Miracle-dz/UniFAR-FTUs huggingface dataset:
Change in the Australian desert culture: a reanalysis of tulas from Puntutjarpa

Abstract Claims for long‐term conservatism of an Australian desert adaptation are assessed by re‐examining one component of the stone artefact assemblage from Puntutjarpa, a rocksheiter in the Western Desert. It is concluded that significant technological changes occur and especially that adzing tools are absent from the early Holocene levels of the site. This finding confirms recent discoveries of demographic, settlement, and technological change elsewhere in the Australian arid zone; and it necessitates the rejection of perceptions of cultural continuity since the Western Desert was first occupied.
The Hidden Diversity of Vascular Patterns in Flower Heads

Vascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flowers heads. We imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism. The vascular system in the head of the model plant Gerbera hybrida is qualitatively different from those of Bellis perennis and Helianthus annuus, characterized previously. Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, and Tanacetum vulgare represent variants of the Bellis and Helianthus systems. In each species the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values. In spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature.
The Bearing of Rolled Garnets on the Concept of b-lineation in Moine Rocks

Abstract A preliminary examination of Moine rocks containing rolled garnets from three widely spaced localities in the North-West Highlands indicates that the lineation in all cases is parallel to b. This is in accord with Phillips' theory that the metamorphism of the Moine schists was due to movement in a north-easterly or south-westerly direction. A Caledonian age for the metamorphism of the Moines therefore appears to be unlikely.
Importin-7-dependent nuclear localization of the Flavivirus core protein is required for infectious virus production

Flaviviridae is a family of positive-stranded RNA viruses, including human pathogens such as Japanese encephalitis virus (JEV), dengue virus (DENV), zika virus (ZIKV), and West Nile virus (WNV). Nuclear localization of the viral core protein is conserved among Flaviviridae, and this feature may be targeted for developing broad-ranging anti-flavivirus drugs. However, the mechanism of core protein translocation to the nucleus and the importance of nuclear localization in the viral life cycle remain unknown. We aimed to identify the molecular mechanism underlying core protein nuclear translocation. We identified importin-7 (IPO7), an importin-β family protein, as a nuclear carrier for Flaviviridae core proteins. Nuclear import assays revealed that core protein was transported into the nucleus via IPO7, whereas IPO7 deletion by CRISPR/Cas9 impaired their nuclear localization. To understand the importance of core protein nuclear localization, we evaluated the production of infectious virus or single-round-infectious-particles in wild-type or IPO7-deficient cells; both processes were significantly impaired in IPO7-deficient cells, whereas intracellular infectious virus levels were equivalent in wild-type and IPO7-deficient cells. These data suggested that IPO7-mediated nuclear localization of core proteins plays a role in the release of infectious virus particles of flaviviruses.
How Fast Are the Tropics Expanding

AbstractDiagnosing the sensitivity of the tropical belt provides one framework for understanding how global precipitation patterns may change in a warming world. This paper seeks to understand boreal winter rates of subtropical dry zone expansion since 1979, and explores physical mechanisms. Various reanalysis estimates based on the latitude where zonal mean precipitation P exceeds evaporation E and the zero crossing latitude for the zonal mean meridional streamfunction () yield tropical width expansion rates in each hemisphere ranging from near zero to over 1° latitude decade−1. Comparisons with 30-yr trends computed from unforced climate model simulations indicate that the range among reanalyses is nearly an order of magnitude greater than the standard deviation of internal climate variability. Furthermore, comparisons with forced climate models indicate that this range is an order of magnitude greater than the forced change signal since 1979. Rapid widening rates during 1979–2009 derived from some rean.
Heterozygous expression of a Kcnt1 gain-of-function variant has differential effects on SST- and PV-expressing cortical GABAergic neurons

More than twenty recurrent missense gain-of-function (GOF) mutations have been identified in the sodium-activated potassium (KNa) channel gene KCNT1 in patients with severe developmental and epileptic encephalopathies (DEEs), most of which are resistant to current therapies. Defining the neuron types most vulnerable to KCNT1 GOF will advance our understanding of disease mechanisms and provide refined targets for precision therapy efforts. Here, we assessed the effects of heterozygous expression of a Kcnt1 GOF variant (Y777H) on KNa currents and neuronal physiology among cortical glutamatergic and GABAergic neurons in mice, including those expressing vasoactive intestinal polypeptide (VIP), somatostatin (SST), and parvalbumin (PV), to identify and model the pathogenic mechanisms of autosomal dominant KCNT1 GOF variants in DEEs. Although the Kcnt1-Y777H variant had no effects on glutamatergic or VIP neuron function, it increased subthreshold KNa currents in both SST and PV neurons but with opposite effects on neuronal output; SST neurons became hypoexcitable with a higher rheobase current and lower action potential (AP) firing frequency, whereas PV neurons became hyperexcitable with a lower rheobase current and higher AP firing frequency. Further neurophysiological and computational modeling experiments showed that the differential effects of the Y777H variant on SST and PV neurons are not likely due to inherent differences in these neuron types, but to an increased persistent sodium current in PV, but not SST, neurons. The Y777H variant also increased excitatory input onto, and chemical and electrical synaptic connectivity between, SST neurons. Together, these data suggest differential pathogenic mechanisms, both direct and compensatory, contribute to disease phenotypes, and provide a salient example of how a pathogenic ion channel variant can cause opposite functional effects in closely related neuron subtypes due to interactions with other ionic conductances.
The maintenance of genetic polymorphism in sexually antagonistic traits

Selection often favours different trait values in males and females, leading to genetic conflicts between the sexes, or sexual antagonism. Theory suggests that such conflict can maintain genetic variation by generating balancing selection. However, most of this theory is based on insights from models of single loci with fixed fitness effects. It is thus unclear how readily sexual antagonism drives balancing selection at loci where the fitness effects are not arbitrarily set but emerge from the genotype-phenotype map and the fitness landscape. Here we use mathematical models and computer simulations to investigate the evolution of traits that have different optima in males and females and so experience sexually antagonistic selection. We examine the consequences of such selection for the maintenance and nature of genetic variation under different assumptions of genetic architecture and for different fitness landscapes. We show that the conditions necessary to maintain variation are significantly more restrictive than previously appreciated. This is because the majority of typical sex-specific fitness landscapes generate stabilising selection on traits, and so favour the fixation of a single homozygote genotype that encodes the phenotype with the highest sex-averaged fitness. Instead, the maintenance of genetic polymorphism requires extremely, if not implausibly, strong conflict between males and females in order to disfavour extreme and intermediate phenotypes by generating diversifying selection. Furthermore, in all cases, we find that distinctive patterns of genetic variation produced by sexual antagonism arise rarely and are often transient, and so are difficult to observe in genomic data. Taken together, our results indicate that sex-specific selection is not a straightforward source of balanced genetic polymorphism and leaves few traces in the genome. Rather, we suggest that sexual antagonism is most likely to maintain genetic variation when traits are determined by a single large effect locus where genetic constraints lead to a limited range of possible alleles.
Increased circulating CD39+FoxP3+CD4+ regulatory T cells in Early Rheumatoid Arthritis facilitate the antiinflammatory action of methotrexate and associate with the clinical response

OBJECTIVES FoxP3+ regulatory T cells (Tregs) are key to the immune system homeostasis; their CD39+ subset (Treg39+) hydrolises adenine nucleotides released by stressed cells, rendering the antiinflammatory adenosine. Methotrexate (MTX), inhibiting AICAR transformylase (ATIC), enhances the extrusion of adenine nucleotides and hence may help Treg39+ cells control inflammation. Therefore, we examined the relation of CD39 expression on Tregs of early RA (ERA) patients with the effect of MTX. METHODS Freshly isolated lymphocytes from 72 untreated ERA patients (duration <24 weeks) and 72 healthy controls (HCs) were examined by cytometry. Treg cell potency was assessed in cocultures of CD4+CD25+CD127- Treg with CD4+CD25- CD127+ responder T cells (Tresp). RESULTS ERA patients demonstrated a superior frequency of circulating Tregs containing increased proportions of Treg39+ cells. Total ERA Tregs were more potent than HC Tregs and MTX further heightened their potency, with greater amplification in ERA vs HC; differences were reduced by adenosine pathway blockade. The potency of isolated Treg39+ and its enhancement by MTX were comparable for ERA and HC suggesting that the differences seen with total Tregs are due to the increased ERA Treg39+ frequency. Basal Treg39+ cell proportions > 39.3 associated with a good 12 month EULAR response [RR 13.4 (2.9-75.6)]. At 12 months, the ERA Treg39+ frequency had decreased to HC levels but its association with the clinical response remained. CONCLUSION MTX cooperates with Treg39+ cells and the basal Treg39+ frequency is a predictor of clinical response. The increased circulating Treg39+ cells in untreated ERA would further facilitate the action of MTX thereby providing a slot for prompt MTX initiation.
Nd and Sr isotopic signatures of Mesozoic plutons in northeastern North America

Nd and Sr initial isotope ratios are reported for 17 Mesozoic plutons of the Monteregian Hills and White Mountain series provinces in northeastern North America. Some variation in the isotopic ratios at most localities is caused by crustal-contamination processes. When the crustal assimilation effects are taken into account, the initial ratios for apparently uncontaminated, mantle-derived parental magmas show only restricted range in /sup 87/Sr//sup 86/Sr (0.7032 to 0.7040) and epsilon/sub Nd/ (T) (+5.4 to +2.3), which are inversely correlated. These ratios characterize alkaline to subalkaline magmas emplaced over more than 400 km/sup 2/ and about 80 m.y. The isotopic and trace-element characteristics are broadly similar to those of many modern ocean-island basalts, specifically the New England Seamounts, suggesting similar time-integrated, lithophile-element-depleted mantle sources. The results are consistent with plume-related mantle sources deeper than the subcontinental mantle.
FSL-CP: A Benchmark for Small Molecule Activity Few-Shot Prediction using Cell Microscopy Images

Predicting small molecule activities using information from high-throughput microscopy images has been shown to tremendously increase hit rates and chemical diversity of the hits in previous drug discovery projects. However, due to high cost of acquiring data or ethical reasons, data sparsity remains a big challenge in drug discovery. This opens up the opportunity for few-shot prediction: fine-tuning a model on a low-data assay of interest after pretraining on other more populated assays. Previous efforts have been made to establish a benchmark for few-shot learning of molecules based on molecular structure. With cell images as a molecular representation, methods in the computer vision domain are also applicable for activity prediction. In this paper, we make two contributions: a) A public data set for few-shot learning with cell microscopy images for the scientific community, b) A range of baseline models encompassing different existing single-task, multi-task and meta-learning approaches.
Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling

Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior of interface interactions and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces it is challenging to determine which amino acid pair interactions are cooperative. In this work we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with G proteins. Our results reveal a strong co-dependency in the formation of interface GPCR:G protein contacts. This observation indicates that cooperativity of GPCR:G protein interactions is necessary for the coupling and selectivity of G proteins and is thus critical for receptor function. We have identified subnetworks containing polar and hydrophobic interactions that are common among multiple GPCRs coupling to different G protein subtypes (Gs, Gi and Gq). These common subnetworks along with G protein-specific subnetworks together confer selectivity to the G protein coupling. This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.
Prolonged metaphase II arrest weakens Aurora B/C- dependent error correction in mouse oocytes

Chromosome segregation during oocyte meiosis is highly error prone in mammals. Whereas control mechanisms at work during meiosis I have been studied quite extensively, our knowledge of these mechanisms in meiosis II is rather limited. The spindle assembly checkpoint (SAC) and error correction (EC) have to be adapted to the specificities of meiosis II, where attachments to the spindle are bipolar, and not monopolar. Additionally, errors occurring during meiosis I, are carried over into meiosis II. In this study we asked whether oocytes in meiosis II have the capacity to respond to attachments that are under less tension. We found that this was indeed the case, and Aurora B/C-dependent EC through SAC activation can mediate a metaphase delay. We also found that during the extended metaphase II arrest, necessary to await fertilization, spindle tension naturally decreases. However, this occurs concomitantly with a decrease in the sensitivity of EC due to an increase in PP2A at centromeres, with the result that only oocytes in early but not late metaphase II can respond to missing spindle tension.
Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls

A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectation, identifying clear footprints of beneficial allele passage has proven to be surprisingly challenging. We addressed the basic premise underlying this expectation by estimating the ages of large numbers of beneficial and deleterious alleles in a human population genomic data set. Deleterious alleles were found to be young, on average, given their allele frequency. However, beneficial alleles were older on average than non-coding, non-regulatory alleles of the same frequency. This finding is not consistent with directional selection and instead indicates some type of balancing selection. Among derived beneficial alleles, those fixed in the population show higher local recombination rates than those still segregating, consistent with a model in which new beneficial alleles experience an initial period of balancing selection due to linkage disequilibrium with deleterious recessive alleles. Alleles that ultimately fix following a period of balancing selection will leave a modest ‘soft’ sweep impact on the local variation, consistent with the overall paucity of species-wide ‘hard’ sweeps in human genomes. Impact Statement Analyses of allele age and evolutionary impact reveal that beneficial alleles in a human population are often older than neutral controls, suggesting a large role for balancing selection in adaptation.
Inversión extranjera directa y encadenamientos productivos en Costa Rica

Costa Rica es un pequeno pais que ha basado su reciente crecimiento economico en la atraccion de inversiones extranjeras directas (IED) y en una orientacion activa hacia las exportaciones. En las ultimas dos decadas, Costa Rica ha logrado reenfocar parte de su especializacion exportadora, de la agricultura a los productos de alta tecnologia. Se ha dicho que este proceso se ha visto facilitado por la estabilidad politica y macroeconomica alcanzada despues de la crisis de 1980 y por la inversion en capital humano y educacion terciaria lograda antes de la “decada perdida”. En este capitulo analizamos el proceso de desarrollo y de industrializacion en Costa Rica y evaluamos en que medida la reorientacion hacia los sectores de alta tecnologia afecta a la industria y si la misma favorece el desarrollo de encadenamientos productivos o la heterogeneidad estructural.
Social bond dynamics and the evolution of helping

Empiricists often struggle to apply game theory models to real-life cases of animal cooperation. One reason is that many examples of cooperation occur in stable groups, where costs and benefits of helping depend on several factors. Among these are variable investments, fitness interdependencies, learning, memory, reciprocity, and partner choice, including the formation of social bonds with specific group members. Here, we present a game theory model exploring the conditions under which social bonds between group members can promote cooperation, with reciprocal acts of helping. In the model, bonds build up from exchanges of help in a similar way as the strength of association increases in learning, as in the Rescorla-Wagner rule. The bonds in turn affect partner choice and influence helping amounts. The model has a mechanism of reciprocity for bonded pairs, which can evolve towards either loose or strict reciprocation. Several aspects of the model are inspired by observations of food sharing in vampire bats. We find that small social neighbourhoods are required for the evolutionary stability of helping, either as small group sizes, or if members of larger groups can form temporary (daily) smaller groupings. The evolutionary outcome is a fairly low cost helping, while the benefit of receiving help can be substantial. Individuals in need request help based on bond strength, but there is also an evolved preference for initiating bonds with new group members. In contrast, if different groups come into temporary contact with each other, the evolved tendency is to avoid forming bonds between groups. Popular science summary The search for evolutionary explanations of cooperation between members of social groups has long been a high profile endeavour. A case of particular interest is when individuals develop a network of friends and exchange help through these social bonds. The question of helping between friends was given emphasis already from the start of the evolutionary study of cooperation, more than 50 years ago, but it has remained without any decisive progress since that time. Here we present a game-theory analysis of helping through the build-up of social bonds. We find that there is reciprocity in socially bonded pairs, which is neither immediate nor very strict, and that relatively small social neighbourhoods are required for the evolutionary stability of helping.
Volcanic and structural morphology of the south flank of Axial Volcano, Juan de Fuca Ridge: Results from a Sea MARC I side scan sonar survey

A 1500 km2 Sea MARC I side scan sonar survey south of Axial volcano investigated the geological structure and constitution of the South Axial Rift Zone (SARZ) and the northern 30 km of the Vance spreading segment. Relative age assignments based on structural relationships indicate that recent volcanism on the southern flank of Axial volcano has been restricted to the SARZ. The surficial volcanic morphology of the SARZ changes downrift, from linear volcanic ridges (north) to small (1-km diameter) cratered cones (south), perhaps indicating a variation in eruptive vent geometry from fissures to point sources downrift. Recent lavas on the northern and central SARZ erupted along preexisting faults in the underlying crust. By acting as pathways for SARZ magmas, these faults may have controlled the orientation of SARZ volcanic ridges and perhaps the orientation of the entire SARZ edifice. The Vance spreading segment terminates at 45°40′N and is not linked with a transform fault. The axis of spreading between 45°40′N and 46°00′N is offset west of the Vance segment and is constrained to lie between 129°54′W and 130°06′W. A discrete, structurally defined spreading axis, however, is not evident over the southern flank of Axial volcano. The divergent plate boundary may now underlie the SARZ massif, although South Helium Basin (an embayment in the southeast flank of Axial volcano) has undergone, and may continue to accommodate, crustal extension. A 48 km2 lava field discovered east of the SARZ is composed of lavas that are inferred to have erupted from the SARZ. These lavas can be traced eastward from the SARZ into the axial valley of the northern Vance segment and partially fill the valley with lavas up to 60 m thick. The eruption of these lavas, which occupy an estimated volume of 1.8 km3, may have contributed to the formation of Axial volcano's summit caldera.