Miracle-dz/UniFAR-FTUs huggingface dataset:
Topographic deep artificial neural networks reproduce the hallmarks of the primate inferior temporal cortex face processing network

A salient characteristic of monkey inferior temporal (IT) cortex is the IT face processing network. Its hallmarks include: “face neurons” that respond more to faces than non-face objects, strong spatial clustering of those neurons in foci at each IT anatomical level (“face patches”), and the preferential interconnection of those foci. While some deep artificial neural networks (ANNs) are good predictors of IT neuronal responses, including face neurons, they do not explain those face network hallmarks. Here we ask if they might be explained with a simple, metabolically motivated addition to current ANN ventral stream models. Specifically, we designed and successfully trained topographic deep ANNs (TDANNs) to solve real-world visual recognition tasks (as in prior work), but, in addition, we also optimized each network to minimize a proxy for neuronal wiring length within its IT layers. We report that after this dual optimization, the model IT layers of TDANNs reproduce the hallmarks of the IT face network: the presence of face neurons, clusters of face neurons that quantitatively match those found in IT face patches, connectivity between those patches, and the emergence of face viewpoint invariance along the network hierarchy. We find that these phenomena emerge for a range of naturalistic experience, but not for highly unnatural training. Taken together, these results show that the IT face processing network could be a consequence of a basic hierarchical anatomy along the ventral stream, selection pressure on the visual system to accomplish general object categorization, and selection pressure to minimize axonal wiring length.
A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer

Androgen receptor (AR) signaling is the central driver of prostate cancer across disease states. While androgen deprivation therapy (ADT) is effective in the initial treatment of prostate cancer, resistance to ADT or to next-generation androgen pathway inhibitors invariably arises, most commonly through re-activation of the AR axis. Thus, orthogonal approaches to inhibit AR signaling in advanced prostate cancer are essential. Here, via genome-scale CRISPR/Cas9 screening, we identify protein arginine methyltransferase 1 (PRMT1) as a critical mediator of AR expression and signaling. PRMT1 regulates recruitment of AR to genomic target sites and inhibition of PRMT1 impairs AR binding at lineage-specific enhancers, leading to decreased expression of key oncogenes, including AR itself. Additionally, AR-driven prostate cancer cells are uniquely susceptible to combined AR and PRMT1 inhibition. Our findings implicate PRMT1 as a key regulator of AR output and provide a preclinical framework for co-targeting of AR and PRMT1 in advanced prostate cancer.
PARP1 inhibitors trigger innate immunity via PARP1 trapping-induced DNA damage response

It is being increasingly appreciated that the immunomodulatory functions of PARP inhibitors (PARPi) underlie their clinical activities in various BRCA-mutated tumors. PARPi possess both PARP1 inhibition and PARP1 trapping activities. The relative contribution of these two mechanisms toward PARPi-induced innate immune signaling, however, is poorly understood. We find that the presence of the PARP1 protein with uncompromised DNA-binding activities is required for PARPi-induced innate immune response. The activation of cGAS-STING signaling induced by various PARPi closely depends on their PARP1 trapping activities. Finally, we show that a small molecule PARP1 degrader blocks the enzymatic activity of PARP1 without eliciting PARP1 trapping or cGAS-STING activation. Our findings thus identify PARP1 trapping as a major contributor of the immunomodulatory functions of PARPi. Although PARPi-induced innate immunity is highly desirable in human malignancies, the ability of “non-trapping” PARP1 degraders to avoid the activation of innate immune response could be useful in non-oncological diseases.
Suitability of Different Gels as Seed Carriers and Germination and Emergence Promoters in Processing Carrots

Stand establishment is critical for optimizing yield and quality in carrots. Low soil temperatures and moisture conditions often challenge seed germination and emergence. Providing an artificial exosperm with appropriate germination promoters, stress condition- ers and growth invigorators to the seed may facilitate uniform germination and emergence. Germination patterns and velocity of germination of 'Oranza' carrot was studied. Seeds were mixed in different types of gels at various ratios and incubated at either 5 or 20 °C. Gels used were Laponite RD, Laponite RDS, guar gum, algenic acid, and agar. Data on germination percentage was collected and the velocity of germination was calculated. Germination was delayed at 5 °C. Both at 5 and 20 °C, Laponite RD promoted and enhanced germination and vigor, and resulted in the highest mean germination percentage (90% at 20 °C and 89% at 5 °C). Laponite RD at 2.5% has shown an overall advantage in germination percentage (94% at 20 °C and 87% at 5 °C) over other gel types and concentrations. 0.3%, 0.35%, 0.4%, 0.45%, and 0.5% (w/v); 2) Laponite RDS at 10%, 12%, 14%, 15%, and 16% (w/v); 3) Laponite RD at 2.5%, 2.75%, 3.0%, 3.25%, and 3.5% (w/v), 4) guar gum at 0.5%, 0.75%, 1.0%, 1.25%, and 1.5% (w/v); and 5) algenic acid at 2.0%, 2.25%, 2.5%, 2.75%,
Evolutionary conserved multifunctional nitric oxide synthesis proteins responding to bacterial MAMPs are located at the endoplasmic reticulum

Most Eukaryotic organisms produce nitric oxide (NO); however, the mechanisms underpinning NO’s biosynthesis are only known in animals. In animals, there seems to be a non-described additional system for producing NO in many cell types, including blood vessels where NO is essential for blood pressure control. NO is known to be a signalling molecule of the innate immunity system in plants and fungi although no NO generation has yet been described. In the plant pathogenic fungus Fusarium graminearum, we demonstrate an extra NO-producing system in fungi that seems also present in mammals and plants and, thus, likely the evolutionary original. The discovered NO-producing enzymes are already well-known sterol-producing enzymes with more than one function. Both these enzymes are targets for statins and the major fungicides; thus, the NO production of the new system has consequences for agriculture (pathogen resistance and control) and medicine (blood pressure control, immunity and sepsis).
Surface area-to-volume ratio, not cellular rigidity, determines red blood cell traversal through small capillaries

The remarkable deformability of red blood cells (RBCs) depends on the viscoelasticity of the plasma membrane and cell contents and the surface area to volume (SA:V) ratio; however, it remains unclear which of these factors is the key determinant for passage through small capillaries. We used a microfluidic device to examine the traversal of normal, stiffened, swollen, parasitised and immature RBCs. We show that dramatic stiffening of RBCs had no measurable effect on their ability to traverse small channels. By contrast, a moderate decrease in the SA:V ratio had a marked effect on the equivalent cylinder diameter that is traversable by RBCs of similar stiffness. We developed a finite element model that provides a coherent rationale for the experimental observations, based on the nonlinear mechanical behaviour of the RBC membrane skeleton. We conclude that the SA:V ratio should be given more prominence in studies of RBC pathologies.
The Functional Relevance of Task-State Functional Connectivity

Resting-state functional connectivity has provided substantial insight into intrinsic brain network organization, yet the functional importance of task-related change from that intrinsic network organization remains unclear. Indeed, such task-related changes are known to be small, suggesting they may have only minimal functional relevance. Alternatively, despite their small amplitude, these task-related changes may be essential for the ability of the human brain to adaptively alter its functionality via rapid changes in inter-regional relationships. We used activity flow mapping—an approach for building empirically derived network models—to quantify the functional importance of task-state functional connectivity (above and beyond resting-state functional connectivity) in shaping cognitive task activations in the (female and male) human brain. We found that task-state functional connectivity could be used to better predict independent fMRI activations across all 24 task conditions and all 360 cortical regions tested. Further, we found that prediction accuracy was strongly driven by individual-specific functional connectivity patterns, while functional connectivity patterns from other tasks (task-general functional connectivity) still improved predictions beyond resting-state functional connectivity. Additionally, since activity flow models simulate how task-evoked activations (which underlie behavior) are generated, these results may provide mechanistic insight into why prior studies found correlations between task-state functional connectivity and individual differences in behavior. These findings suggest that task-related changes to functional connections play an important role in dynamically reshaping brain network organization, shifting the flow of neural activity during task performance. SIGNIFICANCE STATEMENT Human cognition is highly dynamic, yet the functional network organization of the human brain is highly similar across rest and task states. We hypothesized that, despite this overall network stability, task-related changes from the intrinsic (resting-state) network organization of the brain strongly contribute to brain activations during cognitive task performance. Given that cognitive task activations emerge through network interactions, we leveraged connectivity-based models to predict independent cognitive task activations using resting-state versus task-state functional connectivity. This revealed that task-related changes in functional network organization increased prediction accuracy of cognitive task activations substantially, demonstrating their likely functional relevance for dynamic cognitive processes despite the small size of these task-related network changes.
Survival of the salient: Emotion rescues otherwise forgettable memories via neural reactivation and post-encoding hippocampal connectivity

Emotion’s selective effects on memory go beyond the simple enhancement of threatening or rewarding stimuli. They can also rescue otherwise forgettable memories that share overlapping features. Here, we use functional magnetic resonance imaging (fMRI) to examine the brain mechanisms that support this retrograde memory enhancement. In a two-phase incidental encoding paradigm, participants first view images of neutral tools and animals. During Phase 1, these images are intermixed with neutral scenes, which provides a unique ‘context tag’ for this specific phase of encoding. A few minutes later, during Phase 2, new pictures from one category are paired with a mild shock (fear-conditioned stimulus; CS+), while pictures from the other category are not shocked. fMRI analyses reveal that, across participants, retroactive memory benefits for Phase 1 CS+ items are associated with greater phasic reinstatement of the prior mental context during Phase 2 CS+ items. We also see that greater VTA/SN activation during Phase 2 CS+ items relates to this retroactive memory enhancement, suggesting that emotion promotes both the encoding and ongoing consolidation of overlapping representations. Additionally, we find that emotional experience-dependent changes in post-encoding hippocampal functional coupling with CS+ category-selective cortex relate to the magnitude of the retroactive memory effect. These hippocampal connectivity patterns also mediate the relationship between dopaminergic emotional encoding effects and across-participant variability in the retroactive memory benefit. Collectively, our findings suggest that an interplay between online and offline brain mechanisms may enable emotion to preserve seemingly mundane memories that become significant in the future.
ATP-Citrate lyase fuels axonal transport across species

Microtubule (MT)-based transport is an evolutionary conserved processed finely tuned by posttranslational modifications. Among them, α-tubulin acetylation, which is catalyzed by the α-tubulin N-acetyltransferase 1, Atat1, promotes the recruitment and processivity of molecular motors along MT tracks. However, the mechanisms that controls Atat1 activity remains poorly understood. Here, we show that a pool of vesicular ATP-citrate lyase Acly acts as a rate limiting enzyme to modulate Atat1 activity by controlling availability of Acetyl-Coenzyme-A (Acetyl-CoA). In addition, we showed that Acly expression is reduced upon loss of Elongator activity, further connecting Elongator to Atat1 in the pathway regulating α-tubulin acetylation and MT-dependent transport in projection neurons, across species. Remarkably, comparable defects occur in fibroblasts from Familial Dysautonomia (FD) patients bearing an autosomal recessive mutation in the gene coding for the Elongator subunit ELP1. Our data may thus shine new light on the pathophysiological mechanisms underlying FD.
Age and growth of longtail tuna (Thunnus tonggol) in tropical and temperate waters of the central Indo-Pacific

Age and growth of longtail tuna (Thunnus tonggol) were assessed by examination of annual growth increments in sectioned sagittal otoliths from 461 fish (238–1250 mm fork length, LF) sampled from tropical and temperate waters in the central Indo-Pacific between February 2003 and April 2005. Edge and microincrement analyses (presumed daily increments) suggest that longtail tuna deposit a single annual growth increment mainly between August and October. Age was, therefore, estimated for all fish by counting assumed annual growth increments. Ages ranged from 154 d to 18.7 years, with most fish being 3–9 years. Five growth models were fitted to length-at-age data, all of which indicated that the species is relatively slow-growing and long-lived. Recaptures of two tagged fish at liberty for 6.2 and 10.5 years support this notion. A bias-corrected form of Akaike's Information Criterion determined that the Schnute–Richards model provided the best fit to length-at-age data, with model parameter estimates (sexes combined) of L{infty} = 135.4 cm LF, K = 22.3 year–1, t0 = 0.120 years, {delta} = 150.0, v = 0.019, and {gamma} = 2.7 x 10–8. There was no significant difference in growth between sexes. The results suggest that longtail tuna grow more slowly and live longer than other tuna species of similar size. Coupled with their restricted neritic distribution, longtail tuna may be vulnerable to overexploitation by fisheries, and caution needs to be exercised in managing the species until more reliable biological and catch data are collected to assess the status of the population.
COMPETITION BETWEEN PEROMYSCUS MANICULATUS AND MICROTUS TOWNSENDII IN GRASSLANDS OF COASTAL BRITISH COLUMBIA

Peromyscus maniculatus (Wagner) the deer mouse, can be divided into two subgroups: short-tailed, short-eared, and short-footed subspecies occupying grasslands, and longtailed, long-eared and long-footed subspecies occupying woodlands (Baker 1968). Peromyscus maniculatus austerus (Baird), the subspecies found in coastal British Columbia in the Vancouver region is an enigma. It is a woodland species yet has short-feet and a relatively short tail (Cowan & Guiquet 1956; Sheppe 1961). Grant (1971) has suggested that the deer mouse suffers from competition from microtine rodents in grasslands, and is forced to live in the woods. Baker (1968) also notes that Peromyscus 'usually are secondary to Microtus in north temperate and boreal stands of perennial grasslands'. Grant (1972) reviewed the experimental evidence for competition between Microtus sp. and Peromyscus sp. In his experiments little attention was paid to long-term changes in Peromyscus populations released from competition with Microtus. Grant was mainly interested in short-term changes in the rate of occurrence of Peromyscus in grass-land habitats following the removal of Microtus. During our investigations into the population dynamics of Microtus townsendii (Bachman) and M. oregoni (Bachman) we have found several grassland areas with very low populations of Peromyscus maniculatus. These Peromyscus populations in grasslands could be low because of competition with Microtus. We have tested the competition hypothesis experimentally and report on the results here.
Weed Control in Transplanted Maize in Winter

Seven treatmenls including hand weeding and weedy checks were evaluated in a randomized block design with three replications at Punjab Agricultural University. Ludhiana during 1985 and 1986. Application of atrazine before transplanting (0.625kg/ha) or at 2 or 20 days after transplanting (0.625 and 0.375 kg/ha) effectively controlled the weeds, significantly incieased grain and stover yield. There was no phytotoxic effect on succeeding crops of cowpcas (Vigna sinensis) and Jantar [Sesbania aculcata L).
ACCUMULATION OF CALCIUM OXALATE IN THE MANTLE OF ECTOMYCORRHIZAL ROOTS OF PINUS RADIATA AND EUCALYPTUS MARGINATA

SUMMARY Calcium oxalate crystals occur in the mantle of ectomycorrhizal roots of Firms radiata and Eucalyptus marginata. Dense concentrations of these crystals were observed in association with the fungal symbiont of both tree species. It is suggested that oxalate production may enhance nutrient uptake by ectomycorrhizal roots of forest species growing in nutrient impoverished soils. Concentrations of Ca, S, K and P were similar in mycorrhizal root masses of P. radiata and E. marginata.
Age, but not sex and seasonality, influence Haemosporida prevalence in White-banded Tanagers (Neothraupis fasciata) from central Brazil

Despite many studies on avian blood parasites, we still have a limited understanding of the mechanisms that drive patterns of haemosporidian infection among tropical birds, including effects associated with sex, age, and seasonality. Using molecular and morphological methods for blood-parasite detection, we found that juvenile White-banded Tanagers (Neothraupis fasciata (Lichtenstein, 1823)) had lower haemosporidian prevalence than adults in a population within central Brazil. However, no sex or seasonal differences were detected. Of the 92 White-banded Tanagers analyzed, 67 individuals (72.8% prevalence) were infected with either Haemoproteus or Plasmodium (phylum Sporozoa, class Coccidea, order Haemosporida). Sequencing of a portion of the mitochondrial cytochrome b gene revealed six haemosporidian lineages: two lineages within the genus Haemoproteus and four within the genus Plasmodium. The prevalences of Plasmodium and Haemoproteus parasites were 43.5% and 17.4%, respectively. Our results suggest that.
First Record of Hyposaurus (Dyrosauridae, Crocodyliformes) from the Upper Cretaceous Shendi Formation of Sudan

ABSTRACT We describe a new record of the dyrosaurid crocodyliform genus Hyposaurus, from the ? Campanian— Maastrichtian Shendi Formation of Sudan, based on a partial mandibular symphysis, two posterior portions of the upper jaw, and a fused frontal bone, all belonging to a single individual. The material can be assigned to Hyposaurus on the basis of the elliptical shape of the mandibular symphysis (wider than high) and the overall flat shape of the mandible. At the same time, the fossil material differs from other species of Hyposaurus in having (1) an enlarged eighth alveolus of the dentary relative to the other alveoli; (2) a reduced interalveolar space between the ninth and tenth alveoli; and (3) a prominent ridge and groove sculpturing on the dorsal side of the mandible along the symphyseal region. However, due to the fragmentary nature of the material, we refrain from drawing any higher-resolution taxonomic conclusions. The occurrence of Hyposaurus within the Shendi Formation represents the first record of this genus from the Late Cretaceous of Africa and potentially extends its temporal range to the Campanian. Whereas this occurrence in the Late Cretaceous of Sudan supports previous hypotheses of an African origin for Hyposaurus, more complete material is needed for evaluating these hypotheses in a phylogenetic framework.We also wish to stress that the genus Hyposaurus requires detailed revision.
Ecological Consequences Of Relatedness: The Role Of Competition And Herbivory In The Community Structure Of Co-Occurring Asteraceae

The degree to which species, or individuals within species, are related is likely to play an important role in their interactions, since shared ancestry should be reflected in phenotypic and ecological similarity. Similarity in resource requirements and acquisition, in turn, is expected to influence competitive interactions, one of the key ecological processes that structure communities. Yet, a long-standing prediction that close relatives compete more strongly for resources than more distantly related species or conspecific genotypes has been rarely tested experimentally. We employed a hierarchical approach in studying the effect of relatedness on intraand inter-specific competition with six co-occurring old-field Asteraceae: three species of Solidago (goldenrods) and three species of Symphyotrichum (asters). In pairwise combinations using potted plants in a greenhouse, we manipulated relatedness of the neighbour by selecting 1) conspecific from same maternal line (half-sibling), 2) unrelated conspecific from a different maternal line (non-sibling), 3) heterospecific from the same genus (congener), or 4) heterospecific from the other genus (confamilial). Averaged across the six species, none of the measured variables – above-ground and below-ground biomass, total biomass, and root-shoot ratio – supported the prediction that the intensity of competition (measured as the outcome of the competitive effect) decreased as competing individuals became more distantly related. These results
Close Genetic Relationships between Two American Octopuses: Octopus hubbsorum Berry, 1953, and Octopus mimus Gould, 1852

ABSTRACT The octopuses Octopus hubbsorum and Octopus mimus are two species of octopuses that inhabit shallow waters of the eastern Pacific Ocean. The former species is found in the north, from the Gulf of California to Oaxaca, Mexico, whereas O. mimus lives in the south, from Peru to Chile. To infer the phylogenetic relationships between these species we used the mitochondrial genes cytochrome oxidase subunits I and III, and r16S with the aim of comparing their genetic distances with those of other Octopus sp. The genetic distance values between both species estimated per gene or concatenated were low (0%–1.6%) in comparison with other interspecific distances values (4.6%–18.4%). Application of 10× rule showed there is no overlap between intra- and interspecific octopus distances, whereas the application of the 4× rule confirmed that both octopuses belong to the same lineage. The resolved topologies with maximum parsimony and Bayesian approaches clustered the specimens of O. hubbsorum and O. mimus in a single clade with high bootstrap and posterior probability values (100 and 1.0, respectively). These results allow us to suggest that O. hubbsorum and O. mimus could represent the same species.