bluuebunny/crossref_metadata_2025_split huggingface dataset:
From the origin of life to pandemics: emergent phenomena in complex systems
Authors: Artime Oriol , De Domenico Manlio 
Published: May 2022

When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This non-trivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems—from physical to biological and social—and is often related to collective behaviour. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems’ emergent properties, central theoretical questions to the study of emergence remain unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the theme issueEmergent phenomena in complex physical and socio-technical systems: from cells to societies, where we provide a synthesis of the contents tackled in the issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases.This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.
Emergent entanglement structures and self-similarity in quantum spin chains
Authors: Sokolov Boris , Rossi Matteo A. C. , García-Pérez Guillermo , Maniscalco Sabrina 
Published: May 2022

We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localized communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding and description of new physical phenomena even in models studied for decades.This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.
The ergodicity solution of the cooperation puzzle
Authors: Peters Ole , Adamou Alexander 
Published: May 2022

When two entities cooperate by sharing resources, one relinquishes something of value to the other. This apparent altruism is frequently observed in nature. Why? Classical treatments assume circumstances where combining resources creates an immediate benefit, e.g. through complementarity or thresholds. Here we ask whether cooperation is predictable without such circumstances. We study a model in which resources self-multiply with fluctuations, a null model of a range of phenomena from viral spread to financial investment. Two fundamental growth rates exist: the ensemble-average growth rate, achieved by the average resources of a large population; and the time-average growth rate, achieved by individual resources over a long time. As a consequence of non-ergodicity, the latter is lower than the former by a term which depends on fluctuation size. Repeated pooling and sharing of resources reduces the effective size of fluctuations and increases the time-average growth rate, which approaches the ensemble-average growth rate in the many-cooperator limit. Therefore, cooperation is advantageous in our model for the simple reason that those who do it grow faster than those who do not. We offer this as a candidate explanation for observed cooperation in rudimentary environments, and as a behavioural baseline for cooperation more generally.
This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.
Hybrid social learning in human-algorithm cultural transmission
Authors: Brinkmann L. , Gezerli D. , Kleist K. V. , Müller T. F. , Rahwan I. , Pescetelli N. 
Published: May 2022

Humans are impressive social learners. Researchers of cultural evolution have studied the many biases shaping cultural transmission by selecting who we copy from and what we copy. One hypothesis is that with the advent of superhuman algorithms a hybrid type of cultural transmission, namely from algorithms to humans, may have long-lasting effects on human culture. We suggest that algorithms might show (either by learning or by design) different behaviours, biases and problem-solving abilities than their human counterparts. In turn, algorithmic-human hybrid problem solving could foster better decisions in environments where diversity in problem-solving strategies is beneficial. This study asks whether algorithms with complementary biases to humans can boost performance in a carefully controlled planning task, and whether humans further transmit algorithmic behaviours to other humans. We conducted a large behavioural study and an agent-based simulation to test the performance of transmission chains with human and algorithmic players. We show that the algorithm boosts the performance of immediately following participants but this gain is quickly lost for participants further down the chain. Our findings suggest that algorithms can improve performance, but human bias may hinder algorithmic solutions from being preserved.
This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.
Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-month recovery of COVID-19
Authors: Yin Ying , Liu Xiao-zhao , Tian Qing , Fan Yi-xian , Ye Zhen , Meng Tian-qing , Wei Gong-hong , Xiong Cheng-liang , Li Honggang , He Ximiao , Zhou Li-quan 
Published: May 2022

ABSTRACTComprehensive analyses showed that SARS-CoV-2 infection caused COVID-19 and induced strong immune responses and sometimes severe illnesses. However, cellular features of recovered patients and long-term health consequences remain largely unexplored. In this study, we collected peripheral blood samples from recovered COVID-19 patients (average age of 35.7 years old) from Hubei province, China, 3 months after discharge; and carried out RNA-seq and whole-genome bisulfite sequencing (WGBS) to identify hallmarks of recovered COVID-19 patients. Our analyses showed significant changes both in expression and DNA methylation of genes and transposable elements (TEs) in recovered COVID-19 patients. We identified 639 misregulated genes and 18516 differentially methylated regions (DMRs) in total. Genes with aberrant expression and DMRs were found to be associated with immune responses and other related biological processes, implicating prolonged overreaction of the immune system in response to SARS-CoV-2 infection. Notably, a significant amount of TEs were aberrantly activated and TE activation was positively correlated with COVID-19 severity. Moreover, differentially methylated TEs may regulate adjacent gene expression as regulatory elements. Those identified transcriptomic and epigenomic signatures define and drive the features of recovered COVID-19 patients, helping determine the risks of long COVID-19, and providing guidance for clinical intervention.
Revisiting IgG antibody reactivity to Epstein-Barr virus in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and its potential application to disease diagnosis
Authors: Sepúlveda Nuno , Malato João , Sotzny Franziska , Grabowska Anna D , Fonseca André , Cordeiro Clara , Graça Luís , Biecek Przemyslaw , Behrends Uta , Mautner Josef , Westermeier Francisco , Lacerda Eliana M , Scheibenbogen Carmen 
Published: May 2022

AbstractInfections by the Epstein-Barr virus (EBV) are often at the disease onset of patients suffering from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). However, serological analyses of these infections remain inconclusive when comparing patients with healthy controls. In particular, it is unclear if certain EBV-derived antigens eliciting antibody responses have a biomarker potential for disease diagnosis. With this purpose, we re-analysed a previously published microarray data on the IgG antibody responses against 3,054 EBV-related antigens in 92 patients with ME/CFS and 50 HCs. This re-analysis consisted of constructing different regression models for binary outcomes with the ability to classify patients and HCs. In these models, we tested for a possible interaction of different antibodies with age and gender. When analyzing the whole data set, there were no antibody responses that could be used to distinguish patients from healthy controls. A similar finding was obtained when comparing patients with noninfectious or unknown disease trigger to healthy controls. However, when data analysis was restricted to the comparison between HCs and patients with a putative infection at disease onset, we could identify stronger antibody responses against two candidate antigens (EBNA4_0529 and EBNA6_0070). Using antibody responses to these two antigens together with age and gender, the final classification model had an estimated sensitivity and specificity of 0.833 and 0.720, respectively. This reliable case-control discrimination suggested the use of the antibody levels related to these candidate viral epitopes as biomarkers for disease diagnosis in this subgroup of patients. When a bioinformatic analysis was performed on these epitopes, it revealed a potential molecular mimicry with several human proteins. To confirm these promising findings, a follow-up study will be conducted in a separate cohort of patients.
Coronavirus and incomes: the COVID-19 pandemic dynamics in Africa in February 2022
Authors: Nesteruk Igor , Rodionov Oleksii 
Published: May 2022

ABSTRACTThe relative accumulated and daily characteristics of the COVID-19 pandemic dynamics in Africa were used to find links with the gross domestic product per capita (GDP), percentages of fully vaccinated people and daily numbers of tests per case. A simple statistical analysis of datasets corresponding to February 1, 2022 showed that accumulated and daily numbers of cases per capita, daily numbers of deaths per capita and vaccination levels increase with the increase of GDP. As in the case of Europe, the smoothed daily numbers of new cases per capita in Africa increase with the increasing of the vaccination level. But the increase of the accumulated numbers of cases and daily number of deaths with increasing the vaccination level was revealed in Africa. In comparison with Europe, no significant correlation was revealed between the vaccination level and the number of deaths per case. As in the case of Europe, African countries demonstrate no statistically significant links between the pandemic dynamics characteristics and the daily number of tests per case. It looks that countries with very small GDP are less affected by the COVID-19 pandemic. The cause of this phenomenon requires further research, but it is possible that low incomes limit the mobility of the population and reduce the number of contacts with infected people. In order to overcome the pandemic, quarantine measures and social distance should not be neglected (this also applies to countries with a high level of income and vaccination).
Anti SARS-CoV2 seroprevalence in Zanzibar in 2021 before the Omicron wave
Authors: Salum Salum Seif , Sheikh Mohammed Ali , Hebestreit Antje , Kelm Sørge 
Published: May 2022

AbstractObjectivesFor Tanzania including Zanzibar, the development of the COVID-19 pandemic has remained unclear, since reporting cases was suspended during 2020/21. The present study provides first data on the COVID-19 seroprevalence among Zanzibari before the omicron variant wave starting in late 2021.DesignDuring August through October 2021 representative cross-sectional data were collected from randomly selected households in 120 wards of the two main islands, Unguja and Pemba. Participants voluntarily provided blood samples to test their sera for antibodies against SARS-CoV2 in a semiquantitative enzyme-linked immunosorbent assay (ELISA).Results58.9% of the 2051 sera analysed were positive without significant differences between Unguja and Pemba or between rural and urban areas, similar to observations from other sub-Saharan Africa countries.ConclusionsThe antibody levels observed are most likely to previous infections with SARS-CoV2, since vaccination was basically not available before the survey. Therefore, this study provides first insight, how many Zanzibari have had COVID-19 before the Omicron variant. Further, it provides the appropriate basis for a follow-up survey addressing how this seroprevalence influenced the susceptibility to the Omicron variants, given harmonised methodologies are used.
Antibody response and intra-host viral evolution after plasma therapy in COVID-19 patients pre-exposed or not to B-cell depleting agents
Authors: Gachoud David , Pillonel Trestan , Gerasimos Tsilimidos , Battola Dunia , Dumas Dominique , Opota Onya , Fontana Stefano , Vollenweider Peter , Manuel Oriol , Greub Gilbert , Bertelli Claire , Rufer Nathalie 
Published: May 2022

ABSTRACTBackgroundAdministration of plasma therapy may contribute to viral control and survival of COVID-19 patients receiving B-cell depleting agents that hinder the endogenous humoral response. However, little is known on the impact of anti-CD20 pre-exposition and the use of different sources of plasma (convalescent versus vaccinated) on the kinetics of SARS-CoV-2-specific antibodies and viral evolution after plasma therapy.MethodsEligible COVID-19 patients (n = 36), half of them after anti-CD20 targeted therapy, were treated with therapeutic plasma from convalescent (n = 17) or mRNA-vaccinated (n = 19) donors. Each plasma-transfused patient was thoroughly monitored over time by anti-S IgG quantification and whole-genome SARS-CoV-2 sequencing.ResultsThe majority of anti-CD20 pre-exposed patients (15/18) showed progressive declines of anti-S protein IgG titers following plasma therapy, indicating that they mostly relied on the passive transfer of anti-SARS-CoV-2 antibodies. Such antibody kinetics correlated with prolonged infection before virus clearance, contrasting with the endogenous humoral response predominantly present in patients who had not received B-cell depleting agents (15/18). No relevant differences were observed between patients treated with plasma from convalescent and/or vaccinated donors. Finally, 4/30 genotyped patients showed increased intra-host viral evolution and 3/30 included 1 to 4 spike mutations, potentially associated to immune escape.ConclusionsConvalescent and/or vaccinated plasma therapy may provide anti-SARS-CoV-2 antibodies and clinical benefit to B-cell depleted COVID-19 patients. Only a limited number of patients acquired viral mutations prior to clinical recovery, yet our study further emphasizes the need for long-term surveillance for intra-host variant evolution, to guide best therapeutic strategies.
Hospitalized patients with severe COVID-19 during the Omicron wave in Israel - benefits of a fourth vaccine dose
Authors: Brosh-Nissimov Tal , Hussein Khetam , Wiener-Well Yonit , Orenbuch-Harroch Efrat , Elbaz Meital , Lipman-Arens Shelly , Maor Yasmin , Yagel Yael , Chazan Bibiana , Hershman-Sarafov Mirit , Rahav Galia , Zimhony Oren , Shimshovitz Adi Zaidman , Chowers Michal 
Published: May 2022

AbstractImportanceWaning immunity against COVID-19 in parallel with an increased incidence during the Omicron outbreak led the Israeli Ministry of Health to recommend a second booster dose of BNT162b2 (Pfizer) to high-risk individuals. Israel was the first country to recommend this, allowing evaluation of the added protection of a fourth vaccine dose to hospitalized patients with severe diseases.ObjectiveTo assess the effect of a fourth dose for hospitalized patients with severe/critical breakthrough COVID-19.DesignA cohort study of hospitalized adults from 01/15/2022–01/31/2022.SettingsA multi-center study of 14 medical centers in Israel.ParticipantsHospitalized adult patients with PCR-confirmed severe/critical COVID-19. Excluded were patients lacking data on vaccination status.ExposureCases were divided according to the total number of vaccine doses received up to 7 days before diagnosis. Unvaccinated adults and single-dose recipients were grouped into an unvaccinated group.Main OutcomeA composite of mechanical-ventilation or in-hospital death was defined as poor outcome. Outcomes were compared between 3- and 4-dose vaccinees.ResultsIncluded were 1,049 patients with severe/critical COVID-19, median age 80 (IQR 69-87), 51% males. Among them, 360 unvaccinated, 34, 172, 386 and 88 were after 1, 2, 3 or 4 doses, respectively. Patients after 3 doses were older, had more males and immunosuppression, but with similar outcomes, 49% vs. 51% compared to unvaccinated patients (p=0.72). Patients after 4 doses were similarly older and immunosuppressed, but had improved outcomes compared to unvaccinated patients, 34% vs. 51% (p<0.01). We proceeded to examine independent predictors for poor outcome in fully-vaccinated patients with either 3 doses given a median of 161 (IQR 147-168) days earlier, or 4 doses given a median of 14 (IQR 10-18) days before diagnoses. Receipt of the fourth dose conferred significant protection: OR 0.51 (95%CI 0.30.87).Conclusion and RelevanceWithin a population of hospitalized patients with severe/critical breakthrough COVID-19, a recent fourth dose was associated with significant protection against mechanical ventilation or death, compared to fully vaccinated single-boosted individuals.Key pointsQuestionWhat is the benefit of a fourth vaccine dose (second booster) for hospitalized patients with severe COVID-19?FindingsIn this multicenter cohort study in Israel during the Omicron wave, hospitalized severe COVID-19 patients that received a recent fourth dose had a 49% lower odds for a poor outcome (mechanical ventilation or death) compared with those who received 3 doses approximately 5 months before diagnosis, a significant difference.MeaningA vaccine booster given at the onset of a COVID-19 wave can benefit vulnerable individuals.
Effectiveness of oral aciclovir in preventing maternal chickenpox: A comparison with VZIG
Authors: Sile Bersabeh , Brown Kevin E , Gower Charlotte , Bosowski Johanna , Dennis Amanda , Falconer Michelle , Stowe Julia , Amirthalingam Gayatri 
Published: May 2022

AbstractObjectivesAlthough often presenting as a self-limiting childhood disease, chickenpox can have serious consequences if acquired in pregnancy. The UK recommendations are that varicella immunoglobulin (VZIG) is administered intramuscularly to susceptible pregnant women exposed to chickenpox prior to 20 weeks gestation. Oral aciclovir or VZIG is recommended if exposure occurs at 20+ weeks gestation. Our objective was to compare the effectiveness of oral aciclovir to VZIG in preventing maternal and neonatal chickenpox.MethodsWe identified and followed up 186 pregnant women who were exposed to chickenpox and compared their outcomes.Results171/186 (91.9%) of these women received either VZIG or oral aciclovir. 53 of the 145 (36.6%) women who received VZIG went on to develop chickenpox compared to 8 of the 26 (30.8%) women who received oral aciclovir (p=0.32). No statistical difference was found between the oral aciclovir and VZIG groups even after controlling for maternal age, gestational stage, type of exposure and IgG titre (adjusted OR:0.83; 95%CI:0.26-2.65; p=0.751).ConclusionsThese findings support the use of oral aciclovir as first-line prophylaxis in pregnant women exposed at 20+ weeks, (and possibly second-line <20 weeks) as they suggest its effectiveness at preventing maternal chickenpox is either better or equal to VZIG.
Escape of SARS-CoV-2 variant Omicron to mucosal immunity in vaccinated subjects
Authors: Martinuzzi Emanuela , Boutros Jacques , Benzaquen Jonathan , Glaichenhaus Nicolas , Hofman Paul , Marquette Charles Hugo 
Published: May 2022

AbstractOmicron s escape to vaccine-induced systemic antibody responses has been shown in several studies in Omicron-infected patients and vaccine controls.In the present study we compared mucosal antibody response to Omicron to mucosal antibody response to ancestral strain and Delta variant. This was done on nasal epithelial lining fluid (NELF) prospectively collected in 84 otherwise healthy healthcare workers who had never exhibited PCR-documented COVID-19 and had received three doses of the Pfizer-BioNTech COVID-19 mRNA vaccine. NELF was collected prior to Omicron detection in the geographical area of inclusion.We show that NELF antibodies from vaccinated individuals were less efficient at inhibiting the binding of the Omicron Spike protein to ACE-2 compared to those of Delta or the ancestral strain.These findings may explain the increased risk of onward transmission of Omicron, consistent with its successful global displacement of Delta in countries with a high vaccination coverage.
Use of c-peptide as a measure of cephalic phase insulin release in humans
Authors: Pullicin Alexa J. , Newsom Sean A. , Robinson Matthew M. , Lim Juyun 
Published: May 2022

AbstractCephalic phase insulin release (CPIR) is a rapid pulse of insulin secreted within minutes of food-related sensory stimulation. Understanding the mechanisms underlying CPIR in humans has been hindered by its small observed effect size and high variability within and between studies. One contributing factor to these limitations may be the use of peripherally measured insulin as an indicator of secreted insulin, since a substantial portion of insulin is metabolized by the liver before delivery to peripheral circulation. Here, we investigated the use of c-peptide, which is co-secreted in equimolar amounts to insulin from pancreatic beta cells, as a proxy for insulin secretion during the cephalic phase period. Changes in insulin and c-peptide were monitored in 18 adults over two repeated sessions following oral stimulation with a sucrose-containing gelatin stimulus. We found that on average, insulin and c-peptide release followed a similar time course over the cephalic phase period, but that c-peptide showed a greater effect size. Importantly, when insulin and c-peptide concentrations were compared across sessions, we found that changes in c-peptide were significantly correlated at the 2 minute (r = 0.50, p = 0.03) and 4 minute (r = 0.65, p = 0.003) time points, as well as when individuals’ peak c-peptide concentrations were considered (r = 0.64, p = 0.004). In contrast, no significant correlations were observed for changes in insulin measured from the sessions (r = −0.06-0.35, p < 0.05). Herein, we detail the individual variability of insulin and c-peptide release during the cephalic phase period, and discuss why c-peptide may be a more appropriate metric to represent insulin secretion.