Assembly of alternative prothrombinase by extracellular histones initiates and disseminates intravascular coagulation.

Thrombin generation is pivotal to both physiological blood clot formation and pathological development of disseminated intravascular coagulation (DIC). In critical illness, extensive cell damage can release histones into the circulation, which can increase thrombin generation and cause DIC, but the molecular mechanism is not clear. Typically, thrombin is generated by the prothrombinase complex, comprising activated factor X (FXa), activated cofactor V (FVa), and phospholipids to cleave prothrombin in the presence of calcium. In this study, we found that in the presence of extracellular histones, an alternative prothrombinase could form without FVa and phospholipids. Histones directly bind to prothrombin fragment 1 (F1) and fragment 2 (F2) specifically to facilitate FXa cleavage of prothrombin to release active thrombin, unlike FVa, which requires phospholipid surfaces to anchor the classical prothrombinase complex. In vivo, histone infusion into mice induced DIC, which was significantly abrogated when prothrombin F1 + F2 were infused prior to histones, to act as decoy. In a cohort of intensive care unit patients with sepsis (n = 144), circulating histone levels were significantly elevated in patients with DIC. These data suggest that histone-induced alternative prothrombinase without phospholipid anchorage may disseminate intravascular coagulation and reveal a new molecular mechanism of thrombin generation and DIC development. In addition, histones significantly reduced the requirement for FXa in the coagulation cascade to enable clot formation in factor VIII (FVIII)- and FIX-deficient plasma, as well as in FVIII-deficient mice. In summary, this study highlights a novel mechanism in coagulation with therapeutic potential in both targeting systemic coagulation activation and correcting coagulation factor deficiency.

Non-Hermitian cavity quantum electrodynamics-configuration interaction singles approach for polaritonic structure with ab initio molecular Hamiltonians.

We combine ab initio molecular electronic Hamiltonians with a cavity quantum electrodynamics model for dissipative photonic modes and apply mean-field theories to the ground- and excited-states of resulting polaritonic systems. In particular, we develop a non-Hermitian configuration interaction singles theory for mean-field ground- and excited-states of the molecular system strongly interacting with a photonic mode and apply these methods to elucidating the phenomenology of paradigmatic polaritonic systems. We leverage the Psi4Numpy framework to yield open-source and accessible reference implementations of these methods.

Cross Talk Pathways Between Coagulation and Inflammation.

Anatomic pathology studies performed over 150 years ago revealed that excessive activation of coagulation occurs in the setting of inflammation. However, it has taken over a century since these seminal observations were made to delineate the molecular mechanisms by which these systems interact and the extent to which they participate in the pathogenesis of multiple diseases. There is, in fact, extensive cross talk between coagulation and inflammation, whereby activation of one system may amplify activation of the other, a situation that, if unopposed, may result in tissue damage or even multiorgan failure. Characterizing the common triggers and pathways are key for the strategic design of effective therapeutic interventions. In this review, we highlight some of the key molecular interactions, some of which are already showing promise as therapeutic targets for inflammatory and thrombotic disorders.

Comparing the yields of organic and conventional agriculture.

Numerous reports have emphasized the need for major changes in the global food system: agriculture must meet the twin challenge of feeding a growing population, with rising demand for meat and high-calorie diets, while simultaneously minimizing its global environmental impacts. Organic farming­a system aimed at producing food with minimal harm to ecosystems, animals or humans­is often proposed as a solution. However, critics argue that organic agriculture may have lower yields and would therefore need more land to produce the same amount of food as conventional farms, resulting in more widespread deforestation and biodiversity loss, and thus undermining the environmental benefits of organic practices. Here we use a comprehensive meta-analysis to examine the relative yield performance of organic and conventional farming systems globally. Our analysis of available data shows that, overall, organic yields are typically lower than conventional yields. But these yield differences are highly contextual, depending on system and site characteristics, and range from 5% lower organic yields (rain-fed legumes and perennials on weak-acidic to weak-alkaline soils), 13% lower yields (when best organic practices are used), to 34% lower yields (when the conventional and organic systems are most comparable). Under certain conditions­that is, with good management practices, particular crop types and growing conditions­organic systems can thus nearly match conventional yields, whereas under others it at present cannot. To establish organic agriculture as an important tool in sustainable food production, the factors limiting organic yields need to be more fully understood, alongside assessments of the many social, environmental and economic benefits of organic farming systems.

Closing yield gaps through nutrient and water management.

In the coming decades, a crucial challenge for humanity will be meeting future food demands without undermining further the integrity of the Earth's environmental systems. Agricultural systems are already major forces of global environmental degradation, but population growth and increasing consumption of calorie- and meat-intensive diets are expected to roughly double human food demand by 2050 (ref. 3). Responding to these pressures, there is increasing focus on 'sustainable intensification' as a means to increase yields on underperforming landscapes while simultaneously decreasing the environmental impacts of agricultural systems. However, it is unclear what such efforts might entail for the future of global agricultural landscapes. Here we present a global-scale assessment of intensification prospects from closing 'yield gaps' (differences between observed yields and those attainable in a given region), the spatial patterns of agricultural management practices and yield limitation, and the management changes that may be necessary to achieve increased yields. We find that global yield variability is heavily controlled by fertilizer use, irrigation and climate. Large production increases (45% to 70% for most crops) are possible from closing yield gaps to 100% of attainable yields, and the changes to management practices that are needed to close yield gaps vary considerably by region and current intensity. Furthermore, we find that there are large opportunities to reduce the environmental impact of agriculture by eliminating nutrient overuse, while still allowing an approximately 30% increase in production of major cereals (maize, wheat and rice). Meeting the food security and sustainability challenges of the coming decades is possible, but will require considerable changes in nutrient and water management.

Social equity and primary healthcare financing: lessons from New Zealand.

This paper reviews the effect of a primary care financing scheme introduced in New Zealand as a component of the New Zealand Primary Health Care Strategy, a comprehensive reform of the way that primary healthcare was governed, financed and delivered. The population-based funding formulae incorporated an area-based measure of social deprivation and ethnicity in an explicit attempt to improve access to care for certain population groups and fund social interventions aimed at addressing conditions that lead to improved health outcomes. The New Zealand experience shows that introducing a nationwide, comprehensive program to improve access and reduce health disparities is possible. However, the effect of this effort on reducing health disparities is not entirely clear because success ultimately relies on local implementation of a complex set of interventions that need to be evaluated more rigorously. In addition, the partial subsidies for first contact care that came with the Strategy have been shown to improve access, but, the success of this approach relies on compliance by private-practising general practitioners with a fee reduction regimen, which is subject to local variation.

Plasmin(ogen) at the Nexus of Fibrinolysis, Inflammation, and Complement.

The diverse mechanisms by which the plasmin(ogen) system is involved in human physiology and pathology are constantly being delineated. For many years, the plasmin(ogen) system was chiefly known as the system responsible for vascular fibrinolysis. Although this is an important function of the plasmin(ogen) system, we now recognize that plasmin(ogen) is critically important as a mediator of inflammation and the innate immune system, which impacts upon a diverse set of mechanisms underlying the pathologies of many diseases. The current review focuses on recent developments in plasmin(ogen) system activation and regulation and how dysregulation of this finely tuned system may contribute to inflammatory disease (atherosclerosis), impaired wound healing, and infection.

Solutions for a cultivated planet.

Increasing population and consumption are placing unprecedented demands on agriculture and natural resources. Today, approximately a billion people are chronically malnourished while our agricultural systems are concurrently degrading land, water, biodiversity and climate on a global scale. To meet the world's future food security and sustainability needs, food production must grow substantially while, at the same time, agriculture's environmental footprint must shrink dramatically. Here we analyse solutions to this dilemma, showing that tremendous progress could be made by halting agricultural expansion, closing 'yield gaps' on underperforming lands, increasing cropping efficiency, shifting diets and reducing waste. Together, these strategies could double food production while greatly reducing the environmental impacts of agriculture.

Global agriculture and carbon trade-offs.

Feeding a growing and increasingly affluent world will require expanded agricultural production, which may require converting grasslands and forests into cropland. Such conversions can reduce carbon storage, habitat provision, and other ecosystem services, presenting difficult societal trade-offs. In this paper, we use spatially explicit data on agricultural productivity and carbon storage in a global analysis to find where agricultural extensification should occur to meet growing demand while minimizing carbon emissions from land use change. Selective extensification saves ∼ 6 billion metric tons of carbon compared with a business-as-usual approach, with a value of approximately $1 trillion (2012 US dollars) using recent estimates of the social cost of carbon. This type of spatially explicit geospatial analysis can be expanded to include other ecosystem services and other industries to analyze how to minimize conflicts between economic development and environmental sustainability.

Procoagulant activity in stored units of red blood cells.

The procoagulant activity (PA) of stored units of red blood cells (RBC) increases over time, which is related to the expression/exposure of tissue factor (TF). However, there is a discrepancy between the TF measured and changes in PA observed, suggesting that other blood components contribute to this activity. Our goal was to evaluate changes in PA of stored RBCs and to determine possible contributors to it. RBC units from 4 healthy donors were prepared and stored at 4 °C. On selected days, RBC aliquots were reconstituted with autologous plasma and tested in the thromboelastography assay. Corresponding supernatants were tested in a clotting assay. For all donors, the clotting time (CT) of reconstituted RBC units decreased from ∼3000-4000s on day 1 to ∼1000-1600s on day 30, with the most dramatic changes occurring between days 1 and 5. Anti-TF antibody slightly prolonged the CT. The concentration of TF did not change significantly over time and was within the range of 0.3-2.3 pM. Bovine lactadherin (LTD) prolonged the CT of the RBC (by 2.4-3.4-fold in days 3-5 and by 1.3-1.8-fold at day 30). Anti-TF antibody together with LTD had a cumulative effect on the CT prolongation. CT of supernatants responded to both anti-TF and anti-FXIa antibodies. Three contributors to the PA of stored RBC were identified, i.e. FXIa in solution and phosphatidylserine and TF exposed on blood cells and microparticles. Failure of LTD and antibodies to completely eliminate PA suggests that other components of blood could contribute to it.

Targeting ultrasound remission in early rheumatoid arthritis: the results of the TaSER study, a randomised clinical trial.

OBJECTIVE: To investigate whether an intensive early rheumatoid arthritis (RA) treat-to-target (T2T) strategy could be improved through the use of musculoskeletal ultrasound (MSUS) assessment of disease activity. METHODS: 111 newly diagnosed patients with RA or undifferentiated arthritis (symptom duration <1 year) were randomised to strategies that aimed to attain either DAS28-erythrocyte sedimentation rate (ESR)<3.2 (control) or a total power Doppler joint count≤1 during a combined DAS28-ESR/MSUS assessment (intervention). MSUS examination was indicated if: DAS28-ESR<3.2 or DAS28-ESR≥3.2 with two swollen joints. Step-up disease-modifying antirheumatic drug (DMARD) escalation was standardised: methotrexate monotherapy, triple therapy and then etanercept/triple therapy. American College of Rheumatology (ACR) core-set variables were assessed 3 monthly by a metrologist blinded to group allocation. MRI of dominant hand and wrist, and plain radiographs of hands and feet were undertaken at baseline and 18 months for grading by two readers using the Outcome Measures in Rheumatology (OMERACT) Rheumatoid Arthritis MRI Scoring System (RAMRIS) and van der Heijde/Sharp Score, respectively. The coprimary outcomes were mean change from baseline of DAS44 and RAMRIS erosion score. RESULTS: Groups were matched for baseline clinical, demographic and radiographic features. The intervention group received more intensive DMARD therapy. Both groups demonstrated significant improvements in DAS44 (mean change: control -2.58, intervention -2.69; 95% CI difference between groups -0.70 to 0.48; p=0.72). There were no significant between-group differences for any ACR core-set variables, except DAS44 remission after 18 months (control 43%, intervention 66%; p=0.03). There was minimal progression of MRI and radiographic erosions and no difference in imaging outcomes or serious adverse event rates. CONCLUSIONS: In early RA, a MSUS-driven T2T strategy led to more intensive treatment, but was not associated with significantly better clinical or imaging outcomes than a DAS28-driven strategy. TRIAL REGISTRATION NUMBER: NCT00920478.

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci.

While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. However, the exact contribution of these two factors in regulating expression noise has not been explored. Using a dual-reporter lentiviral model system, we deconvolved the influence of the promoter sequence to systematically study the contribution of the chromatin environment at different genomic locations in regulating expression noise. By integrating a large-scale analysis to quantify mRNA levels by smFISH and protein levels by flow cytometry in single cells, we found that mean expression and noise are uncorrelated across genomic locations. Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. Finally, we showed that genomic locations displaying higher expression noise are associated with more repressed chromatin, thereby indicating the contribution of the chromatin environment in regulating expression noise.

Polyphosphate suppresses complement via the terminal pathway.

Polyphosphate, synthesized by all cells, is a linear polymer of inorganic phosphate. When released into the circulation, it exerts prothrombotic and proinflammatory activities by modulating steps in the coagulation cascade. We examined the role of polyphosphate in regulating the evolutionarily related proteolytic cascade complement. In erythrocyte lysis assays, polyphosphate comprising more than 1000 phosphate units suppressed total hemolytic activity with a concentration to reduce maximal lysis to 50% that was 10-fold lower than with monophosphate. In the ion- and enzyme-independent terminal pathway complement assay, polyphosphate suppressed complement in a concentration- and size-dependent manner. Phosphatase-treated polyphosphate lost its ability to suppress complement, confirming that polymer integrity is required. Sequential addition of polyphosphate to the terminal pathway assay showed that polyphosphate interferes with complement only when added before formation of the C5b-7 complex. Physicochemical analyses using native gels, gel filtration, and differential scanning fluorimetry revealed that polyphosphate binds to and destabilizes C5b,6, thereby reducing the capacity of the membrane attack complex to bind to and lyse the target cell. In summary, we have added another function to polyphosphate in blood, demonstrating that it dampens the innate immune response by suppressing complement. These findings further establish the complex relationship between coagulation and innate immunity.

Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.

Custom-made zinc-finger nucleases (ZFNs) can induce targeted genome modifications with high efficiency in cell types including Drosophila, C. elegans, plants, and humans. A bottleneck in the application of ZFN technology has been the generation of highly specific engineered zinc-finger arrays. Here we describe OPEN (Oligomerized Pool ENgineering), a rapid, publicly available strategy for constructing multifinger arrays, which we show is more effective than the previously published modular assembly method. We used OPEN to construct 37 highly active ZFN pairs which induced targeted alterations with high efficiencies (1%-50%) at 11 different target sites located within three endogenous human genes (VEGF-A, HoxB13, and CFTR), an endogenous plant gene (tobacco SuRA), and a chromosomally integrated EGFP reporter gene. In summary, OPEN provides an "open-source" method for rapidly engineering highly active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN technology for biological research and gene therapy.

Design of emitter structures based on resonant perfect absorption for thermophotovoltaic applications.

We report a class of thermophotovoltaic emitter structures built upon planar films that support resonant modes, known as perfectly-absorbing modes, that facilitate an exceptional optical response for selective emission. These planar structures have several key advantages over previously-proposed designs for TPV applications: they are simple to fabricate, are stable across a range of temperatures and conditions, and are capable of achieving some of the highest spectral efficiencies reported of any class of emitter structure. Utilization of these emitters leads to exceptionally high device efficiencies under low operating temperature conditions, which should open new opportunities for waste heat management. We present a theoretical framework for understanding this performance, and show that this framework can be leveraged as a search algorithm for promising candidate structures. In addition to providing an efficient theoretical methodology for identifying high-performance emitter structures, our methodology provides new insight into underlying design principles and should pave way for future design of structures that are simple to fabricate, temperature stable, and possess exceptional optical properties.

Hi-Fi SELEX: A High-Fidelity Digital-PCR Based Therapeutic Aptamer Discovery Platform.

Current technologies for aptamer discovery typically leverage the systematic evolution of ligands by exponential enrichment (SELEX) concept by recursively panning semi-combinatorial ssDNA or RNA libraries against a molecular target. The expectation is that this iterative selection process will be sufficiently stringent to identify a candidate pool of specific high-affinity aptamers. However, failure of this process to yield promising aptamers is common, due in part to (i) limitations in library designs, (ii) retention of non-specific aptamers during screening rounds, (iii) excessive accumulation of amplification artifacts, and (iv) the use of screening criteria (binding affinity) that does not reflect therapeutic activity. We report a new selection platform, High-Fidelity (Hi-Fi) SELEX, that introduces fixed-region blocking elements to safeguard the functional diversity of the library. The chemistry of the target-display surface and the composition of the equilibration solvent are engineered to strongly inhibit non-specific retention of aptamers. Partition efficiencies approaching 10(6) are thereby realized. Retained members are amplified in Hi-Fi SELEX by digital PCR in a manner that ensures both elimination of amplification artifacts and stoichiometric conversion of amplicons into the single-stranded library required for the next selection round. Improvements to aptamer selections are first demonstrated using human α-thrombin as the target. Three clinical targets (human factors IXa, X, and D) are then subjected to Hi-Fi SELEX. For each, rapid enrichment of ssDNA aptamers offering an order-nM mean equilibrium dissociation constant (Kd) is achieved within three selection rounds, as quantified by a new label-free qPCR assay reported here. Therapeutic candidates against factor D are identified.

Reversible Modulation of Surface Plasmons in Gold Nanoparticles Enabled by Surface Redox Chemistry.

Switchable surface redox chemistry is demonstrated in gold@iron/iron oxide core-shell nanoparticles with ambient oxidation and plasmon-mediated reduction to modulate the oxidation state of shell layers. The iron shell can be oxidized to iron oxide through ambient oxidation, leading to an enhancement and red-shift of the gold surface plasmon resonance (SPR). This enhanced gold SPR can drive reduction of the iron oxide shell under broadband illumination to reversibly blue-shift and significantly dampen gold SPR absorption. The observed phenomena provide a unique mechanism for controlling the plasmonic properties and surface chemistry of small metal nanoparticles.

Solulin increases clot stability in whole blood from humans and dogs with hemophilia.

Solulin is a soluble form of thrombomodulin that is resistant to proteolysis and oxidation. It has been shown to increase the clot lysis time in factor VIII (fVIII)-deficient plasma by an activated thrombin-activatable fibrinolysis inhibitor (TAFIa)-dependent mechanism. In the present study, blood was drawn from humans and dogs with hemophilia, and thromboelastography was used to measure tissue factor-initiated fibrin formation and tissue-plasminogen activator-induced fibrinolysis. The kinetics of TAFI and protein C activation by the thrombin-Solulin complex were determined to describe the relative extent of anticoagulation and antifibrinolysis. In severe hemophilia A, clot stability increased by > 4-fold in the presence of Solulin while minimally affecting clot lysis time. Patients receiving fVIII/fIX prophylaxis showed a similar trend of increased clot stability in the presence of Solulin. The catalytic efficiencies of TAFI and protein C activation by the thrombin-Solulin complex were determined to be 1.53 and 0.02/µM/s, respectively, explaining its preference for antifibrinolysis over anticoagulation at low concentrations. Finally, hemophilic dogs given Solulin had improved clot strength in thromboelastography assays. In conclusion, the antifibrinolytic properties of Solulin are exhibited in hemophilic human (in vitro) and dog (in vivo/ex vivo) blood at low concentrations. Our findings suggest the therapeutic utility of Solulin at a range of very low doses.

An in-vitro assessment of tranexamic acid as an adjunct to rFVIII or rFVIIa treatment in haemophilia A.

Haemophilia is characterised by defective thrombin generation, reduced clot stability and spontaneous bleeding. Treatment with factor VIII (FVIII) concentrate or bypassing agents (e.g. recombinant factor VIIa (rFVIIa)) is generally effective. Occasionally, haemostasis is not achieved, which may reflect a failure of factor concentrate to normalise clot stability. Tranexamic acid (TXA) is often used to aid haemostasis in surgery (e.g. joint replacements and dental procedures). Used routinely as an adjunct, it may enhance clot stability and allow effective, reliable, and cost-effective treatment at lower doses of factor concentrate. This study hypothesised that clot stabilising adjunct TXA is required in addition to factor substitution to normalise clot stability in whole blood from patients with severe haemophilia A. The in vitro effect of varying concentrations of recombinant FVIII or recombinant FVIIa and adjunct TXA on whole blood clot stability was measured by thromboelastometry. Coagulation was triggered by tissue factor and clots were challenged with tissue plasminogen activator. The area under the elasticity curve was the primary endpoint. High concentrations of FVIII and rFVIIa increased clot stability to levels that were not significantly different from controls (Mean ± SD: control 112,694 ± 84,115; FVIII 78,662 ± 74,126; rFVIIa 95,918 ± 88,492). However, the response was highly variable between individuals and demonstrates why some patients show clinical resistance to treatment. Addition of TXA resulted in normalised clot stability in all individuals, even when combined with the lowest doses of factor concentrate. The results support the concept that a more efficient, reliable and cost effective treatment may be obtained if TXA is combined with factor concentrates to treat individuals with haemophilia.

Interfaced metal heterodimers in the quantum size regime.

Synthesis of nanoparticle dimers made of asymmetric compositions is very challenging because of the difficulty in manipulating the nanoparticles' surface chemistries in order to control the assembly and/or growth of different nanoparticles. In this Letter, we report a seed-mediated, surface-confined epitaxial overgrowth strategy that enables the synthesis of high-quality interfaced Au-Ag heterodimers in the quantum size regime (diameters <10 nm). Au and Ag share a common face-centered cubic lattice and have nearly identical lattice constants, which facilitates epitaxial overgrowth and allows direct contact between the Au and Ag domains. Quantum size effects, formation of the Au/Ag interfaces, and chemical interactions with surfactant molecules strongly influence the optical properties of the dimers and lead to the observation of unique surface plasmon resonances. In particular, we find an unusual enhancement of the characteristic Au surface plasmon resonance and the emergence of a charge transfer plasmon across the Au/Ag domains, which together lead to broad-band absorption spanning visible to near-infrared wavelengths. A model that captures the changes in optical behavior due to chemical interactions and quantum size effects is used to calculate the absorption spectra of the interfaced heterodimers, resulting in good agreement with experimental measurements.