Complex network analysis of arboviruses in the same geographic domain: Differences and similarities.

Arbovirus can cause diseases with a broad spectrum from mild to severe and long-lasting symptoms, affecting humans worldwide and therefore considered a public health problem with global and diverse socio-economic impacts. Understanding how they spread within and across different regions is necessary to devise strategies to control and prevent new outbreaks. Complex network approaches have widespread use to get important insights on several phenomena, as the spread of these viruses within a given region. This work uses the motif-synchronization methodology to build time varying complex networks based on data of registered infections caused by Zika, chikungunya, and dengue virus from 2014 to 2020, in 417 cities of the state of Bahia, Brazil. The resulting network sets capture new information on the spread of the diseases that are related to the time delay in the synchronization of the time series among different municipalities. Thus the work adds new and important network-based insights to previous results based on dengue dataset in the period 2001-2016. The most frequent synchronization delay time between time series in different cities, which control the insertion of edges in the networks, ranges 7 to 14 days, a period that is compatible with the time of the individual-mosquito-individual transmission cycle of these diseases. As the used data covers the initial periods of the first Zika and chikungunya outbreaks, our analyses reveal an increasing monotonic dependence between distance among cities and the time delay for synchronization between the corresponding time series. The same behavior was not observed for dengue, first reported in the region back in 1986, either in the previously 2001-2016 based results or in the current work. These results show that, as the number of outbreaks accumulates, different strategies must be adopted to combat the dissemination of arbovirus infections.

Biosaline agriculture: an agronomic proposal for onion (Allium cepa L.) production.

NOVELTY STATEMENT: The onion crop with brackish irrigation but accompanied by halophytes is productive, so halophytoremediation is an excellent agronomic proposal for areas where there is poor quality water used for irrigation.

Optimized second-generation CRY2-CIB dimerizers and photoactivatable Cre recombinase.

Arabidopsis thaliana cryptochrome 2 (AtCRY2), a light-sensitive photosensory protein, was previously adapted for use in controlling protein-protein interactions through light-dependent binding to a partner protein, CIB1. While the existing CRY2-CIB dimerization system has been used extensively for optogenetic applications, some limitations exist. Here, we set out to optimize function of the CRY2-CIB system by identifying versions of CRY2-CIB that are smaller, show reduced dark interaction, and maintain longer or shorter signaling states in response to a pulse of light. We describe minimal functional CRY2 and CIB1 domains maintaining light-dependent interaction and new signaling mutations affecting AtCRY2 photocycle kinetics. The latter work implicates an α13-α14 turn motif within plant CRYs whose perturbation alters signaling-state lifetime. Using a long-lived L348F photocycle mutant, we engineered a second-generation photoactivatable Cre recombinase, PA-Cre2.0, that shows five-fold improved dynamic range, allowing robust recombination following exposure to a single, brief pulse of light.

Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma.

Melanoma and other cancers harbor oncogenic mutations in the protein kinase B-Raf, which leads to constitutive activation and dysregulation of MAP kinase signaling. In order to elucidate molecular determinants responsible for B-Raf control of cancer phenotypes, we present a method for phosphoprotein profiling, using negative ionization mass spectrometry to detect phosphopeptides based on their fragment ion signature caused by release of PO(3)(-). The method provides an alternative strategy for phosphoproteomics, circumventing affinity enrichment of phosphopeptides and isotopic labeling of samples. Ninety phosphorylation events were regulated by oncogenic B-Raf signaling, based on their responses to treating melanoma cells with MKK1/2 inhibitor. Regulated phosphoproteins included known signaling effectors and cytoskeletal regulators. We investigated MINERVA/FAM129B, a target belonging to a protein family with unknown category and function, and established the importance of this protein and its MAP kinase-dependent phosphorylation in controlling melanoma cell invasion into three-dimensional collagen matrix.

An agent-based model for studying the temperature changes on environments exposed to magnetic fluid hyperthermia.

Magnetic fluid hyperthermia (MFH) is a technique whose results show promise in the treatment against cancer, but which still faces obstacles such as controlling the spatial distribution of temperature. The present study developed an agent-based model in order to simulate the temperature changes in an aqueous environment submitted to the magnetic fluid hyperthermia technique. The developed model was built with its parameters based on the clinical treatment protocol for glioblastoma multiforme (GBM). Using thermodynamic properties of magnetic fluid and tissues, we define a specific thermal parameter (α) and evaluate its influence, together with the intensity of the external magnetic field (H), on the dynamics of the temperature of the cancer environment. The temperature evolution generated by the model was in accordance with experimental results known from the subject literature. The parameters evaluation indicates that the temperature stabilization of the tumor environment during MFH treatment is due to the local interactions of energy diffusion, as well as indicating that the α-parameter is a key factor for controlling the temperature and heating speed.

Activation of the IKK2/NF-κB pathway in VSMCs inhibits calcified vascular stiffness in CKD.

IKK2/NF-κB pathway-mediated inflammation in vascular smooth muscle cells (VSMCs) has been proposed to be an etiologic factor in medial calcification and stiffness. However, the role of the IKK2/NF-κB pathway in medial calcification remains to be elucidated. In this study, we found that chronic kidney disease (CKD) induces inflammatory pathways through the local activation of the IKK2/NF-κB pathway in VMSCs associated with calcified vascular stiffness. Despite reducing the expression of inflammatory mediators, complete inhibition of the IKK2/NF-κB pathway in vitro and in vivo unexpectedly exacerbated vascular mineralization and stiffness. In contrast, activation of NF-κB by SMC-specific IκBα deficiency attenuated calcified vascular stiffness in CKD. Inhibition of the IKK2/NF-κB pathway induced cell death of VSMCs by reducing anti-cell death gene expression, whereas activation of NF-κB reduced CKD-dependent vascular cell death. In addition, increased calcification of extracellular vesicles through the inhibition of the IKK2/NF-κB pathway induced mineralization of VSMCs, which was significantly reduced by blocking cell death in vitro and in vivo. This study reveals that activation of the IKK2/NF-κB pathway in VSMCs plays a protective role in CKD-dependent calcified vascular stiffness by reducing the release of apoptotic calcifying extracellular vesicles.

Modularity map of the network of human cell differentiation.

Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified. Alternatively, a large-scale approach in search of different organizational features of the growth stages promises to reveal its modular global structure with the goal of discovering previously unknown relations between cell types. Here, we sort and analyze a large set of scattered data to construct the network of human cell differentiation (NHCD) based on cell types (nodes) and differentiation steps (links) from the fertilized egg to a developed human. We discover a dynamical law of critical branching that reveals a self-similar regularity in the modular organization of the network, and allows us to observe the network at different scales. The emerging picture clearly identifies clusters of cell types following a hierarchical organization, ranging from sub-modules to super-modules of specialized tissues and organs on varying scales. This discovery will allow one to treat the development of a particular cell function in the context of the complex network of human development as a whole. Our results point to an integrated large-scale view of the network of cell types systematically revealing ties between previously unrelated domains in organ functions.

Tonic pain reduces autonomic responses and EEG functional connectivity elicited by affective stimuli.

Most pain studies have focused on only two aspects of pain: the influence of pain on attentional processing and the modulation of pain perception by affective stimuli. However, the influence of tonic pain on the attentional processing of affective stimuli has not been studied. In this study, we investigated the effects of tonic pain on the attentional processing of affective stimuli, focusing on autonomic responses and their relationship with both EEG power and functional connectivity. Forty participants (20 men and 20 women) received tonically painful and nonpainful thermal stimulation while viewing blocks of pleasant, unpleasant, or neutral images. The galvanic skin conductance response (SCR), electrocardiographic activity, and electroencephalographic (EEG) activity in the delta and theta bands were recorded. Participants rated the unpleasantness of the pain at the end of each block. Typical affective SCR and heart rate (HR) patterns were found in the no-pain condition, but when the pain was delivered, these patterns disappeared. EEG power and functional connectivity results showed that tonic pain affected the delta band in the central region during pleasant and unpleasant image blocks. Our findings suggest that tonic pain captured attentional focus and reduced the cognitive resources available for processing affective stimuli, altering the emotional experience associated with pain.

Modulation of Gap Junction Coupling Within the Islet of Langerhans During the Development of Type 1 Diabetes.

In type 1 diabetes (T1D), islet dysfunction occurs prior to diabetes onset. Pro-inflammatory cytokines can disrupt insulin secretion and Ca2+ homeostasis. Connexin36 (Cx36) gap junctions electrically couple ß-cells to coordinate glucose-stimulated Ca2+ and insulin secretion. Cx36 gap junction coupling can also protect against cytokine-induced apoptosis. Our goal was to determine how islet gap junction coupling and Ca2+ dynamics are altered in mouse models of T1D prior to diabetes. Glucose tolerance was assessed in NOD and immunodeficient NOD-RAG1KO mice at 6-12 weeks age. Glucose-stimulated insulin secretion, Ca2+ dynamics, and gap junction coupling were measured in islets isolated at each age. Gap junction coupling was also measured in islets from mice that underwent transfer of diabetogenic splenocytes and from chromograninA knockout NOD mice. Cell death was measured in islets isolated from wild-type, Cx36 knockout or Cx36 over-expression mice, each treated with a cocktail of pro-inflammatory cytokines and KATP or SERCA activators/inhibitors. NOD mice over-expressing Cx36 were also monitored for diabetes development, and islets assessed for insulitis and apoptosis. NOD and NOD-RAG1KO controls showed similar glucose tolerance at all ages. Ca2+ dynamics and gap junction coupling were disrupted in islets of NOD mice at 9 weeks, compared to controls. Transfer of diabetogenic splenocytes also decreased gap junction coupling. Islets from chromograninA knockout mice displayed normal coupling. Overexpression of Cx36 protected islets from cytokine-induced apoptosis. A knockout of Cx36 amplified cytokine-induced apoptosis, which was reversed by KATP activation or SERCA activation. Cx36 overexpression in NOD mice delayed diabetes development compared to NOD controls. However, apoptosis and insulitis were not improved. Decreases in islet gap junction coupling occur prior to T1D onset. Such decreases alter islet susceptibility to apoptosis due to altered Ca2+. Future studies will determine if increasing Cx36 gap junction coupling in combination with restoring Ca2+ homeostasis protects against islet decline in T1D.

Dynamic changes in ß-cell [Ca2+] regulate NFAT activation, gene transcription, and islet gap junction communication.

OBJECTIVE: Diabetes occurs because of insufficient insulin secretion due to ß-cell dysfunction within the islet of Langerhans. Elevated glucose levels trigger ß-cell membrane depolarization, action potential generation, and slow sustained free-Ca2+ ([Ca2+]) oscillations, which trigger insulin release. Nuclear factor of activated T-cell (NFAT) is a transcription factor, which is regulated by the increases in [Ca2+] and calceineurin (CaN) activation. NFAT regulation links cell activity with gene transcription in many systems and regulates proliferation and insulin granule biogenesis within the ß-cell. However, the link between the regulation of ß-cell electrical activity and oscillatory [Ca2+] dynamics with NFAT activation and downstream transcription is poorly understood. Here, we tested whether dynamic changes to ß-cell electrical activity and [Ca2+] regulate NFAT activation and downstream transcription. METHODS: In cell lines, mouse islets, and human islets, including those from donors with type 2 diabetes, we applied both agonists/antagonists of ion channels together with optogenetics to modulate ß-cell electrical activity. We measured the dynamics of [Ca2+] and NFAT activation as well as performed whole transcriptome and functional analyses. RESULTS: Both glucose-induced membrane depolarization and optogenetic stimulation triggered NFAT activation as well as increased the transcription of NFAT targets and intermediate early genes (IEGs). Importantly, slow, sustained [Ca2+] oscillation conditions led to NFAT activation and downstream transcription. In contrast, in human islets from donors with type2 diabetes, NFAT activation by glucose was diminished, but rescued upon pharmacological stimulation of electrical activity. NFAT activation regulated GJD2 expression and increased Cx36 gap junction permeability upon elevated oscillatory [Ca2+] dynamics. However, it is unclear if NFAT directly binds the GJD2 gene to regulate expression. CONCLUSIONS: This study provides an insight into the specific patterns of electrical activity that regulate NFAT activation, gene transcription, and islet function. In addition, it provides information on how these factors are disrupted in diabetes.

Qigong Training Positively Impacts Both Posture and Mood in Breast Cancer Survivors With Persistent Post-surgical Pain: Support for an Embodied Cognition Paradigm.

Theories of embodied cognition hypothesize interdependencies between psychological well-being and physical posture. The purpose of this study was to assess the feasibility of objectively measuring posture, and to explore the relationship between posture and affect and other patient centered outcomes in breast cancer survivors (BCS) with persistent postsurgical pain (PPSP) over a 12-week course of therapeutic Qigong mind-body training. Twenty-one BCS with PPSP attended group Qigong training. Clinical outcomes were pain, fatigue, self-esteem, anxiety, depression, stress and exercise self-efficacy. Posture outcomes were vertical spine and vertical head angles in the sagittal plane, measured with a 3D motion capture system in three conditions: eyes open (EO), eyes open relaxed (EOR) and eyes closed (EC). Assessments were made before and after the Qigong training. The association between categorical variables (angle and mood) was measured by Cramer's V. In the EO condition, most participants who improved in fatigue and anxiety scales also had better vertical head values. For the EOR condition, a moderate correlation was observed between changes in vertical head angle and changes in fatigue scale. In the EC condition, most of the participants who improved in measures of fatigue also improved vertical head angle. Additionally, pain severity decreased while vertical spine angle improved. These preliminary findings support that emotion and other patient centered outcomes should be considered within an embodied framework, and that Qigong may be a promising intervention for addressing biopsychosocially complex interventions such as PPSP in BCSs.

Zinc transporter 8 haploinsufficiency protects against beta cell dysfunction in type 1 diabetes by increasing mitochondrial respiration.

OBJECTIVE: Zinc transporter 8 (ZnT8) is a major humoral target in human type 1 diabetes (T1D). Polymorphic variants of Slc30A8, which encodes ZnT8, are also associated with protection from type 2 diabetes (T2D). The current study examined whether ZnT8 might play a role beyond simply being a target of autoimmunity in the pathophysiology of T1D. METHODS: The phenotypes of NOD mice with complete or partial global loss of ZnT8 were determined using a combination of disease incidence, histological, transcriptomic, and metabolic analyses. RESULTS: Unexpectedly, while complete loss of ZnT8 accelerated spontaneous T1D, heterozygosity was partially protective. In vivo and in vitro studies of ZnT8 deficient NOD.SCID mice suggested that the accelerated disease was due to more rampant autoimmunity. Conversely, beta cells in heterozygous animals uniquely displayed increased mitochondrial fitness under mild proinflammatory conditions. CONCLUSIONS: In pancreatic beta cells and immune cell populations, Zn2+ plays a key role as a regulator of redox signaling and as an independent secondary messenger. Importantly, Zn2+ also plays a major role in maintaining mitochondrial homeostasis. Our results suggest that regulating mitochondrial fitness by altering intra-islet zinc homeostasis may provide a novel mechanism to modulate T1D pathophysiology.

Synchronized spread of COVID-19 in the cities of Bahia, Brazil.

The COVID-19 pandemic, caused by the highly transmissible SARS-CoV-2 virus, has overloaded health systems in many contexts Conant and Wolfe (2008). Brazil has experienced more than 345,000 deaths, as of April/2021 Conant and Wolfe (2008), with dire consequences for the country's public and private health systems. This paper aims to estimate the synchronization graph between the cities' contagion waves from public COVID-19 data records. For this purpose, the Motif-Synchronization method Magwire et al. (2011) was applied to publicly available COVID-19 data records to determine the sequential relationship of occurrence of the waves among Bahia's cities. We find synchronization between waves of infection between cities, suggesting diffusion of the disease in Bahia and a potential role for inter-city transportation Saba et al. (2018), Saba et al. (2014), Araújo et al. (2018) in the dynamics of this phenomenon McKee and Stuckler (2020), Chinazzi et al. (2020), Tizzoni et al. (2014). Our main contribution lies in the use of the Motif-Synchronization method applied to COVID-19 data records, with the results revealing a pattern of disease spread that extends beyond city boundaries.

A Critical Analysis of the COVID-19 Hospitalization Network in Countries with Limited Resources.

To effectively combat the COVID-19 pandemic, countries with limited resources could only allocate intensive and non-intensive care units to a low number of regions. In this work, we evaluated the actual displacement of infected patients in search of care, aiming to understand how the networks of planned and actual hospitalizations take place. To assess the flow of hospitalizations outside the place of residence, we used the concepts of complex networks. Our findings indicate that the current distribution of health facilities in Bahia, Brazil, is not sufficient to effectively reduce the distances traveled by patients with COVID-19 who require hospitalization. We believe that unnecessary trips to distant hospitals can put both the sick and the healthy involved in the transport process at risk, further delaying the stabilization of the COVID-19 pandemic in each region of the state of Bahia. From the results found, we concluded that, to mitigate this situation, the implementation of health units in countries with limited resources should be based on scientific methods, and international collaborations should be established.

The Therapeutic Effects of Whole-Body Vibration in Patients With Fibromyalgia. A Randomized Controlled Trial.

Fibromyalgia is a chronic pain disease with few effective therapeutic options. We evaluated the efficacy of a 12-weeks therapy program that involves the use of whole body vibration in patients with fibromyalgia. The experimental group (N = 20 patients) participated in a neuromuscular training with a rotational whole body vibration platform for 12 weeks. The control group (N = 20 patients) received no physiotherapy treatment. The following variables were assessed before, after and 3 months after the therapy program: Fibromyalgia impact questionnaire, pain intensity, quality of life, sensitivity measurements (pressure pain thresholds, vibration thresholds), motor function tasks (Berg scale, 6-min walk test, isometric back muscle strength), and static and dynamic balance. We found improvements in the indexes of functional disability, static equilibrium and vibration sensitivity and a reduction of pain sensitivity. Our results showed that the intervention group improved almost all parameters immediately after the therapy program, in contrast to the control group that showed no changes. These improvements were not maintained in the follow-up. The whole body vibration therapy can be an effective therapy in patients with fibromyalgia and it can improve symptomatology and quality of life in these patients.

Investigating extradomiciliary transmission of tuberculosis: An exploratory approach using social network patterns of TB cases and controls and the genotyping of Mycobacterium tuberculosis.

Extradomiciliary contacts have been overlooked in the study of TB transmission due to difficulties in identifying actual contacts in large populations. Complex network analysis provides a framework to model the structure of contacts, specially extradomiciliary ones. We conducted a study of incident sputum-positive TB cases and healthy controls occurring in a moderate TB burden city. Cases and controls were interviewed to obtain data regarding the usual locations of residence, work, study, and leisure. Mycobacterium tuberculosis isolated from sputum was genotyped. The collected data were used to build networks based on a framework of putative social interactions indicating possible TB transmission. A user-friendly open source environment (GraphTube) was setup to extract information from the collected data. Networks based on the likelihood of patient-patient, patient-healthy, and healthy-healthy contacts were setup, depending on a constraint of geographical distance of places attended by the volunteers. Using a threshold for the geographical distance of 300 m, the differences between TB cases and controls are revealed. Several clusters formed by social network nodes with high genotypic similarity were characterized. The developed framework provided consistent results and can be used to support the targeted search of potentially infected individuals and to help to understand the TB transmission.

Integrating Computational Methods to Investigate the Macroecology of Microbiomes.

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.

Fractal and Multifractal Properties of Electrographic Recordings of Human Brain Activity: Toward Its Use as a Signal Feature for Machine Learning in Clinical Applications.

The quantification of brain dynamics is essential to its understanding. However, the brain is a system operating on multiple time scales, and characterization of dynamics across time scales remains a challenge. One framework to study such dynamics is that of fractal geometry; and currently there exist several methods for the study of brain dynamics using fractal geometry. We aim to highlight some of the practical challenges of applying fractal geometry to brain dynamics-and as a putative feature for machine learning applications, and propose solutions to enable its wider use in neuroscience. Using intracranially recorded electroencephalogram (EEG) and simulated data, we compared monofractal and multifractal methods with regards to their sensitivity to signal variance. We found that both monofractal and multifractal properties correlate closely with signal variance, thus not being a useful feature of the signal. However, after applying an epoch-wise standardization procedure to the signal, we found that multifractal measures could offer non-redundant information compared to signal variance, power (in different frequency bands) and other established EEG signal measures. We also compared different multifractal estimation methods to each other in terms of reliability, and we found that the Chhabra-Jensen algorithm performed best. Finally, we investigated the impact of sampling frequency and epoch length on the estimation of multifractal properties. Using epileptic seizures as an example event in the EEG, we show that there may be an optimal time scale (i.e., combination of sampling frequency and epoch length) for detecting temporal changes in multifractal properties around seizures. The practical issues we highlighted and our suggested solutions should help in developing robust methods for the application of fractal geometry in EEG signals. Our analyses and observations also aid the theoretical understanding of the multifractal properties of the brain and might provide grounds for new discoveries in the study of brain signals. These could be crucial for the understanding of neurological function and for the developments of new treatments.

Altered Functional Performance in Patients with Fibromyalgia.

Fibromyalgia is a common chronic pain condition that exerts a considerable impact on patients' daily activities and quality of life. Objectives: The main objective of the present study was to evaluate kinematic parameters of gait, functional performance, and balance in women with fibromyalgia syndrome. Methods: The study included 26 female patients with fibromyalgia (49.2 ± 8.0 years) according to the criteria of the American College of Rheumatology, as well as 16 pain-free women (43.5 ± 8.5 years). Gait and balance parameters were extracted from video recordings of participants performing several motor tasks. Non-linear dynamic of body sway time series was also analyzed by computing the Hurst exponent. In addition, functional performance and clinical pain were obtained by using standardized motor tests (Berg's balance scale, 6-min walking test, timed up and go task, Romberg's balance test) and self-report questionnaires (Fibromyalgia Impact Questionnaire). Results: Walking speed was significantly diminished (p < 0.001) in FM patients as compared to pain-free controls, probably due to significant reductions in stride length (p < 0.001) and cycle frequency (p < 0.001). Analyses of balance also revealed significant differences between fibromyalgia and pain-free controls on body sway in the medial-lateral and anterior-posterior axes (all ps < 0.01). Several parameters of gait and balance were significantly associated with high levels of pain, depression, stiffness, anxiety, and fatigue in fibromyalgia. Conclusion: Our data revealed that both gait and balance were severely impaired in FM, and that subjective complaints associated with FM could contribute to functional disability in these patients. These findings suggest that optimal rehabilitation and fall prevention in fibromyalgia require a comprehensive assessment of both psychological responses to pain and physical impairments during postural control and gait.

Neighborhood properties of complex networks.

A concept of neighborhood in complex networks is addressed based on the criterion of the minimal number of steps to reach other vertices. This amounts to, starting from a given network R1, generating a family of networks Rl, l = 2, 3,... such that, the vertices that are l steps apart in the original R1, are only 1 step apart in Rl. The higher order networks are generated using Boolean operations among the adjacency matrices Ml that represent Rl. The families originated by the well known linear and the Erdös-Renyi networks are found to be invariant, in the sense that the spectra of Ml are the same, up to finite size effects. A further family originated from small world network is identified.