Peridotite, kimberlite, and carbonatite explained in the system CaO-MgO-SiO_2-CO_2

The key to the origin of carbonatite and kimberlite lies in the system CaO-MgO-SiO_2-CO_2. Increase in pressure causes a carbonation reaction in the peridotite assemblage as follows: forsterite + clinopyroxene + CO_2 ⇌ orthopyroxene + carbonate (Ca:Mg::70:30). This reaction passes through 15 kb–960°C with slope 45 b/°C and terminates at an invariant point near 25 kb-1200°C, where melting begins. This intersection of the carbonation reaction with the solidus introduces primary carbonate minerals alongside peridotite minerals on the liquidus surface. At 20 kb the melting temperature of the peridotite assemblage Fo + Opx + Cpx is lowered 75°C by solution of about 5 wt percent CO_2. The liquid corresponds to undersilicated basic magma. Stabilization of carbonate increases CO_2 solubility in the liquid, and above 25 kb the liquidus reaction involving Fo + Opx + Cpx + CO_2 sweeps down through 400°C via a pressure maximum at 32 kb to meet the invariant point at 25 kb. The peridotite solidus curve at higher pressures involves fusion of silicates and carbonates, producing a carbonatitic liquid with more than 45 wt percent CO_2. Progressive fusion produces a kimberlitic liquid. There is an intricate series of reactions between 25 kb and 35 kb involving changes in silicate and carbonate phase fields on the CO_2-saturated liquidus surface. Fractional crystallization of CO_2-bearing under-silicated basic magmas at most pressures yields residual kimberlite and carbonatite. Kimberlite and carbonatite magmas rising from the asthenosphere evolve CO_2 as they reach a reaction boundary at a depth of about 100 to 80 km. This contributes to their explosive eruption. Free CO_2 cannot coexist with subsolidus mantle peridotite with normal temperature distributions. CO_2 appears to be as effective as H_2O in causing incipient melting in the asthenosphere

List-Decoding Homomorphism Codes with Arbitrary Codomains

The codewords of the homomorphism code aHom(G,H) are the affine homomorphisms between two finite groups, G and H, generalizing Hadamard codes. Following the work of Goldreich-Levin (1989), Grigorescu et al. (2006), Dinur et al. (2008), and Guo and Sudan (2014), we further expand the range of groups for which local list-decoding is possible up to mindist, the minimum distance of the code. In particular, for the first time, we do not require either G or H to be solvable. Specifically, we demonstrate a poly(1/epsilon) bound on the list size, i. e., on the number of codewords within distance (mindist-epsilon) from any received word, when G is either abelian or an alternating group, and H is an arbitrary (finite or infinite) group. We conjecture that a similar bound holds for all finite simple groups as domains; the alternating groups serve as the first test case. The abelian vs. arbitrary result permits us to adapt previous techniques to obtain efficient local list-decoding for this case. We also obtain efficient local list-decoding for the permutation representations of alternating groups (the codomain is a symmetric group) under the restriction that the domain G=A_n is paired with codomain H=S_m satisfying m < 2^{n-1}/sqrt{n}. The limitations on the codomain in the latter case arise from severe technical difficulties stemming from the need to solve the homomorphism extension (HomExt) problem in certain cases; these are addressed in a separate paper (Wuu 2018). We introduce an intermediate "semi-algorithmic" model we call Certificate List-Decoding that bypasses the HomExt bottleneck and works in the alternating vs. arbitrary setting. A certificate list-decoder produces partial homomorphisms that uniquely extend to the homomorphisms in the list. A homomorphism extender applied to a list of certificates yields the desired list

An integrated cell-free metabolic platform for protein production and synthetic biology

Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements

Cell cycle analysis and synchronization of pluripotent hematopoietic progenitor stem cells

Hematopoietic stem cells purified from mouse bone marrow are quiescent with less than 2% of Lin- Hoechst(low)/Rhodamine(low) (Lin- Ho(low)/Rho(low)) and 10% to 15% of Lin-/Sca+ cells in S phase. These cells enter proliferative cycle and progress through G1 and into S phase in the presence of cytokines and 5% heat-inactivated fetal calf serum (HI-FCS). Cytokine-stimulated Lin- Ho(low)/Rho(low) cells took 36 to 40 hours to complete first division and only 12 hours to complete each of 5 subsequent divisions. These cells require 16 to 18 hours to transit through G0/G1 period and 28 to 30 hours to enter into mid-S phase during the first cycle. Up to 56% of Lin- Rho(low)/Ho(low) cells are high-proliferative potential (7 factor-responsive) colony-forming cells (HPP-CFC). At isolation, HPP-CFC are quiescent, but after 28 to 30 hours of culture, greater than 60% are in S phase. Isoleucine-deprivation of Lin- Ho(low)/Rho(low) cells in S phase of first cycle reversibly blocked them from entering into second cycle. After the release from isoleucine-block, these cells exhibited a G1 period of less than 2 hours and entered into mid-S phase by 12 hours. Thus, the duration of G1 phase of the cells in second cycle is 4 to 5 times shorter than that observed in their first cycle. Similar cell cycle kinetics are observed with Lin-/Sca+ population of bone marrow cells. Stem cell factor (SCF) alone, in the presence of HI-FCS, is as effective as a cocktail of 2 to 7 cytokines in inducing quiescent Lin-/Sca+ cells to enter into proliferative cycle. Aphidicolin treatment reversibly blocked cytokine-stimulated Lin-/Sca+ cells at G1/S boundary, allowing their tight synchrony as they progress through first S phase and enter into second G1. For these cells also, SCF alone is sufficient for their progression through S phase. These studies indicate a very short G1 phase for stem cells induced to proliferate and offer experimental approaches to synchronize murine hematopoietic stem cells

Rising CO₂ drives divergence in water use efficiency of evergreen and deciduous plants

Intrinsic water use efficiency (iWUE), defined as the ratio of photosynthesis to stomatal conductance, is a key variable in plant physiology and ecology. Yet, how rising atmospheric CO2 concentration affects iWUE at broad species and ecosystem scales is poorly understood. In a field-based study of 244 woody angiosperm species across eight biomes over the past 25 years of increasing atmospheric CO2 (~45 ppm), we show that iWUE in evergreen species has increased more rapidly than in deciduous species. Specifically, the difference in iWUE gain between evergreen and deciduous taxa diverges along a mean annual temperature gradient from tropical to boreal forests and follows similar observed trends in leaf functional traits such as leaf mass per area. Synthesis of multiple lines of evidence supports our findings. This study provides timely insights into the impact of Anthropocene climate change on forest ecosystems and will aid the development of next-generation trait-based vegetation models

Humoral response to neurofilaments and dipeptide repeats in ALS progression

Abstract Objective To appraise the utility as biomarkers of blood antibodies and immune complexes to neurofilaments and dipeptide repeat proteins, the products of translation of the most common genetic mutation in amyotrophic lateral sclerosis (ALS). Methods Antibodies and immune complexes against neurofilament light, medium, heavy chains as well as poly‐(GP)‐(GR) dipeptide repeats were measured in blood samples from the ALS Biomarkers (n = 107) and the phenotype–genotype biomarker (n = 129) studies and in 140 healthy controls. Target analyte levels were studied longitudinally in 37 ALS cases. Participants were stratified according to the rate of disease progression estimated before and after baseline and C9orf72 genetic status. Survival and longitudinal analyses were undertaken with reference to matched neurofilament protein expression. Results Compared to healthy controls, total neurofilament proteins and antibodies, neurofilament light immune complexes (p < 0.0001), and neurofilament heavy antibodies (p = 0.0061) were significantly elevated in ALS, patients with faster progressing disease (p < 0.0001) and in ALS cases with a C9orf72 mutation (p < 0.0003). Blood neurofilament light protein discriminated better ALS from healthy controls (AUC: 0.92; p < 0.0001) and faster from slower progressing ALS (AUC: 0.86; p < 0.0001) compared to heavy‐chain antibodies and light‐chain immune complexes (AUC: 0.79; p < 0.0001 and AUC: 0.74; p < 0.0001). Lower neurofilament heavy antibodies were associated with longer survival (Log‐rank Chi‐square: 7.39; p = 0.0065). Increasing levels of antibodies and immune complexes between time points were observed in faster progressing ALS. Conclusions We report a distinctive humoral response characterized by raising antibodies against neurofilaments and dipeptide repeats in faster progressing and C9orf72 genetic mutation carriers ALS patients. We confirm the significance of plasma neurofilament proteins in the clinical stratification of ALS

Bounded version vectors

Version vectors play a central role in update tracking under optimistic distributed systems, allowing the detection of obsolete or inconsistent versions of replicated data. Version vectors do not have a bounded representation; they are based on integer counters that grow indefinitely as updates occur. Existing approaches to this problem are scarce; the mechanisms proposed are either unbounded or operate only under specific settings. This paper examines version vectors as a mechanism for data causality tracking and clarifies their role with respect to vector clocks. Then, it introduces bounded stamps and proves them to be a correct alternative to integer counters in version vectors. The resulting mechanism, bounded version vectors, represents the first bounded solution to data causality tracking between replicas subject to local updates and pairwise symmetrical synchronization.FCT project POSI/ICHS/44304/2002, FCT under grant BSAB/390/2003

An integrated cell-free metabolic platform for protein production and synthetic biology

Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements