Synchronous Context-Free Grammars and Optimal Linear Parsing Strategies

Synchronous Context-Free Grammars (SCFGs), also known as syntax-directed translation schemata, are unlike context-free grammars in that they do not have a binary normal form. In general, parsing with SCFGs takes space and time polynomial in the length of the input strings, but with the degree of the polynomial depending on the permutations of the SCFG rules. We consider linear parsing strategies, which add one nonterminal at a time. We show that for a given input permutation, the problems of finding the linear parsing strategy with the minimum space and time complexity are both NP-hard

Shell reworking impacts on climate variability reconstructions using individual foraminiferal analyses

Particle mixing by benthic fauna beneath the sediment‐water interface (or bioturbation) fundamentally challenges the proxy based retrieval of past climatic conditions from deep‐sea sediment cores. Previous efforts targeted the impacts of bioturbation on the nature of paleoceanographic changes gleaned from the proxy record, whereas impacts on seasonal and/or interannual variability reconstructions have received less attention. We present TurbIFA (Tracking uncertainty of reworking & bioturbation on IFA), a software that adapts and combines existing algorithms to quantitatively estimate the impact of sediment reworking and other uncertainties and assess significance of ocean and climate variability reconstructions based on individual foraminiferal analyses (IFA). Building upon previous idealized investigations of bioturbation using hydroclimate‐sediment simulations, TurbIFA advances the IFA proxy system modeling such that users may directly assess the sensitivity of their data to various local parameters related to shell reworking across the global ocean. Using the output of state‐of‐the‐art coupled atmosphere‐ocean general circulation models, TurbIFA simulates planktic foraminiferal δ 18 O or Mg/Ca‐temperature signal carriers and evaluates uncertainties in the sample size, analytical protocols along with as those arising from bioturbation. Application of TurbIFA to synthetic and existing data sets indicates that the significance of IFA‐based reconstructions can be assessed once the impacts of sediment accumulation rates, sediment mixed layer depths, length of time integrated by the chosen IFA sampling interval, and changes in the amplitude of climate variability (i.e., the targeted environmental signal) are comprehensively evaluated. We contend that TurbIFA can aid quantitative assessments of past seasonal and interannual variability gleaned from the paleoceanographic record.Universidade de Vigo/CISUGMinisterio de Universidades | Ref. BG20-00157Agencia Estatal de Investigación | Ref. PID2019‐109653RB‐10

Effects of membrane and biological target on the structural and allosteric properties of recoverin: a computational approach

Recoverin (Rec) is a prototypical calcium sensor protein primarily expressed in the vertebrate retina. The binding of two Ca2+ ions to the functional EF-hand motifs induces the extrusion of a myristoyl group that increases the affinity of Rec for the membrane and leads to the formation of a complex with rhodopsin kinase (GRK1). Here, unbiased all-atom molecular dynamics simulations were performed to monitor the spontaneous insertion of the myristoyl group into a model multicomponent biological membrane for both isolated Rec and for its complex with a peptide from the GRK1 target. It was found that the functional membrane anchoring of the myristoyl group is triggered by persistent electrostatic protein-membrane interactions. In particular, salt bridges between Arg43, Arg46 and polar heads of phosphatidylserine lipids are necessary to enhance the myristoyl hydrophobic packing in the Rec-GRK1 assembly. The long-distance communication between Ca2+-binding EF-hands and residues at the interface with GRK1 is significantly influenced by the presence of the membrane, which leads to dramatic changes in the connectivity of amino acids mediating the highest number of persistent interactions (hubs). In conclusion, specific membrane composition and allosteric interactions are both necessary for the correct assembly and dynamics of functional Rec-GRK1 complex

A model for archaeologically relevant Holocene climate impacts in the Aegean-Levantine region (easternmost Mediterranean)

A repeating pattern of multi-centennial-scale Holocene climate events has been widely (globally) documented, and they were termed Rapid Climate Change (RCC) events. Non-seasalt potassium ion (K+) series in Greenland ice cores provide well-constrained timings for the events, and a direct timing relationship has been inferred between these events and the frequency of northerly cold polar/continental air outbreaks over the eastern Mediterranean Sea through gaps in the mountain ranges along the northern margin of the basin. There also appears to be a remarkable timing agreement with major archaeological turnover events in the Aegean/Levantine region. Yet no physically consistent assessment exists for understanding the regional climatic impacts of the events around this critical region. We present a simple 2-dimensional Lagrangian model, which yields a broad suite of physically coherent simulations of the impacts of frequency changes in winter-time northerly air outbreaks over the Aegean/Levantine region. We validate this with existing reconstructions from palaeoclimate proxy data, with emphasis on well-validated sea-surface temperature reconstructions and a highly resolved cave speleothem stable oxygen isotope record from Lebanon. Given that the RCCs were clearly marked by negative sea surface temperature anomalies in the region, we find that the predominant climatic impacts of this winter-time mechanism were “cold and wet,” in contrast with intercalated “warmer and more arid” conditions of non-RCC periods. More specifically, the RCCs are found to be periods of highly variable conditions, with an overall tendency toward cold and wet conditions with potential for flash flooding and for episodic snow-cover at low altitudes, at least in the lower-altitude (lower 1–1.5 km) regions of Crete and the Levant. The modelled winter-anomaly process cannot address underlying longer-term, astronomically forced trends, or the relatively warm and arid anomalies in between RCCs. The latter require further study, for example with respect to potential (summer-time?) extension of evaporative subtropical conditions over the region. Finally, our results imply that the “amount effect” observed in Levantine cave δ18O (and precipitation or drip-water δ18O) may not reflect the conventional concept related to temperature-dependent fractionation and Rayleigh distillation. Instead, it appears to arise from a complex and somewhat counter-intuitive mixing, in shifting proportionalities, between advected (external) and evaporated (Mediterranean) moisture.Australian Laureate Fellowship | Ref. FL120100050Universidade de Vig

Quantification of african monsoon runoff during last interglacial sapropel S5

Organic‐rich sapropel layers punctuate the eastern Mediterranean sedimentary sequence, recording deep‐sea anoxic events. The timing of sapropel deposition coincides with precession minima, which are associated with the northward migration of the monsoon rain belt over North Africa. The resultant increase in monsoon precipitation over the Sahara caused an increase in low‐δ 18 O freshwater runoff into eastern Mediterranean surface waters, which is reflected by negative δ 18 O anomalies in the records of planktic foraminiferal calcite. However, despite extensive research on sapropels, the magnitude of monsoon intensification and freshwater runoff, along with its influence on δ 18 O, remains elusive. Here, we present a quantification of African monsoon freshwater runoff into the eastern Mediterranean for the period of deposition of last interglacial sapropel S5 (~128.3–121.5 ka). Our method uses a box model of the Mediterranean Sea, which represents different water masses, and has been calibrated using δ 18 O from planktic foraminiferal species of different depth and seasonal habitats. The model was constrained with existing records of sea level and sea surface temperature then inverted to deconvolve the δ 18 O signal of the surface‐dwelling foraminiferal species Globigerinoides ruber (w) and calculate the freshwater runoff volume. Our calculated African monsoon runoff suggests large increases in freshwater discharge to the eastern Mediterranean (up to ~8.8 times the modern pre‐Aswan Nile discharge). Rapid onset of S5 deposition following the estimated increase in runoff strongly suggests a preconditioning of the eastern Mediterranean for sapropel deposition. Our study also provides insight into the stratification and warming of eastern Mediterranean surface waters during the S5 interval.Australian Research Council | Ref. FL120100050Australian Research Council | Ref. DE190100042Australia-New Zealand IODP Consortium | Ref. LE140100047Australia-New Zealand IODP Consortium | Ref. LE16010006

Prep1.1 has essential genetic functions in hindbrain development and cranial neural crest cell differentiation

In this study we analysed the function of the Meinox gene prep1.1 during zebrafish development. Meinox proteins form heterotrimeric complexes with Hox and Pbx members, increasing the DNA binding specificity of Hox proteins in vitro and in vivo. However, a role for a specific Meinox protein in the regulation of Hox activity in vivo has not been demonstrated. In situ hybridization showed that prep1.1 is expressed maternally and ubiquitously up to 24 hours post-fertilization (hpf), and restricted to the head from 48 hpf onwards. Morpholino-induced prep1.1 loss-of-function caused significant apoptosis in the CNS. Hindbrain segmentation and patterning was affected severely, as revealed by either loss or defective expression of several hindbrain markers ( foxb1.2/mariposa , krox20 , pax2.1 and pax6.1 ), including anteriorly expressed Hox genes ( hoxb1a , hoxa2 and hoxb2 ), the impaired migration of facial nerve motor neurons, and the lack of reticulospinal neurons (RSNs) except Mauthner cells. Furthermore, the heads of prep1.1 morphants lacked all pharyngeal cartilages. This was not caused by the absence of neural crest cells or their impaired migration into the pharyngeal arches, as shown by expression of dlx2 and snail1 , but by the inability of these cells to differentiate into chondroblasts. Our results indicate that prep1.1 has a unique genetic function in craniofacial chondrogenesis and, acting as a member of Meinox-Pbc-Hox trimers, it plays an essential role in hindbrain development