Single Sustained Inflation followed by Ventilation Leads to Rapid Cardiorespiratory Recovery but Causes Cerebral Vascular Leakage in Asphyxiated Near-Term Lambs

BackgroundA sustained inflation (SI) rapidly restores cardiac function in asphyxic, bradycardic newborns but its effects on cerebral haemodynamics and brain injury are unknown. We determined the effect of different SI strategies on carotid blood flow (CaBF) and cerebral vascular integrity in asphyxiated near-term lambs.MethodsLambs were instrumented and delivered at 139 ± 2 d gestation and asphyxia was induced by delaying ventilation onset. Lambs were randomised to receive 5 consecutive 3 s SI (multiple SI; n = 6), a single 30 s SI (single SI; n = 6) or conventional ventilation (no SI; n = 6). Ventilation continued for 30 min in all lambs while CaBF and respiratory function parameters were recorded. Brains were assessed for gross histopathology and vascular leakage.ResultsCaBF increased more rapidly and to a greater extent during a single SI (p = 0.01), which then decreased below both other groups by 10 min, due to a higher cerebral oxygen delivery (p = 0.01). Blood brain barrier disruption was increased in single SI lambs as indicated by increased numbers of blood vessel profiles with plasma protein extravasation (p = 0.001) in the cerebral cortex. There were no differences in CaBF or cerebral oxygen delivery between the multiple SI and no SI lambs.ConclusionsVentilation with an initial single 30 s SI improves circulatory recovery, but is associated with greater disruption of blood brain barrier function, which may exacerbate brain injury suffered by asphyxiated newborns. This injury may occur as a direct result of the initial SI or to the higher tidal volumes delivered during subsequent ventilation.     

Function and regulation of tau conformations in the development and treatment of traumatic brain injury and neurodegeneration

One of the two common hallmark lesions of Alzheimer’s disease (AD) brains is neurofibrillary tangles (NFTs), which are composed of hyperphosphorylated tau protein (p-tau). NFTs are also a defining feature of other neurodegenerative disorders and have recently been identified in the brains of patients suffering from chronic traumatic encephalopathy (CTE). However, NFTs are not normally observed in traumatic brain injury (TBI) until months or years after injury. This raises the question of whether NFTs are a cause or a consequence of long-term neurodegeneration following TBI. Two conformations of phosphorylated tau, cis p-tau and trans p-tau, which are regulated by the peptidyl-prolyl isomerase Pin1, have been previously identified. By generating a polyclonal and monoclonal antibody (Ab) pair capable of distinguishing between cis and trans isoforms of p-tau (cis p-tau and trans p-tau, respectively), cis p-tau was identified as a precursor of tau pathology and an early driver of neurodegeneration in AD, TBI and CTE. Histological studies shows the appearance of robust cis p-tau in the early stages of human mild cognitive impairment (MCI), AD and CTE brains, as well as after sport- and military-related TBI. Notably, cis p-tau appears within hours after closed head injury and long before other known pathogenic p-tau conformations including oligomers, pre-fibrillary tangles and NFTs. Importantly, cis p-tau monoclonal antibody treatment not only eliminates cis p-tau induction and tau pathology, but also restores many neuropathological and functional outcome in TBI mouse models. Thus, cis p-tau is an early driver of tau pathology in TBI and CTE and detection of cis p-tau in human bodily fluids could potentially provide new diagnostic and prognostic tools. Furthermore, humanization of the cis p-tau antibody could ultimately be developed as a new treatment for AD, TBI and CTE.     

Into the deep: the functionality of mesopelagic excursions by an oceanic apex predator

Comprehension of ecological processes in marine animals requires information regarding dynamic vertical habitat use. While many pelagic predators primarily associate with epipelagic waters, some species routinely dive beyond the deep scattering layer. Actuation for exploiting these aphotic habitats remains largely unknown. Recent telemetry data from oceanic whitetip sharks (Carcharhinus longimanus) in the Atlantic show a strong association with warm waters (>20°C) less than 200 m. Yet, individuals regularly exhibit excursions into the meso‐ and bathypelagic zone. In order to examine deep‐diving behavior in oceanic whitetip sharks, we physically recovered 16 pop‐up satellite archival tags and analyzed the high‐resolution depth and temperature data. Diving behavior was evaluated in the context of plausible functional behavior hypotheses including interactive behaviors, energy conservation, thermoregulation, navigation, and foraging. Mesopelagic excursions (n = 610) occurred throughout the entire migratory circuit in all individuals, with no indication of site specificity. Six depth‐versus‐time descent and ascent profiles were identified. Descent profile shapes showed little association with examined environmental variables. Contrastingly, ascent profile shapes were related to environmental factors and appear to represent unique behavioral responses to abiotic conditions present at the dive apex. However, environmental conditions may not be the sole factors influencing ascents, as ascent mode may be linked to intentional behaviors. While dive functionality remains unconfirmed, our study suggests that mesopelagic excursions relate to active foraging behavior or navigation. Dive timing, prey constituents, and dive shape support foraging as the most viable hypothesis for mesopelagic excursions, indicating that the oceanic whitetip shark may regularly survey extreme environments (deep depths, low temperatures) as a foraging strategy. At the apex of these deep‐water excursions, sharks exhibit a variable behavioral response, perhaps, indicating the presence or absence of prey.     

Multigeneration Cross-Contamination of Mail with Bacillus anthracis Spores

The release of biological agents, including those which could be used in biowarfare or bioterrorism in large urban areas, has been a concern for governments for nearly three decades. Previous incidents from Sverdlosk and the postal anthrax attack of 2001 have raised questions on the mechanism of spread of Bacillus anthracis spores as an aerosol or contaminant. Prior studies have demonstrated that Bacillus atrophaeus is easily transferred through simulated mail handing, but no reports have demonstrated this ability with Bacillus anthracis spores, which have morphological differences that may affect adhesion properties between spore and formite. In this study, equipment developed to simulate interactions across three generations of envelopes subjected to tumbling and mixing was used to evaluate the potential for cross-contamination of B. anthracis spores in simulated mail handling. In these experiments, we found that the potential for cross-contamination through letter tumbling from one generation to the next varied between generations while the presence of a fluidizer had no statistical impact on the transfer of material. Likewise, the presence or absence of a fluidizer had no statistically significant impact on cross-contamination levels or reaerosolization from letter opening.     

A Multiple Case Study of Mental Health Interventions in Middle Income Countries: Considering the Science of Delivery

In the debate in global mental health about the most effective models for developing and scaling interventions, there have been calls for the development of a more robust literature regarding the "non-specific", science of delivery aspects of interventions that are locally, contextually, and culturally relevant. This study describes a rigorous, exploratory, qualitative examination of the key, non-specific intervention strategies of a diverse group of five internationally-recognized organizations addressing mental illness in middle income countries (MICs). A triangulated approach to inquiry was used with semi-structured interviews conducted with service recipients, service providers and leaders, and key community partners (N = 159). The interview focus was upon processes of implementation and operation. A grounded theory-informed analysis revealed cross cutting themes of: a holistic conceptualization of mental health problems, an intensive application of principles of leverage and creating the social, cultural, and policy “space” within which interventions could be applied and resourced. These findings aligned with key aspects of systems dynamic theory suggesting that it might be a helpful framework in future studies of mental health service implementation in MICs.     

Contrasting Role of Temperature in Structuring Regional Patterns of Invasive and Native Pestilential Stink Bugs

Objectives

Assessment and identification of spatial structures in the distribution and abundance of invasive species is important for unraveling the underlying ecological processes. The invasive agricultural insect pest Halyomorpha halys that causes severe economic losses in the United States is currently expanding both within United States and across Europe. We examined the drivers of H. halys invasion by characterizing the distribution and abundance patterns of H. halys and native stink bugs (Chinavia hilaris and Euschistus servus) across eight different spatial scales. We then quantified the interactive and individual influences of temperature, and measures of resource availability and distance from source populations, and their relevant spatial scales. We used Moran’s Eigenvector Maps based on Gabriel graph framework to quantify spatial relationships among the soybean fields in mid-Atlantic Unites States surveyed for stink bugs.

Findings

Results from the multi-spatial scale, multivariate analyses showed that temperature and its interaction with resource availability and distance from source populations structures the patterns in H. halys at very broad spatial scale. H. halys abundance decreased with increasing average June temperature and distance from source population. H. halys were not recorded at fields with average June temperature higher than 23.5°C. In parts with suitable climate, high H. halys abundance was positively associated with percentage developed open area and percentage deciduous forests at 250m scale. Broad scale patterns in native stink bugs were positively associated with increasing forest cover and, in contrast to the invasive H. halys, increasing mean July temperature. Our results identify the contrasting role of temperature in structuring regional patterns in H. halys and native stink bugs, while demonstrating its interaction with resource availability and distance from source populations for structuring H. halys patterns.

Conclusion

These results help predicting the pest potential of H. halys and vulnerability of agricultural systems at various regions, given the climatic conditions, and its interaction with resource availability and distance from source populations. Monitoring and control efforts within parts of the United States and Europe with more suitable climate could focus in areas of peri-urban developments with deciduous forests and other host plants, along with efforts to reduce propagule pressure.     

OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery

The Zika virus outbreak in the Americas has caused global concern. To help accelerate this fight against Zika, we launched the OpenZika project. OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds against crystal structures and homology models of Zika proteins (and other related flavivirus targets). This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus. The docking data is being made openly accessible so that all members of the global research community can use it to further advance drug discovery studies against Zika and other related flaviviruses.The Zika virus (ZIKV) has emerged as a major public health threat to the Americas as of 2015 [1]. We have previously suggested that it represents an opportunity for scientific collaboration and open scientific exchange [2]. The health of future generations may very well depend on the decisions we make, our willingness to share our findings quickly, and open collaboration to rapidly find a cure for this disease. Since February 1, 2016, when the World Health Organization deemed the cluster of microcephaly cases, Guillain-Barré, and other neurological disorders associated with ZIKV in Latin America and the Caribbean as constituting a Public Health Emergency of International Concern [3] (PHEIC), we have seen a rapid increase in publications (S1 References and main references). We [2] and others [4,5] described steps that could be taken to initiate a drug discovery program on ZIKV. For example, computational approaches, such as virtual screening of chemical libraries or focused screening to repurpose FDA and/or EU-approved drugs, can be used to help accelerate the discovery of an anti-ZIKV drug. An antiviral drug discovery program can be initiated using structure-based design, based on homology models of the key ZIKV proteins. With the lack of structural information regarding the proteins of ZIKV, we built homology models for all the ZIKV proteins, based on close homologs such as dengue virus, using freely available software [6] (S1 Table). These were made available online on March 3, 2016. We also predicted the site of glycosylation of glycoprotein E as Asn154, which was recently experimentally verified [7].Since the end of March 2016, we have now seen two cryo-EM structures and 16 crystal structures of five target classes (S1 Table). These structures, alongside the homology models, represent potential starting points for docking-based virtual screening campaigns to help find molecules that are predicted to have high affinity with ZIKV proteins. These predictions can then be tested against the virus in cell-based assays and/or using individual protein-based assays. There are millions of molecules available that can be assayed, but which ones are likely to work, and how should we prioritize them?In March, we initiated a new open collaborative project called OpenZika (Fig 1), with IBM’s World Community Grid (WCG, worldcommunitygrid.org), which has been used previously for distributed computing projects (S2 Table). On May 18, 2016, the OpenZika project began the virtual screening of ~6 million compounds that are in the ZINC database (Fig 1), as well as the FDA-approved drugs and the NIH clinical collection, using AutoDock Vina and the homology models and crystal structures (S1 Table, S1 Text, S1 References), to discover novel candidate compounds that can potentially be developed into new drugs for treating ZIKV. These will be followed by additional virtual screens with a new ZINC library of ~38 million compounds, and the PubChem database (at most ~90 million compounds), after their structures are prepared for docking.Open in a separate windowFig 1Workflow for the OpenZika project.A. Docking input files of the targets and ligands are prepared, and positive control docking studies are performed. The crystallographic binding mode of a known inhibitor is shown as sticks with dark purple carbon atoms, while the docked binding mode against the NS5 target from HCV has cyan carbons. Our pdbqt files of the libraries of compounds we screen are also openly accessible (http://zinc.docking.org/pdbqt/). B. We have already prepared the docking input files for ~6 million compounds from ZINC (i.e., the libraries that ALP previously used in the GO Fight Against Malaria project on World Community Grid), which are currently being used in the initial set of virtual screens on OpenZika. C. IBM’s World Community Grid is an internet-distributed network of millions of computers (Mac, Windows, and Linux) and Android-based tablets or smartphones in over 80 countries. Over 715,000 volunteers donate their dormant computer time (that would otherwise be wasted) towards different projects that are both (a) run by an academic or nonprofit research institute, and (b) are devoted to benefiting humanity. D. OpenZika is harnessing World Community Grid to dock millions of commercially available compounds against multiple ZIKV homology models and crystal structures (and targets from related viruses) using AutoDock Vina (AD Vina). This ultimately produces candidates (virtual hits that produced the best docking scores and displayed the best interactions with the target during visual inspection) against individual proteins, which can then be prioritized for in vitro testing by collaborators. After it is inspected, all computational data against ZIKV targets will be made open to the public on our website (http://openzika.ufg.br/experiments/#tab-id-7), and OpenZika results are also available upon request. The computational and experimental data produced will be published as quickly as possible.Initially, compounds are being screened against the ZIKV homologs of drug targets that have been well-validated in research against dengue and hepatitis C viruses, such as NS5 and Glycoprotein E (S1 Table, S1 Text, S1 References). These may allow us to identify broad-spectrum antivirals against multiple flaviviruses, such as dengue virus, West Nile virus, and yellow fever virus. In addition, docking against the crystal structure of a related protein from a different pathogen can sometimes discover novel hits against the pathogen of interest [8].As well as applying docking-based filters, the compounds virtually screened on OpenZika will also be filtered using machine learning models (S1 Text, S1 References). These should be useful selection criteria for subsequent tests by our collaborators in whole-cell ZIKV assays, to verify their antiviral activity for blocking ZIKV infection or replication. Since all OpenZika docking data will be in the public domain soon after they are completed and verified, we and other labs can then advance the development of some of these new virtual candidates into experimentally validated hits, leads, and drugs through collaborations with wet labs.This exemplifies open science, which should help scientists around the world as they address the long and arduous process of discovering and developing new drugs. Screening millions of compounds against many different protein models in this way would take far more resources and time than any academic researcher could generally obtain or spend. As of August 16, 2016, we have submitted 894 million docking jobs. Over 6,934 CPU years have been donated to us, enabling over 439 million different docking jobs. We recently selected an initial batch of candidates for NS3 helicase (data openly available at http://openzika.ufg.br/experiments/#tab-id-7), for in vitro testing. Without the unique community of volunteers and tremendous resources provided by World Community Grid, this project would have been very difficult to initiate in a reasonable time frame at this scale.The OpenZika project will ultimately generate several billion docking results, which could make it the largest computational drug discovery project ever performed in academia. The potential challenges we foresee will be finding laboratories with sufficient funding to pursue compounds, synthesize analogs, and develop target-based assays to validate our predictions and generate SAR (Structure-Activity Relationship) data to guide the process of developing the new hits into leads and then drugs. Due to the difficult nature of drug discovery and the eventual evolution of drug resistance, funding of ZIKV research once initiated will likely need to be sustained for several years, if not longer (e.g., HIV research has been funded for decades). As with other WCG projects, once scientists identify experimentally validated leads, finding a company to license them and pursue them in clinical trials and beyond will need incentives such as the FDA Tropical Disease Priority voucher, [9] which has a financial value on the open market [10].By working together and opening our research to the scientific community, many other labs will also be able to take promising molecular candidates forward to accelerate progress towards defeating the ZIKV outbreak. We invite any interested researcher to join us (send us your models or volunteer to assay the candidates we identify through this effort against any of the flaviviruses), and we hope new volunteers in the general public will donate their dormant, spare computing cycles to this cause. We will ultimately report the full computational and experimental results of this collaboration.

Advantages and Disadvantages of OpenZika

Advantages

• Open Science could accelerate the discovery of new antivirals using docking and virtual screening
• Docking narrows down compounds to test, which saves time and money
• Free to use distributed computing on World Community Grid, and the workflow is simpler than using conventional supercomputers

Disadvantages

• Concern around intellectual property ownership and whether companies will develop drugs coming from effort
• Need for experimental assays will always be a factor
• Testing in vitro and in vivo is not free, nor are the samples of the compounds

     

The Effects of Sub-Regional Climate Velocity on the Distribution and Spatial Extent of Marine Species Assemblages

Many studies illustrate variable patterns in individual species distribution shifts in response to changing temperature. However, an assemblage, a group of species that shares a common environmental niche, will likely exhibit similar responses to climate changes, and these community-level responses may have significant implications for ecosystem function. Therefore, we examine the relationship between observed shifts of species in assemblages and regional climate velocity (i.e., the rate and direction of change of temperature isotherms). The assemblages are defined in two sub-regions of the U.S. Northeast Shelf that have heterogeneous oceanography and bathymetry using four decades of bottom trawl survey data and we explore temporal changes in distribution, spatial range extent, thermal habitat area, and biomass, within assemblages. These sub-regional analyses allow the dissection of the relative roles of regional climate velocity and local physiography in shaping observed distribution shifts. We find that assemblages of species associated with shallower, warmer waters tend to shift west-southwest and to shallower waters over time, possibly towards cooler temperatures in the semi-enclosed Gulf of Maine, while species assemblages associated with relatively cooler and deeper waters shift deeper, but with little latitudinal change. Conversely, species assemblages associated with warmer and shallower water on the broad, shallow continental shelf from the Mid-Atlantic Bight to Georges Bank shift strongly northeast along latitudinal gradients with little change in depth. Shifts in depth among the southern species associated with deeper and cooler waters are more variable, although predominantly shifts are toward deeper waters. In addition, spatial expansion and contraction of species assemblages in each region corresponds to the area of suitable thermal habitat, but is inversely related to assemblage biomass. This suggests that assemblage distribution shifts in conjunction with expansion or contraction of thermal habitat acts to compress or stretch marine species assemblages, which may respectively amplify or dilute species interactions to an extent that is rarely considered. Overall, regional differences in climate change effects on the movement and extent of species assemblages hold important implications for management, mitigation, and adaptation on the U.S. Northeast Shelf.