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Gameiro J, Branco T, Lopes JA. Artificial Intelligence in Acute Kidney Injury Risk Prediction. J Clin Med 2020; 9:jcm9030678. [PMID: 32138284 PMCID: PMC7141311 DOI: 10.3390/jcm9030678] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/23/2022] Open
Abstract
Acute kidney injury (AKI) is a frequent complication in hospitalized patients, which is associated with worse short and long-term outcomes. It is crucial to develop methods to identify patients at risk for AKI and to diagnose subclinical AKI in order to improve patient outcomes. The advances in clinical informatics and the increasing availability of electronic medical records have allowed for the development of artificial intelligence predictive models of risk estimation in AKI. In this review, we discussed the progress of AKI risk prediction from risk scores to electronic alerts to machine learning methods.
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Lefler Y, Campagner D, Branco T. The role of the periaqueductal gray in escape behavior. Curr Opin Neurobiol 2019; 60:115-121. [PMID: 31864105 DOI: 10.1016/j.conb.2019.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 02/01/2023]
Abstract
Escape behavior is a defensive action deployed by animals in response to imminent threats. In mammalian species, a variety of different brain circuits are known to participate in this crucial survival behavior. One of these circuits is the periaqueductal gray, a midbrain structure that can command a variety of instinctive behaviors. Recent experiments using modern systems neuroscience techniques have begun to elucidate the specific role of the periaqueductal gray in controlling escape. These have shown that periaqueductal gray neurons are crucial units for gating and commanding the initiation of escape, specifically activated in situations of imminent, escapable threat. In addition, it is becoming clear that the periaqueductal gray integrates brain-wide information that can modulate escape initiation to generate flexible defensive behaviors.
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Ujfalussy BB, Makara JK, Lengyel M, Branco T. Global and Multiplexed Dendritic Computations under In Vivo-like Conditions. Neuron 2019; 100:579-592.e5. [PMID: 30408443 PMCID: PMC6226578 DOI: 10.1016/j.neuron.2018.08.032] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/07/2018] [Accepted: 08/21/2018] [Indexed: 10/27/2022]
Abstract
Dendrites integrate inputs nonlinearly, but it is unclear how these nonlinearities contribute to the overall input-output transformation of single neurons. We developed statistically principled methods using a hierarchical cascade of linear-nonlinear subunits (hLN) to model the dynamically evolving somatic response of neurons receiving complex, in vivo-like spatiotemporal synaptic input patterns. We used the hLN to predict the somatic membrane potential of an in vivo-validated detailed biophysical model of a L2/3 pyramidal cell. Linear input integration with a single global dendritic nonlinearity achieved above 90% prediction accuracy. A novel hLN motif, input multiplexing into parallel processing channels, could improve predictions as much as conventionally used additional layers of local nonlinearities. We obtained similar results in two other cell types. This approach provides a data-driven characterization of a key component of cortical circuit computations: the input-output transformation of neurons during in vivo-like conditions.
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Evans DA, Stempel AV, Vale R, Branco T. Cognitive Control of Escape Behaviour. Trends Cogn Sci 2019; 23:334-348. [PMID: 30852123 PMCID: PMC6438863 DOI: 10.1016/j.tics.2019.01.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
When faced with potential predators, animals instinctively decide whether there is a threat they should escape from, and also when, how, and where to take evasive action. While escape is often viewed in classical ethology as an action that is released upon presentation of specific stimuli, successful and adaptive escape behaviour relies on integrating information from sensory systems, stored knowledge, and internal states. From a neuroscience perspective, escape is an incredibly rich model that provides opportunities for investigating processes such as perceptual and value-based decision-making, or action selection, in an ethological setting. We review recent research from laboratory and field studies that explore, at the behavioural and mechanistic levels, how elements from multiple information streams are integrated to generate flexible escape behaviour.
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Masaracchia C, Hnida M, Gerhardt E, Lopes da Fonseca T, Villar-Pique A, Branco T, Stahlberg MA, Dean C, Fernández CO, Milosevic I, Outeiro TF. Membrane binding, internalization, and sorting of alpha-synuclein in the cell. Acta Neuropathol Commun 2018; 6:79. [PMID: 30107856 PMCID: PMC6090819 DOI: 10.1186/s40478-018-0578-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/28/2018] [Indexed: 12/31/2022] Open
Abstract
Alpha-synuclein (aSyn) plays a crucial role in Parkinson's disease (PD) and other synucleinopathies, since it misfolds and accumulates in typical proteinaceous inclusions. While the function of aSyn is thought to be related to vesicle binding and trafficking, the precise molecular mechanisms linking aSyn with synucleinopathies are still obscure. aSyn can spread in a prion-like manner between interconnected neurons, contributing to the propagation of the pathology and to the progressive nature of synucleinopathies. Here, we investigated the interaction of aSyn with membranes and trafficking machinery pathways using cellular models of PD that are amenable to detailed molecular analyses. We found that different species of aSyn can enter cells and form high molecular weight species, and that membrane binding properties are important for the internalization of aSyn. Once internalized, aSyn accumulates in intracellular inclusions. Interestingly, we found that internalization is blocked in the presence of dynamin inhibitors (blocked membrane scission), suggesting the involvement of the endocytic pathway in the internalization of aSyn. By screening a pool of small Rab-GTPase proteins (Rabs) which regulate membrane trafficking, we found that internalized aSyn partially colocalized with Rab5A and Rab7. Initially, aSyn accumulated in Rab4A-labelled vesicles and, at later stages, it reached the autophagy-lysosomal pathway (ALP) where it gets degraded. In total, our study emphasizes the importance of membrane binding, not only as part of the normal function but also as an important step in the internalization and subsequent accumulation of aSyn. Importantly, we identified a fundamental role for Rab proteins in the modulation of aSyn processing, clearance and spreading, suggesting that targeting Rab proteins may hold important therapeutic value in PD and other synucleinopathies.
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Vale R, Evans D, Branco T. A Behavioral Assay for Investigating the Role of Spatial Memory During Instinctive Defense in Mice. J Vis Exp 2018. [PMID: 30080198 PMCID: PMC6126525 DOI: 10.3791/56988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Evolution has selected a repertoire of defensive behaviors that are essential for survival across all animal species. These behaviors are often stereotyped actions elicited in response to innately aversive sensory stimuli, but their success requires enough flexibility for adapting to different spatial environments, which can change rapidly. Here, we describe a behavioral assay to evaluate the influence of learned spatial knowledge on defensive behaviors in mice. We have adapted the widely used Barnes maze spatial memory assay to investigate how mice navigate to a shelter during escape responses to innately aversive sensory stimuli in a novel environment, and how they adapt to acute changes in the environment. This new assay is an ethological paradigm that does not require training and exploits the natural exploration patterns and navigation strategies in mice. We propose that the set of protocols described here are a powerful means of studying goal-directed behaviors and stimulus-triggered navigation, which should be of interest to both the fields of instinctive behaviors and spatial memory.
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Grillo FW, Neves G, Walker A, Vizcay-Barrena G, Fleck RA, Branco T, Burrone J. A Distance-Dependent Distribution of Presynaptic Boutons Tunes Frequency-Dependent Dendritic Integration. Neuron 2018; 99:275-282.e3. [PMID: 29983327 PMCID: PMC6078905 DOI: 10.1016/j.neuron.2018.06.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 03/23/2018] [Accepted: 06/08/2018] [Indexed: 11/28/2022]
Abstract
How presynaptic inputs and neurotransmitter release dynamics are distributed along a dendritic tree is not well established. Here, we show that presynaptic boutons that form onto basal dendrites of CA1 pyramidal neurons display a decrease in active zone (AZ) size with distance from the soma, resulting in a distance-dependent increase in short-term facilitation. Our findings suggest that the spatial distribution of short-term facilitation serves to compensate for the electrotonic attenuation of subthreshold distal inputs during repeated stimulation and fine-tunes the preferred input frequency of dendritic domains. Presynaptic inputs decrease in size with distance along CA1 basal dendrites Release probability decreases with distance along basal dendrites Short-term facilitation increases with distance along basal dendrites Increased synaptic facilitation offsets passive decay and boosts supralinear events
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Evans DA, Stempel AV, Vale R, Ruehle S, Lefler Y, Branco T. A synaptic threshold mechanism for computing escape decisions. Nature 2018; 558:590-594. [PMID: 29925954 PMCID: PMC6235113 DOI: 10.1038/s41586-018-0244-6] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 05/11/2018] [Indexed: 11/09/2022]
Abstract
Escaping from imminent danger is an instinctive behaviour that is fundamental for survival, and requires the classification of sensory stimuli as harmless or threatening. The absence of threat enables animals to forage for essential resources, but as the level of threat and potential for harm increases, they have to decide whether or not to seek safety 1 . Despite previous work on instinctive defensive behaviours in rodents2-11, little is known about how the brain computes the threat level for initiating escape. Here we show that the probability and vigour of escape in mice scale with the saliency of innate threats, and are well described by a model that computes the distance between the threat level and an escape threshold. Calcium imaging and optogenetics in the midbrain of freely behaving mice show that the activity of excitatory neurons in the deep layers of the medial superior colliculus (mSC) represents the saliency of the threat stimulus and is predictive of escape, whereas glutamatergic neurons of the dorsal periaqueductal grey (dPAG) encode exclusively the choice to escape and control escape vigour. We demonstrate a feed-forward monosynaptic excitatory connection from mSC to dPAG neurons, which is weak and unreliable-yet required for escape behaviour-and provides a synaptic threshold for dPAG activation and the initiation of escape. This threshold can be overcome by high mSC network activity because of short-term synaptic facilitation and recurrent excitation within the mSC, which amplifies and sustains synaptic drive to the dPAG. Therefore, dPAG glutamatergic neurons compute escape decisions and escape vigour using a synaptic mechanism to threshold threat information received from the mSC, and provide a biophysical model of how the brain performs a critical behavioural computation.
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Dos Santos MP, Do Vale MM, Branco T, Klein DR, Santos JPA. HEAT STRESS IN BROILERS AND THE NEED OF CLIMATIZATION SYSTEMS. REVISTA BRASILEIRA DE ENGENHARIA DE BIOSSISTEMAS 2017. [DOI: 10.18011/bioeng2017v11n3p265-272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Broilers have better production rates when housed in thermal comfort conditions, outside of this zone the poultry need to maintain homeothermy. The heat production and thermal exchanges are related to body weight and available surface for heat exchange. The genetic evolution of broilers ensured high production with improvement in the feed conversion and reducing the slaughter time. The faster weight gain difficult sensible heat exchange, increasing the needs for climatization systems, in days with high temperatures. Changes in heat waves frequency and days with extreme temperatures are challenging situations for ventilation and evaporative cooling systems in broiler facilities. This review discusses heat exchanges of broilers and the challenges in maintaining the thermal comfort zone in poultry facilities, in a reality of increase of heat stress conditions.
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Schmidt-Hieber C, Toleikyte G, Aitchison L, Roth A, Clark BA, Branco T, Häusser M. Active dendritic integration as a mechanism for robust and precise grid cell firing. Nat Neurosci 2017. [PMID: 28628104 DOI: 10.1038/nn.4582] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding how active dendrites are exploited for behaviorally relevant computations is a fundamental challenge in neuroscience. Grid cells in medial entorhinal cortex are an attractive model system for addressing this question, as the computation they perform is clear: they convert synaptic inputs into spatially modulated, periodic firing. Whether active dendrites contribute to the generation of the dual temporal and rate codes characteristic of grid cell output is unknown. We show that dendrites of medial entorhinal cortex neurons are highly excitable and exhibit a supralinear input-output function in vitro, while in vivo recordings reveal membrane potential signatures consistent with recruitment of active dendritic conductances. By incorporating these nonlinear dynamics into grid cell models, we show that they can sharpen the precision of the temporal code and enhance the robustness of the rate code, thereby supporting a stable, accurate representation of space under varying environmental conditions. Our results suggest that active dendrites may therefore constitute a key cellular mechanism for ensuring reliable spatial navigation.
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Vale R, Evans DA, Branco T. Rapid Spatial Learning Controls Instinctive Defensive Behavior in Mice. Curr Biol 2017; 27:1342-1349. [PMID: 28416117 PMCID: PMC5434248 DOI: 10.1016/j.cub.2017.03.031] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/19/2022]
Abstract
Instinctive defensive behaviors are essential for animal survival. Across the animal kingdom, there are sensory stimuli that innately represent threat and trigger stereotyped behaviors such as escape or freezing [1-4]. While innate behaviors are considered to be hard-wired stimulus-responses [5], they act within dynamic environments, and factors such as the properties of the threat [6-9] and its perceived intensity [1, 10, 11], access to food sources [12-14], and expectations from past experience [15, 16] have been shown to influence defensive behaviors, suggesting that their expression can be modulated. However, despite recent work [2, 4, 17-21], little is known about how flexible mouse innate defensive behaviors are and how quickly they can be modified by experience. To address this, we have investigated the dependence of escape behavior on learned knowledge about the spatial environment and how the behavior is updated when the environment changes acutely. Using behavioral assays with innately threatening visual and auditory stimuli, we show that the primary goal of escape in mice is to reach a previously memorized shelter location. Memory of the escape target can be formed in a single shelter visit lasting less than 20 s, and changes in the spatial environment lead to a rapid update of the defensive action, including changing the defensive strategy from escape to freezing. Our results show that although there are innate links between specific sensory features and defensive behavior, instinctive defensive actions are surprisingly flexible and can be rapidly updated by experience to adapt to changing spatial environments.
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Real C, Sobreira Fernandes D, Sá Couto P, Correia de Barros F, Esteves S, Aragão I, Fonseca L, Aguiar J, Branco T, Fernandes Moreira Z. Survival Predictors in Liver Transplantation: Time-Varying Effect of Red Blood Cell Transfusion. Transplant Proc 2017; 48:3303-3306. [PMID: 27931573 DOI: 10.1016/j.transproceed.2016.08.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 08/01/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Many attempts have been undertaken to better predict outcome after liver transplantation. The aim of this study was to identify the pre- and intraoperative variables that may influence the survival after liver transplantation, at a single institution. METHODS Anesthetic records from 543 consecutive patients who underwent liver transplantation from June 2006 to June 2014 were reviewed in this retrospective study. Patients undergoing retransplantation were excluded from the analysis, as were patients with familial amyloid polyneuropathy. Preoperative variables studied were age, sex, Model for End-Stage Liver Disease score, primary diagnosis, cold ischemia time, preoperative international normalized ratio, serum albumin, and and hemoglobin levels. Intraoperative variables included were norepinephrine consumption, blood loss, red blood cell transfusion, and surgical time. Variables significant in the univariate analysis with a P value of <.2 were included in a multivariate Cox regression model. RESULTS Only red blood cell transfusion (hazard ratio [HR], 1.16; 95% confidence interval [CI], 1.04-1.29) and female sex (HR, 1.71; 95% CI, 1.10-2.65) were identified as significant independent predictors for survival after liver transplantation. Because of proportionality assumption violation, the multivariate Cox regression model was subsequently upgraded by adding a time-varying interaction between red blood cell transfusion and time since liver transplantation. As a result, we found that at 3 months after liver transplantation, the rate of dying increased 14% (95% CI, 2%-26%) for each unit transfused, and at 6 months it increased 12% (95% CI, 0.3%-24%). CONCLUSIONS Red blood cell transfusion ceased to influence survival from 1 year onward.
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Lagarto F, Gomes B, Couto PS, Correia de Barros F, Moreira Z, Branco T, Fonseca L, Aguiar J, Aragão I, Miranda HP, Daniel J, Esteves S. Perioperative Predictors of Survival After Liver Transplantation for Familial Amyloid Polyneuropathy in a Portuguese Center. Transplant Proc 2017; 48:2098-101. [PMID: 27569952 DOI: 10.1016/j.transproceed.2016.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/05/2016] [Accepted: 04/27/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Liver transplantation (LT) has been the treatment of choice to halt the progression of familial amyloid polyneuropathy (FAP). Few studies have identified prognostic factors for post-LT survival in FAP. Our aim was to assess survival rate and to identify independent factors for survival after LT. METHODS This retrospective cohort study of FAP patients transplanted for the first time analyzed 116 transplantations from 2006 to 2014. The median follow-up period was 45.5 months. RESULTS The overall survival rates at 1 month, 1 year, and 5 years were 89%, 82% and 79%, respectively. On multivariate analysis, only number of red blood cell (RBC) units transfused during surgery, operation time, and body mass index were independent prognostic factors for patient survival. Only 30% of patients were transfused during surgery, and, in these, each RBC unit transfused increased mortality by 53%. The operation time increased mortality by 20% for every 15 minutes of surgery. CONCLUSIONS This study suggests that operation time and RBC transfused are predominant factors affecting post-LT survival in our FAP patients.
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Branco T, Tozer A, Magnus CJ, Sugino K, Tanaka S, Lee AK, Wood JN, Sternson SM. Near-Perfect Synaptic Integration by Nav1.7 in Hypothalamic Neurons Regulates Body Weight. Cell 2017; 165:1749-1761. [PMID: 27315482 PMCID: PMC4912688 DOI: 10.1016/j.cell.2016.05.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 03/27/2016] [Accepted: 04/26/2016] [Indexed: 01/20/2023]
Abstract
Neurons are well suited for computations on millisecond timescales, but some neuronal circuits set behavioral states over long time periods, such as those involved in energy homeostasis. We found that multiple types of hypothalamic neurons, including those that oppositely regulate body weight, are specialized as near-perfect synaptic integrators that summate inputs over extended timescales. Excitatory postsynaptic potentials (EPSPs) are greatly prolonged, outlasting the neuronal membrane time-constant up to 10-fold. This is due to the voltage-gated sodium channel Nav1.7 (Scn9a), previously associated with pain-sensation but not synaptic integration. Scn9a deletion in AGRP, POMC, or paraventricular hypothalamic neurons reduced EPSP duration, synaptic integration, and altered body weight in mice. In vivo whole-cell recordings in the hypothalamus confirmed near-perfect synaptic integration. These experiments show that integration of synaptic inputs over time by Nav1.7 is critical for body weight regulation and reveal a mechanism for synaptic control of circuits regulating long term homeostatic functions. Hypothalamic neurons that regulate body weight are near-perfect synaptic integrators Near-perfect synaptic integration is observed in hypothalamic neurons in vivo Near-perfect synaptic integration depends on the voltage-gated sodium channel Nav1.7 Loss of Nav1.7 in hypothalamic neurons disrupts regulation of body weight
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Klein DR, Vale MM, Silva LP, Santos JPA, Branco T, Fernandes MO. Bioimpedance as a Non-Invasive Method to Evaluate Eggs and Poultry. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2016. [DOI: 10.1590/1806-9061-2015-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mussini C, Antinori A, Bhagani S, Branco T, Brostrom M, Dedes N, Bereczky T, Girardi E, Gökengin D, Horban A, Lacombe K, Lundgren JD, Mendao L, Mocroft A, Oprea C, Porter K, Podlekareva D, Battegay M, d'Arminio Monforte A. European AIDS Clinical Society Standard of Care meeting on HIV and related coinfections: The Rome Statements. HIV Med 2015; 17:445-52. [PMID: 26492497 DOI: 10.1111/hiv.12347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
Abstract
OBJECTIVES The objective of the 1st European AIDS Clinical Society meeting on Standard of Care in Europe was to raise awareness of the European scenario and come to an agreement on actions that could be taken in the future. METHODS Data-driven presentations were given on specific topics followed by interactive panel discussions. RESULTS In Eastern European countries, the epidemic is largely driven by injecting drug use, in contrast with Western Europe where the infection mainly occurs through heterosexual contact. A high proportion of people living with HIV remain unaware of their infection. Substantial differences exist in Eastern Europe and Central Asia with respect to treatment coverage, regimen availability and continuity of drug supply. In 2012, tuberculosis case notification rates were 5-10 times higher in Eastern Europe compared with Western Europe, with an alarming proportion of newly diagnosed multi-drug-resistant cases. Hepatitis C is widespread in selected geographical areas and risk groups. CONCLUSIONS The key conclusion from the meeting was that a high-priority group of actions could be identified, including: increasing HIV awareness and testing, improving training for health care providers, ensuring equitable patient access to treatments and diagnostics for HIV and comorbidities, and implementing best practices in infection control and treatment of HIV-infected patients coinfected with tuberculosis and hepatitis C virus, for whom direct acting antiviral treatment. should be considered.
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Henry FE, Sugino K, Tozer A, Branco T, Sternson SM. Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss. eLife 2015; 4. [PMID: 26329458 PMCID: PMC4595745 DOI: 10.7554/elife.09800] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/02/2015] [Indexed: 12/13/2022] Open
Abstract
Molecular and cellular processes in neurons are critical for sensing and responding to energy deficit states, such as during weight-loss. Agouti related protein (AGRP)-expressing neurons are a key hypothalamic population that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific transcriptomics can be used to identify pathways that counteract weight-loss, and here we report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived young adult mice. For comparison, we also analyzed Proopiomelanocortin (POMC)-expressing neurons, an intermingled population that suppresses appetite and body weight. We find that AGRP neurons are considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion channels, neuropeptides, and receptors. Combined with methods to validate and manipulate these pathways, this resource greatly expands molecular insight into neuronal regulation of body weight, and may be useful for devising therapeutic strategies for obesity and eating disorders. DOI:http://dx.doi.org/10.7554/eLife.09800.001 Humans and other animals must get adequate nutrition in order to survive. As a result, the body has several systems that work side by side to maintain a healthy body weight and ensure that enough food gets eaten to provide the energy that the body needs. Problems with these systems can contribute towards obesity and other eating disorders. Certain types of cells in the brain play important roles in controlling weight and appetite, although the genes and cellular mechanisms that underlie these abilities are not well understood. When an animal is deprived of food, so-called AGRP neurons produce molecules that increase appetite and make it easier to gain weight. These neurons also go through structural changes and increase their electrical activity during weight loss. Another group of cells, called the POMC neurons, becomes less active when an animal is deprived of energy. Using a technique called cell type-specific transcriptomics, Henry, Sugino et al. have now revealed that the expression of hundreds of genes in AGRP and POMC neurons changes depending on whether mice are well fed or food deprived. Food deprivation also affects more genes in AGRP neurons than has been seen in other types of brain cell, and the AGRP neurons are also more sensitive to a change in food intake than POMC neurons. In the future, this gene expression data and knowledge of the pathways affected by the genes could help researchers to develop new treatments for obesity and other disorders that affect appetite. Henry, Sugino et al. then mapped how these changes in gene expression trigger molecular “pathways” in the neurons that alter how the cells work. These affect many parts of the cells, including ion channels, transcription factors, receptors, and secreted proteins. In addition, food deprivation activated pathways in AGRP neurons that protect the cells from damage and death caused by elevated neuron activity and also triggered signaling pathways that increase body weight. In the future, this gene expression data and knowledge of the pathways affected by the genes could help researchers to develop new treatments for obesity and other disorders that affect appetite. DOI:http://dx.doi.org/10.7554/eLife.09800.002
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Ujfalussy BB, Makara JK, Branco T, Lengyel M. Dendritic nonlinearities are tuned for efficient spike-based computations in cortical circuits. eLife 2015; 4:e10056. [PMID: 26705334 PMCID: PMC4912838 DOI: 10.7554/elife.10056] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/23/2015] [Indexed: 01/27/2023] Open
Abstract
Cortical neurons integrate thousands of synaptic inputs in their dendrites in highly nonlinear ways. It is unknown how these dendritic nonlinearities in individual cells contribute to computations at the level of neural circuits. Here, we show that dendritic nonlinearities are critical for the efficient integration of synaptic inputs in circuits performing analog computations with spiking neurons. We developed a theory that formalizes how a neuron's dendritic nonlinearity that is optimal for integrating synaptic inputs depends on the statistics of its presynaptic activity patterns. Based on their in vivo preynaptic population statistics (firing rates, membrane potential fluctuations, and correlations due to ensemble dynamics), our theory accurately predicted the responses of two different types of cortical pyramidal cells to patterned stimulation by two-photon glutamate uncaging. These results reveal a new computational principle underlying dendritic integration in cortical neurons by suggesting a functional link between cellular and systems--level properties of cortical circuits.
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Kohl J, Ng J, Cachero S, Ciabatti E, Dolan MJ, Sutcliffe B, Tozer A, Ruehle S, Krueger D, Frechter S, Branco T, Tripodi M, Jefferis GSXE. Ultrafast tissue staining with chemical tags. Proc Natl Acad Sci U S A 2014; 111:E3805-14. [PMID: 25157152 PMCID: PMC4246963 DOI: 10.1073/pnas.1411087111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetically encoded fluorescent proteins and immunostaining are widely used to detect cellular and subcellular structures in fixed biological samples. However, for thick or whole-mount tissue, each approach suffers from limitations, including limited spectral flexibility and lower signal or slow speed, poor penetration, and high background labeling, respectively. We have overcome these limitations by using transgenically expressed chemical tags for rapid, even, high-signal and low-background labeling of thick biological tissues. We first construct a platform of widely applicable transgenic Drosophila reporter lines, demonstrating that chemical labeling can accelerate staining of whole-mount fly brains by a factor of 100. Using viral vectors to deliver chemical tags into the mouse brain, we then demonstrate that this labeling strategy works well in mice. Thus this tag-based approach drastically improves the speed and specificity of labeling genetically marked cells in intact and/or thick biological samples.
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Ratnayaka A, Marra V, Bush D, Burden JJ, Branco T, Staras K. Recruitment of resting vesicles into recycling pools supports NMDA receptor-dependent synaptic potentiation in cultured hippocampal neurons. J Physiol 2012; 590:1585-97. [PMID: 22271866 PMCID: PMC3413500 DOI: 10.1113/jphysiol.2011.226688] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Most presynaptic terminals in the central nervous system are characterized by two functionally distinct vesicle populations: a recycling pool, which supports action potential-driven neurotransmitter release via vesicle exocytosis, and a resting pool. The relative proportions of these two pools are highly variable between individual synapses, prompting speculation on their specific relationship, and on the possible functions of the resting pool. Using fluorescence imaging of FM-styryl dyes and synaptophysinI-pHluorin (sypHy) as well as correlative electron microscopy approaches, we show here that Hebbian plasticity-dependent changes in synaptic strength in rat hippocampal neurons can increase the recycling pool fraction at the expense of the resting pool in individual synaptic terminals. This recruitment process depends on NMDA-receptor activation, nitric oxide signalling and calcineurin and is accompanied by an increase in the probability of neurotransmitter release at individual terminals. Blockade of actin-mediated intersynaptic vesicle exchange does not prevent recycling pool expansion demonstrating that vesicle recruitment is intrasynaptic. We propose that the conversion of resting pool vesicles to the functionally recycling pool provides a rapid mechanism to implement long-lasting changes in presynaptic efficacy.
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Carvalho AC, Valadas E, França L, Carvalho C, Aleixo MJ, Mendez J, Marques R, Sarmento A, Doroana M, Antunes F, Branco T, Aguas M, Sarmento E Castro R, Lazarus JV, Barros H. Population mobility and the changing epidemics of HIV-2 in Portugal. HIV Med 2011; 13:219-25. [PMID: 22136745 DOI: 10.1111/j.1468-1293.2011.00963.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2011] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Portugal is the European country with the highest frequency of HIV-2 infection, which is mainly concentrated in West Africa. The cumulative number of notified HIV-2 infections in Portugal was 1813 by the end of December 2008. To better characterize the dynamics of HIV-2 infection in the country and to obtain data that may be of use in the prevention of the spread of HIV-2, we evaluated a large pooled sample of patients. PATIENTS AND METHODS Five Portuguese hospitals provided data on HIV-2-infected patients from 1984 to the end of 2007. Data concerning demographic characteristics and clinical variables were extracted. Patients were stratified according to date of diagnosis in approximately 5-year categories. RESULTS The sample included 442 patients, accounting for 37% of all HIV-2 infections notified in Portugal during that period. HIV-2-infected patients showed clearly different characteristics according to the period of diagnosis. Until 2000, the majority of HIV-2-infected patients were Portuguese-born males living in the north of the country. From 2000 to 2007, most of the patients diagnosed with HIV-2 infection had a West African origin, were predominantly female and were living in the capital, Lisbon. The average age at diagnosis and loss to follow-up significantly increased over time. CONCLUSION HIV-2 infection has been documented in Portugal since the early 1980s and its epidemiology appears to reflect changes in population movement. These include the movements of soldiers and repatriates from African territories during the independence wars and, later, migration and mobility from high-endemicity areas. The findings of this study stress the importance of promoting migrant-sensitive health care.
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Ratnayaka A, Marra V, Branco T, Staras K. Extrasynaptic vesicle recycling in mature hippocampal neurons. Nat Commun 2011; 2:531. [PMID: 22068598 DOI: 10.1038/ncomms1534] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 10/05/2011] [Indexed: 11/09/2022] Open
Abstract
Fast neuronal signalling relies on highly regulated vesicle fusion and recycling at specialized presynaptic terminals. Recently, examples of non-classical neurotransmission have also been reported, where fusion of vesicles can occur at sites remote from conventional synapses. This has potentially broad biological implications, but the underlying mechanisms are not well established. Here we show that a complete vesicle recycling pathway can occur at discrete axonal sites in mature hippocampal neurons and that extrasynaptic fusion is a robust feature of native tissue. We demonstrate that laterally mobile vesicle clusters trafficking between synaptic terminals become transiently stabilized by evoked action potentials and undergo complete but delayed Ca(2+)-dependent fusion along axons. This fusion is associated with dynamic actin accumulation and, subsequently, vesicles can be locally recycled, re-acidified and re-used. Immunofluorescence and ultrastructural work demonstrates that extrasynaptic fusion sites can have apposed postsynaptic specializations, suggesting that mobile vesicle recycling may underlie highly dynamic neuron-neuron communication.
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Branco T. Eppendorf winner. The language of dendrites. Science 2011; 334:615-6. [PMID: 22053040 DOI: 10.1126/science.1215079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Branco T, Marra V, Staras K. Examining size-strength relationships at hippocampal synapses using an ultrastructural measurement of synaptic release probability. J Struct Biol 2010; 172:203-10. [PMID: 19895891 PMCID: PMC3084449 DOI: 10.1016/j.jsb.2009.10.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 09/25/2009] [Accepted: 10/27/2009] [Indexed: 11/19/2022]
Abstract
Release probability (p(r)) is a fundamental presynaptic parameter which is critical in defining synaptic strength. Knowledge of how synapses set and regulate their p(r) is a fundamental step in understanding synaptic transmission and communication between neurons. Despite its importance, p(r) is difficult to measure directly at single synapses. One important strategy to achieve this has relied on the application of fluorescence-based imaging methods, but this is always limited by the lack of detailed information on the morphological and structural properties of the individual synapses under study, and thus precludes an investigation of the relationship between p(r) and synaptic anatomy. Here we outline a powerful methodology based on using FM-styryl dyes, photoconversion and correlative ultrastructural analysis in dissociated hippocampal cultured neurons, which provides both a direct readout of p(r) as well as nanoscale detail on synaptic organization and structure. We illustrate the value of this approach by investigating, at the level of individual reconstructed terminals, the relationship between release probability and defined vesicle pools. We show that in our population of synapses, p(r) is highly variable, and while it is positively correlated with the number of vesicles docked at the active zone it shows no relationship with the total number of synaptic vesicles. The lack of a direct correlation between total synaptic size and performance in these terminals suggests that factors other than the absolute magnitude of the synapse are the most important determinants of synaptic efficacy.
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Branco T, Clark BA, Häusser M. Dendritic discrimination of temporal input sequences in cortical neurons. Science 2010; 329:1671-5. [PMID: 20705816 DOI: 10.1126/science.1189664] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The detection and discrimination of temporal sequences is fundamental to brain function and underlies perception, cognition, and motor output. By applying patterned, two-photon glutamate uncaging, we found that single dendrites of cortical pyramidal neurons exhibit sensitivity to the sequence of synaptic activation. This sensitivity is encoded by both local dendritic calcium signals and somatic depolarization, leading to sequence-selective spike output. The mechanism involves dendritic impedance gradients and nonlinear synaptic N-methyl-D-aspartate receptor activation and is generalizable to dendrites in different neuronal types. This enables discrimination of patterns delivered to a single dendrite, as well as patterns distributed randomly across the dendritic tree. Pyramidal cell dendrites can thus act as processing compartments for the detection of synaptic sequences, thereby implementing a fundamental cortical computation.
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