bluuebunny/crossref_metadata_2025_split huggingface dataset:
SBMLDiagrams: a python package to process and visualize SBML layout and render
Authors: Xu Jin , Jiang Jessie , Sauro Herbert M 
Published: November 2022

Abstract

Summary
The systems biology markup language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical model as a pathway diagram. However, up to now, there has been little support to help users easily add and retrieve such information from SBML. In this application note, we describe a new Python package called SBMLDiagrams. This package allows a user to add a layout and render information or retrieve it using a straightforward Python API. The package uses skia-python to support the rendering of the diagrams, allowing export to commons formats such as PNG or PDF.

Availability and implementation
SBMLDiagrams is publicly available and licensed under the liberal MIT open-source license. The package is available for all major platforms. The source code has been deposited at GitHub (github.com/sys-bio/SBMLDiagrams). Users can install the package using the standard pip installation mechanism: pip install SBMLDiagrams.

Supplementary information
Supplementary data are available at Bioinformatics online.
B cells in human lymphoid structures
Authors: Montorsi Lucia , Siu Jacqueline H Y , Spencer Jo 
Published: November 2022

SummaryMost B cells in the human body are present in tissues where they support immune responses to pathogens, vaccines, autoantigens, and tumours. Despite their clear importance, they are very difficult to study and there are many areas of uncertainty that are difficult to resolve because of limited tissue access.In this review, we consider the zonal structure of lymphoid tissues, the B cell subsets they contain, and how these are regulated. We also discuss the impact that methods of deep interrogation have made on our current knowledge base, especially with respect to studies of cells from dissociated tissues. We discuss in some detail the controversial B cells with marginal zone distribution that some consider being archived memory B cells.We anticipate that more we understand of B cells in tissues and the niches they create, the more opportunities will be identified to harness their potential for therapeutic benefit.
Cortical networks show characteristic recruitment patterns after somatosensory stimulation by pneumatically evoked repetitive hand movements in newborn infants
Authors: Ahtola Eero , Leikos Susanna , Tuiskula Anna , Haataja Leena , Smeds Eero , Piitulainen Harri , Jousmäki Veikko , Tokariev Anton , Vanhatalo Sampsa 
Published: November 2022

AbstractControlled assessment of functional cortical networks is an unmet need in the clinical research of noncooperative subjects, such as infants. We developed an automated, pneumatic stimulation method to actuate naturalistic movements of an infant’s hand, as well as an analysis pipeline for assessing the elicited electroencephalography (EEG) responses and related cortical networks. Twenty newborn infants with perinatal asphyxia were recruited, including 7 with mild-to-moderate hypoxic–ischemic encephalopathy (HIE). Statistically significant corticokinematic coherence (CKC) was observed between repetitive hand movements and EEG in all infants, peaking near the contralateral sensorimotor cortex. CKC was robust to common sources of recording artifacts and to changes in vigilance state. A wide recruitment of cortical networks was observed with directed phase transfer entropy, also including areas ipsilateral to the stimulation. The extent of such recruited cortical networks was quantified using a novel metric, Spreading Index, which showed a decrease in 4 (57%) of the infants with HIE. CKC measurement is noninvasive and easy to perform, even in noncooperative subjects. The stimulation and analysis pipeline can be fully automated, including the statistical evaluation of the cortical responses. Therefore, the CKC paradigm holds great promise as a scientific and clinical tool for controlled assessment of functional cortical networks.
Cognitive flexibility: neurobehavioral correlates of changing one’s mind
Authors: Zühlsdorff Katharina , Dalley Jeffrey W , Robbins Trevor W , Morein-Zamir Sharon 
Published: November 2022

Abstract
Behavioral and cognitive flexibility allow adaptation to a changing environment. Most tasks used to investigate flexibility require switching reactively in response to deterministic task-response rules. In daily life, flexibility often involves a volitional decision to change behavior. This can be instigated by environmental signals, but these are frequently unreliable. We report results from a novel “change your mind” task, which assesses volitional switching under uncertainty without the need for rule-based learning. Participants completed a two-alternative choice task, and following spurious feedback, were presented with the same stimulus again. Subjects had the opportunity to repeat or change their response. Forty healthy participants completed the task while undergoing a functional magnetic resonance imaging scan. Participants predominantly repeated their choice but changed more when their first response was incorrect or when the feedback was negative. Greater activations for changing were found in the inferior frontal junction, anterior insula (AI), anterior cingulate, and dorsolateral prefrontal cortex. Changing responses were also accompanied by reduced connectivity from the AI and orbitofrontal cortices to the occipital cortex. Using multivariate pattern analysis of brain activity, we predicted with 77% reliability whether participants would change their mind. These findings extend our understanding of cognitive flexibility in daily life by assessing volitional decision-making.
Anonymity in sharing morally salient news: the causal role of the temporoparietal junction
Authors: Cui Fang , Zhong Yijia , Feng Chenghu , Peng Xiaozhe 
Published: November 2022

Abstract
Considering the crucial role of morality in shaping one’s reputation, exploring factors that modulate people’s decision to share morally salient news is important. Previous studies suggested that self-expression and socializing are 2 key factors for news-sharing behaviors, suggesting the key role of anonymity in such decisions. Using functional magnetic resonance imaging (fMRI) and transcranial direct current stimulation (tDCS), the present study focused on how anonymity modulates the sharing of morally salient information, as well as its neural mechanisms. Results showed that compared to moral news, people were more reluctant to share immoral news, especially when they share it with their real names shown. On the neural level, we found that this effect was associated with the activity of the left temporoparietal junction (TPJ), as well as its functional connection to its right counterpart. Dynamic causal modeling analysis revealed the moral valence of news and the anonymity of sharing modulated the effective connectivity between the left TPJ and the middle frontal gyrus as well as the medial frontal gyrus. There was no significant difference when sharing news anonymously. Further, a followed-up tDCS experiment supported the causal role of the left TPJ in this behavioral effect. Taken together, these results suggested that people concern more about social repercussion, when they share the news with their real-names shown, especially when sharing immoral news, and this effect is associated with stronger neural activation in the left TPJ, as well as changes in its functional connectivity with other brain regions.
Nutritional needs and mortality risk combine to shape foraging decisions in ants
Authors: Barbee Bryce , Pinter-Wollman Noa 
Published: November 2022

Abstract
When foraging, internal needs for particular nutrients might affect food choice, and external constraints, such as predation risk, might impact trade-offs between foraging and risk avoidance. Examining both internal and external constraints simultaneously can provide important insights into how animals make decisions. We examined how internal nutritional needs and external cues of mortality risk jointly impact the foraging behavior of ants. Ant colonies require carbohydrates to support workers energetically and proteins to raise brood. Furthermore, colonies adjust their foraging activity in response to the environment, such as food availability and the presence of predators or heterospecifics. Here we examine the foraging decisions of groups of Argentine ants Linepithema humile, which differ in their nutritional needs in high-risk environments. We starved groups of ants for either proteins or carbohydrates and determined the foraging choices that ants made when cues of heterospecifics were present. We found that ants preferentially forage for carbohydrates in high-risk conditions. Furthermore, starvation for carbohydrates increased the ants’ preference for carbohydrates, even when cues of heterospecifics were present at both carbohydrates and protein resources. Starvation for protein also resulted in preferential foraging for carbohydrates, but it increased visitation to a protein food source in high-risk environments compared to when ants were starved for carbohydrates or for both resources. Examining the effect of both nutrition and mortality risk on foraging simultaneously provides insights about state-dependent risk-taking behavior that may have important implications for predicting the invasion of species into novel habitats.
Monitoring and diagnosis of intermittent arrhythmias: evidence-based guidance and role of novel monitoring strategies
Authors: Carrington Mafalda , Providência Rui , Chahal C Anwar A , Ricci Fabrizio , Epstein Andrew E , Gallina Sabina , Fedorowski Artur , Sutton Richard , Khanji Mohammed Y 
Published: November 2022

Abstract
Technological advances have made diagnosis of heart rhythm disturbances much easier, with a wide variety of options, including single-lead portable devices, smartphones/watches to sophisticated implantable cardiac monitors, allowing accurate data to be collected over different time periods depending on symptoms frequency. This review provides an overview of the novel and existing heart rhythm testing options, including a description of the supporting evidence for their use. A description of each of the tests is provided, along with discussion of their advantages and limitations. This is intended to help clinicians towards choosing the most appropriate test, thus improving diagnostic yield management of patients with suspected arrhythmias.
Decolonizing Cyprus 60 Years after Independence: An Assessment of the Legality of the Sovereign Base Areas
Authors: Hadjigeorgiou Nasia 
Published: November 2022

Abstract
The Sovereign Base Areas (SBA) are two parts on the island of Cyprus, with a combined territory of 99 square miles, over which the United Kingdom exercises sovereignty. They were created by the Treaty of Establishment 1960, which is also the international agreement that granted the Republic of Cyprus its independence. This article maps out the implications of the Chagos Archipelago advisory opinion for the SBA. It argues that the process through which they were created disregarded the wishes of the Cypriot people and, therefore, was not in accordance with the right to self-determination.
Computed tomography to replace invasive coronary angiography? The DISCHARGE trial
Authors: Bolognese Leonardo , Reccia Matteo Rocco 
Published: November 2022

Abstract
Ongoing advancements of coronary computed tomographic angiography (CTA) continue to challenge the role of invasive coronary angiography (ICA) as the gold standard for the evaluation of coronary artery disease (CAD). To investigate the comparative effectiveness of ICA when compared with CTA as an initial diagnostic imaging strategy the DISCHARGE Trial enrolled 3561 patients with stable chest pain and an intermediate pre-test probability of obstructive CAD. The study showed no difference between CTA and ICA in the incidence of the primary composite outcome of cardiovascular death, non-fatal myocardial infarction, or non-fatal stroke during 3.5 years of follow up. As with many trials that advance a field, this trial raises several additional questions of interest that will be discussed. Furthermore, recent studies focused on the discrepancies of CTA vs. ICA indicate that the status of CTA remains unchanged in its ability to rule out disease but at present cannot be considered a substitute for ICA when coronary lesions are documented. Thus, a change in clinical practice patterns likely requires evidence from clinical studies demonstrating equivalence of CT to ICA for guiding medical management. Developments, however, are swift, and CT technology is catching up on its invasive counterpart.
The myocardial bridge: incidence, diagnosis, and prognosis of a pathology of uncertain clinical significance
Authors: Santucci Andrea , Jacoangeli Francesca , Cavallini Sara , d’Ammando Matteo , de Angelis Francesca , Cavallini Claudio 
Published: November 2022

Abstract
The myocardial bridge (MB) is a common anomaly of the coronary tree, very often clinically silent. The artery typically involved is the left anterior descending in its proximal and/or middle portion. MB can cause ischaemia with various mechanisms, directly proportional to the degree of compression of the intra-myocardial tract, which impairs the coronary flow. It is a dynamic phenomenon that is affected by the adrenergic tone and is therefore often brought by physical exercise. MB, when symptomatic, often begins with angina from exertion; some patients have more severe conditions such as unstable angina or myocardial infarction. Coronary vasospasm related to MB-induced endothelial dysfunction can explain a number of cases that come to observation even with catastrophic pictures such as ventricular fibrillation caused by ischaemia. The diagnostic workup includes the non-invasive study using computed tomography angiography and the invasive study of the haemodynamic impact using pressure and Doppler guides. In symptomatic cases, drug therapy with a beta-blocker is enough to manage angina. When it fails, there is the option of coronary angioplasty or surgical treatment techniques.
Treatment in patients with severe asymptomatic aortic stenosis: is it best not to wait?
Authors: Di Pietro Elena , Frittitta Valentina , Motta Silvia , Strazzieri Orazio , Valvo Roberto , Reddavid Claudia , Costa Giuliano , Tamburino Corrado 
Published: November 2022

Abstract
New insights into the natural history and pathophysiology of patients with aortic stenosis (AS), coupled with the dramatic evolution of transcatheter aortic valve implantation (TAVI), are fuelling intense interest in the management of asymptomatic patients with severe AS. This patient presenting for elective intervention poses a unique challenge. These patients are not traditionally offered surgical aortic valve replacement or TAVI given their lack of symptoms; however, they are at increased risk given the severity of their AS. Furthermore, clinical experience has shown that symptoms can be challenging to ascertain in many sedentary, deconditioned, and/or elderly patients. In addition, evolving data based on imaging and biomarker evidence of adverse ventricular remodelling, hypertrophy, inflammation, or fibrosis may radically transform existing clinical decision paradigms. However, management of asymptomatic severe AS is otherwise controversial and the decision to intervene requires careful assessment of the benefits and risks in an individual patient. Further randomized trials [EARLY TAVI (NCT03042104), AVATAR (NCT02436655), EVOLVED (NCT03094143)] will help determine future recommendations.
Cardiac complications of COVID-19 vaccination: now we know more
Authors: Verdecchia Paolo , Coiro Stefano , Notaristefano Francesco , Santucci Andrea , De Angelis Francesca , D’Ammando Matteo , Angeli Fabio 
Published: November 2022

Abstract
The proliferation of good quality observational studies on the potential adverse effects of COVID-19 vaccination has greatly increased our knowledge on myocarditis and pericarditis, and also, more recently, on arterial hypertension. According to some recent studies, the incidence of a significant increase in blood pressure after COVID-19 vaccination is about 3.2% (95% CI: 1.62–6.21). The incidence of serious hypertensive emergencies or stage III hypertension has been reported as 0.6%. It is well known that the ‘spike protein’ of the Sars-CoV-2 virus, the synthesis of which is induced by vaccines, binds to ACE2 receptors, inducing their migration towards the inside of the cell. This would result in a lack of ACE2 activity on cell surfaces and therefore a relative deficiency of angiotensin1-7 with a relative excess of angiotensin II, which could explain, at least in part, the blood pressure increases. Regarding myo-pericarditis, there is evidence that the advantages of COVID-19 vaccination over non-vaccination remain preponderant in terms of prevented hospitalizations and serious complications of COVID-19, compared with the risk of developing myocarditis. In the age group most at risk of COVID-19 vaccine myocarditis (12–29 years), for every 100 000 vaccinated, compared to about four more cases of myocarditis we have 56 fewer hospitalizations, 13.8 admissions to intensive care and 0.6 fewer deaths. Several studies have shown that post vaccine myocarditis/pericarditis are generally short-lasting phenomena with favourable clinically course.
The treatment of amyloidosis is being refined
Authors: Cantone Anna , Sanguettoli Federico , Dal Passo Beatrice , Serenelli Matteo , Rapezzi Claudio 
Published: November 2022

AbstractThe therapy of transthyretin (TTR)-related cardiac amyloidosis consists, on the one hand, of the prevention and management of complications (supportive therapy) and on the other of treatments aimed at interrupting or slowing down the production and deposition of fibrils (disease-modifying therapy). This definition includes drugs that act on different phases of amyloidogenesis: (i) silencing of the gene encoding TTR (small interfering RNA: patisiran, vutrisiran; antisense oligonucleotides: inotersen, eplontersen; new CRISPR Cas-9 drug technology for editing in vivo DNA); (ii) stabilization of circulating TTR to inhibit its dissociation and subsequent assembly of the resulting monomers in amyloidotic fibrils (tafamidis, acoramidis, and tolcapone); (iii) destruction and re-absorption of already formed amyloid tissue deposits. Drugs related to the latter strategy (antibodies) are still the subject of Phase 1 or 2 studies.
The cohesin complex of yeasts: sister chromatid cohesion and beyond
Authors: Choudhary Karan , Kupiec Martin 
Published: November 2022

AbstractEach time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
Seismic wavefield reconstruction based on compressed sensing using data-driven reduced-order model
Authors: Nagata T , Nakai K , Yamada K , Saito Y , Nonomura T , Kano M , Ito S , Nagao H 
Published: November 2022

SUMMARYReconstruction of the distribution of ground motion due to an earthquake is one of the key technologies for the prediction of seismic damage to infrastructure. Particularly, the immediate reconstruction of the spatially continuous wavefield is valuable for decision-making of disaster response decisions in the initial phase. For a fast and accurate reconstruction, utilization of prior information is essential. In fluid mechanics, full-state recovery, which recovers the full state from sparse observation using a data-driven model reduced-order model, is actively used. In this study, the framework developed in the field of fluid mechanics is applied to seismic wavefield reconstruction. A seismic wavefield reconstruction framework based on compressed sensing using the data-driven reduced-order model (ROM) is proposed and its characteristics are investigated through numerical experiments. The data-driven ROM is generated from the data set of the wavefield using the singular value decomposition. The spatially continuous seismic wavefield is reconstructed from the sparse and discrete observation and the data-driven ROM. The observation sites used for reconstruction are effectively selected by the sensor optimization method for linear inverse problems based on a greedy algorithm. The proposed framework was applied to simulation data of theoretical waveform with the subsurface structure of the horizontally stratified three layers. The validity of the proposed method was confirmed by the reconstruction based on the noise-free observation. Since the ROM of the wavefield is used as prior information, the reconstruction error is reduced to an approximately lower error bound of the present framework, even though the number of sensors used for reconstruction is limited and randomly selected. In addition, the reconstruction error obtained by the proposed framework is much smaller than that obtained by the Gaussian process regression. For the numerical experiment with noise-contaminated observation, the reconstructed wavefield is degraded due to the observation noise, but the reconstruction error obtained by the present framework with all available observation sites is close to a lower error bound, even though the reconstructed wavefield using the Gaussian process regression is fully collapsed. Although the reconstruction error is larger than that obtained using all observation sites, the number of observation sites used for reconstruction can be reduced while minimizing the deterioration and scatter of the reconstructed data by combining it with the sensor optimization method. Hence, a better and more stable reconstruction of the wavefield than randomly selected observation sites can be realized, even if the reconstruction is carried out with a smaller number of observations with observation noise, by combining it with the sensor optimization method.