided as a Docker container. Using d-StructMAn, we annotated several very large sets of human genetic variants, including all variants from ClinVar and all amino acid positions in the human proteome. We were able to provide annotation for more than 46% of positions in the human proteome representing over 60% proteins.

Conclusions
d-StructMAn is the first of its kind and a highly efficient tool for structural annotation of protein-coding genetic variation in the context of observed and potential intermolecular interactions. d-StructMAn is readily applicable to proteome-scale datasets and can be an instrumental building machine-learning tool for predicting genotype-to-phenotype relationships.
A consistent multiparameter Bayesian full waveform inversion scheme for imaging heterogeneous isotropic elastic media
Authors: Kan Li-Yu , Chevrot Sébastien , Monteiller Vadim 
Published: September 2022

SUMMARY
The inversion of complete seismic waveforms offers new perspectives to better constrain the elastic properties of Earth’s interior. However, models of density and seismic velocities obtained from full waveform inversions are generally characterized by very different and uneven spatial resolutions. Because the 3-D structure of the Earth represents small deviations from average reference Earth models, the absolute values of density, VP and VS in the Earth are strongly correlated. Here, we exploit this strong correlation between model parameters as a priori information introduced into a new full waveform inversion algorithm, by considering a non-diagonal 3-D model covariance matrix in which the spatial correlations of elastic properties are described with an exponential covariance function. The inverse of such a model covariance matrix is easy to compute, and we thus have all the ingredients to construct a consistent Bayesian full waveform inversion scheme. We show that taking into account the correlations between density and seismic velocities can lead to dramatic improvements on the reconstructed models of density, seismic velocities and VP/VS ratio. This new imaging approach opens new perspectives for refining tomographic images of density and seismic velocities in the lithosphere and upper mantle on a regional scale by full waveform inversion of teleseismic body waves.
Can GPS and GRACE data be used to separate past and present-day surface loading in a data-driven approach?
Authors: Ziegler Yann , Vishwakarma Bramha Dutt , Brady Aoibheann , Chuter Stephen , Royston Sam , Westaway Richard M , Bamber Jonathan L 
Published: September 2022

SUMMARY
Glacial isostatic adjustment (GIA) and the hydrological cycle are both associated with mass changes and vertical land motion (VLM), which are observed by GRACE and GPS, respectively. Hydrology-related VLM results from the instantaneous response of the elastic solid Earth to surface loading by freshwater, whereas GIA-related VLM reveals the long-term response of the viscoelastic Earth mantle to past ice loading history. Thus, observations of mass changes and VLM are interrelated, making GIA and hydrology difficult to quantify and study independently. In this work, we investigate the feasibility of separating these processes based on GRACE and GPS observations, in a fully data-driven and physically consistent approach. We take advantage of the differences in the spatio-temporal characteristics of the GIA and hydrology fields to estimate the respective contributions of each component using a Bayesian hierarchical modelling framework. A closed-loop synthetic test confirms that our method successfully solves this source separation problem. However, there are significant challenges when applying the same approach with actual observations and the answer to the main question of this study is more nuanced. In particular, in regions where GPS station coverage is sparse, the lack of informative data becomes a limiting factor.