Miracle-dz/UniFAR-FTUs huggingface dataset:
Wiring Up Vision: Minimizing Supervised Synaptic Updates Needed to Produce a Primate Ventral Stream

After training on large datasets, certain deep neural networks are surprisingly good models of the neural mechanisms of adult primate visual object recognition. Nevertheless, these models are poor models of the development of the visual system because they posit millions of sequential, precisely coordinated synaptic updates, each based on a labeled image. While ongoing research is pursuing the use of unsupervised proxies for labels, we here explore a complementary strategy of reducing the required number of supervised synaptic updates to produce an adult-like ventral visual stream (as judged by the match to V1, V2, V4, IT, and behavior). Such models might require less precise machinery and energy expenditure to coordinate these updates and would thus move us closer to viable neuroscientific hypotheses about how the visual system wires itself up. Relative to the current leading model of the adult ventral stream, we here demonstrate that the total number of supervised weight updates can be substantially reduced using three complementary strategies: First, we find that only 2% of supervised updates (epochs and images) are needed to achieve ~80% of the match to adult ventral stream. Second, by improving the random distribution of synaptic connectivity, we find that 54% of the brain match can already be achieved “at birth” (i.e. no training at all). Third, we find that, by training only ~5% of model synapses, we can still achieve nearly 80% of the match to the ventral stream. When these three strategies are applied in combination, we find that these new models achieve ~80% of a fully trained model’s match to the brain, while using two orders of magnitude fewer supervised synaptic updates. These results reflect first steps in modeling not just primate adult visual processing during inference, but also how the ventral visual stream might be “wired up” by evolution (a model’s “birth” state) and by developmental learning (a model’s updates based on visual experience).
Relating Bone Strain to Local Changes in Radius Microstructure Following 12 Months of Axial Forearm Loading in Women

Work in animal models suggest that bone structure adapts to local bone strain, but this relationship has not been comprehensively studied in humans. Here, we quantified the influence of strain magnitude and gradient on bone adaptation in the forearm of premenopausal women performing compressive forearm loading (n=11) and non-loading controls (n=10). High resolution peripheral quantitative computed tomography (HRpQCT) scans of the distal radius acquired at baseline and 12 months of a randomized controlled experiment were used to identify local sites of bone formation and resorption. Bone strain was estimated using validated finite element (FE) models. Trabecular strain magnitude and gradient were higher near (within 200 µm) formation versus resorption (p<0.05). Trabecular formation and resorption occurred preferentially near very high (>95th percentile) versus low (<5th percentile) strain magnitude and gradient elements, and very low strain elements were more likely to be near resorption than formation (p<0.05). In the cortical compartment, strain gradient was higher near formation versus resorption (p<0.05), and both formation and resorption occurred preferentially near very high versus low strain gradient elements (p<0.05). At most, 54% of very high and low strain elements were near formation or resorption only, and similar trends were observed in the control and load groups. These findings suggest that strain, likely in combination with other physiological factors, influences adaptation under normal loads and in response to a novel loading intervention, and represents an important step toward defining exercise interventions to maximize bone strength.
Excitatory effects of dentate gyrus mossy cells and their ability to influence granule cell firing: an optogenetic study in adult mouse hippocampal slices

Glutamatergic dentate gyrus (DG) mossy cells (MCs) innervate the primary cell type, granule cells (GCs), and GABAergic neurons which inhibit GCs. Prior studies suggest that the net effect of MCs is mainly to inhibit GCs, leading one to question why direct excitation of GCs is often missed. We hypothesized that MCs do have excitatory effects, but each GC is only excited weakly, at least under most experimental conditions. To address this hypothesis, MC axons were stimulated optogenetically in slices. A brief optogenetic stimulus to MC axons in the inner molecular layer (IML) led to a short-latency field EPSP (fEPSP) in the IML, suggesting there was a direct excitatory effect on GCs. Population spikes were negligible however, consistent with weak excitation. FEPSPs reflected AMPA/NMDA receptor-mediated EPSPs in GCs. EPSPs reached threshold after GC depolarization or facilitating NMDA receptors. GABAA and GABAB receptor-mediated IPSPs often followed EPSPs. At the network level, an optogenetic stimulus led to a brief, small facilitation of the PP-evoked population spike followed by a longer, greater inhibition. These data are consistent with rapid and selective GC firing by MCs (MC → GC) and disynaptic inhibition (MC → GABAergic neuron → GC). Notably, optogenetic excitation was evoked for both dorsal and ventral MCs, ipsilateral and contralateral MC axons, and two Cre lines. Together the results suggest a way to reconcile past studies and provide new insight into the balance of excitation and inhibition of GCs by MCs. SIGNIFICANCE STATEMENT Mossy cells (MCs) of the dentate gyrus (DG) are glutamatergic and innervate granule cells (GCs). The net effect of MCs has been debated because MCs also innervate GABAergic neurons which inhibit GCs. The results shown here suggest that MCs excite numerous GCs, but excitation is weak at GC resting potentials, and requires specific conditions to trigger GC APs. The results are consistent with a GC network that is designed for selective activation.
Stability of SARS-CoV-2 phylogenies

The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation and/or recombination among viral lineages. We suggest how samples can be screened and problematic mutations removed. We also develop tools for comparing and visualizing differences among phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse. Foreword We wish to thank all groups that responded rapidly by producing these invaluable and essential sequence data. Their contributions have enabled an unprecedented, lightning-fast process of scientific discovery---truly an incredible benefit for humanity and for the scientific community. We emphasize that most lab groups with whom we associate specific suspicious alleles are also those who have produced the most sequence data at a time when it was urgently needed. We commend their efforts. We have already contacted each group and many have updated their sequences. Our goal with this work is not to highlight potential errors, but to understand the impacts of these and other kinds of highly recurrent mutations so as to identify commonalities among the suspicious examples that can improve sequence quality and analysis going forward.
Experimental Modification of the Growth of the Bursa of Fabricius

Abstract THE growth of the bursa of Fabricius in the domestic chicken has recently been characterized by Glick (1956). The bursae of all breeds studied began a period of definite involution during the second to third month after hatching. Several possible factors causing this involution are discussed in this paper. Jolly (1914) reported that rate of bursa involution could be increased in the chicken by fasting and irradiation. It is interesting that Jolly theorized that the sensitivity of the bursa to inanition warranted the supposition that it plays a role in the exchange of nutritives. Bursa involution was delayed, according to Jolly and Pezard (1928), after castration. They caponized 6 chickens at 2 months of age and reported that at 6 months the bursae of the capons were larger than the 4 controls. One control had a larger bursa than the capons. Kirkpatrick and Andrews (1944) were able to increase the …
Zooplankton feeding ecology : Grazing by marine copepods and cladocerans upon phytoplankton and cyanobacteria from Kingston Harbour, Jamaica

Grazing by the copepods Tcworci /irrhiirutu and Acurlicr IiNjehorgii and the marine cladoceran Peiiilin uriro. ~rri. ~ on natural phytoplankton and cyanobacteria assemblages from Kingston Harbour. Jamaica, was examined in summer 1992. Food assemblages were often dominated by an unidentified filamentous cyanobacterium. with abundances of up to 1.16 x lo4 filaments.ml I. Other abundant phytoplankters included microflagellates and diatoms of the genus Nir:schiri. Mean clearance rates for the entire food assemblage ranged from 0.10 to 2.41 ml 'animal -I. h-', although most mean clearance rates were between 0.5 and I.5 ml . animal-' h- I. Patterns of selection of different food items by various grazers on different dates were variable and inconsistent. Microscopic measurements revealed that cyanobacterial filament lengths were shorter in grazed than initial aliquots during a cyanobacterium bloom in August. This suggests that grazers reduced lengths of many filaments by biting otl'portions, in addition to consuming entire filaments. Such 'filament clipping' of cyanobacteria filaments has been recorded previously in freshwater studies and suggests that grazers impact a larger portion of the phytoplankton assemblage than is accounted for by ingestion and clearance rates based only upon removal of filaments. Grazers exhibited no adverse effects from consuming cyanobacteria. Cyano- hacterkd are often considered to be toxic or of poor food quality for planktonic grazers. but due to the high abundance and dominance of filamentous cyanobacteria in Kingston Harbour. if these cyano- bacteria were ungrazed. there would at times be little alternative phytoplankton food for copepods and cladocerans. Our results suggest that the trophic role of tilamentous cyanobacteria in pelagic food webs of the tropical ocean should be further investigated and possibly reconsidered.
Increased nest cofounding and high intra‐colony relatedness in the bee Exoneura bicolor (Hymenoptera: Apidae): Results from an experimental situation

Identifying differences in a key social trait between two populations of the same species is important for understanding the evolution of sociality. Previous studies of new colonies in Exoneura bicolor, an Australian allodapine bee, have shown that there are high levels of kin cofounding in a montane population. The only study to examine intra-colony relatedness in a heathland population has found that new multifemale colonies are not formed by kin. In this study we used an experiment to investigate both cofounding behaviour and intra-colony relatedness in E. bicolor from a heathland population. Nest substrate was placed either 0.05 or 1 m distant from source nests in a novel environment. Although there were no differences in cofounding rate or intra-colony relatedness between the two treatments there was, overall, a high rate of cofounding: 53% of new nests were multifemale, approximately twice as high as found in previous field-based studies. Relatedness among cofoundresses was not only different from zero, r ± SE = 0.597 ± 0.097, but almost identical to that found in montane populations. A constraint, such as nest substrate distribution, is suggested as a proximate factor affecting the expression of cofounding behaviour in E. bicolor. The implication of such proximate constraints for inferring the phylogenetic origins of social behaviour is discussed.
The neural basis of intelligence in fine-grained cortical topographies

Intelligent thought is the product of efficient neural information processing, which is embedded in fine-grained, topographically-organized population responses and supported by fine-grained patterns of connectivity among cortical fields. Previous work on the neural basis of intelligence, however, has focused on coarse-grained features of brain anatomy and function, because cortical topographies are highly idiosyncratic at a finer scale, obscuring individual differences in fine-grained connectivity patterns. We used a computational algorithm, hyperalignment, to resolve these topographic idiosyncrasies, and found that predictions of general intelligence based on fine-grained (vertex-by-vertex) connectivity patterns were markedly stronger than predictions based on coarse-grained (region-by-region) patterns. Intelligence was best predicted by fine-grained connectivity in the default and frontoparietal cortical systems, both of which are associated with self-generated thought. Previous work overlooked fine-grained architecture because existing methods couldn’t resolve idiosyncratic topographies, preventing investigation where the keys to the neural basis of intelligence are more likely to be found.
Drebrin mediates scar formation and astrocyte reactivity during brain injury by inducing RAB8 tubular endosomes

The brain of mammals lacks a significant ability to regenerate neurons and is thus particularly vulnerable. To protect the brain from injury and disease, damage control by astrocytes through astrogliosis and scar formation is vital. Here, we show that brain injury triggers an ad hoc upregulation of the actin-binding protein Drebrin (DBN) in astrocytes, which is essential for the formation and maintenance of glial scars in vivo. In turn, DBN loss leads to defective glial scar formation and excessive neurodegeneration following mild brain injuries. At the cellular level, DBN switches actin homeostasis from ARP2/3-dependent arrays to microtubule-compatible scaffolds and facilitates the formation of RAB8-positive membrane tubules. This injury-specific RAB8 membrane compartment serves as hub for the trafficking of surface proteins involved in astrogliosis and adhesive responses, such as β1-integrin. Our work identifies DBN as pathology-specific actin regulator, and establishes DBN-dependent membrane trafficking as crucial mechanism in protecting the brain from escalating damage following traumatic injuries.
Michigan ZoomIN: validating crowd-sourcing to identify mammals from camera surveys

Camera trap studies have become a popular medium to assess many ecological phenomena including population dynamics, patterns of biodiversity, and monitoring of endangered species. In conjunction with the benefit to scientists, camera traps present an unprecedented opportunity to involve the public in scientific research via image classifications. However, this engagement strategy comes with a myriad of complications. Volunteers vary in their familiarity with wildlife, and thus, the accuracy of user-derived classifications may be biased by the commonness or popularity of species and user-experience. From an extensive multi-site camera trap study across Michigan U.S.A, images were compiled and identified through a public science platform called Michigan ZoomIN. We aggregated responses from 15 independent users per image using multiple consensus methods to assess accuracy by comparing to species identification completed by wildlife experts. We also evaluated how different factors including consensus algorithms, study area, wildlife species, user support, and camera type influenced the accuracy of user-derived classifications. Overall accuracy of user-derived classification was 97%; although, several canid (e.g., Canis lupus, Vulpes vulpes) and mustelid (e.g., Neovison vison) species were repeatedly difficult to identify by users and had lower accuracy. When validating user-derived classification, we found that study area, consensus method, and user support best explained accuracy. To continue to overcome stigma associated with data from untrained participants, we demonstrated their value by showing the accuracy from volunteers was comparable to experts when classifying North American mammals. Our hierarchical workflow that integrated multiple consensus methods lead to more image classifications without extensive training and even when the expertise of the volunteer was unknown. Ultimately, adopting such an approach can harness broader participation, expedite future camera trap data synthesis, and improve allocation of resources by scholars to enhance performance of public participants and increase accuracy of user-derived data.
Use of set-aside land in winter by declining farmland bird species in the UK

Between 1992 and 1993 over 600 000 ha of arable farmland in the UK were set aside under a production control mechanism of the Common Agricultural Policy (CAP) of the European Union. One of the management options for this set-aside land was to leave it as an over-winter fallow with a naturally regenerated green cover. This study was designed to test whether such land was used by seed-eating bird species, populations of many of which have undergone recent severe declines. Five out of six declining species recorded in the study were found in significantly greater numbers on this habitat than would be expected if the birds were randomly distributed over the farmland landscape. The results of this study, covering a wide geographical area, reinforce previous findings of the importance of winter food sources, particularly over-winter stubble fields, to declining farmland seed-eaters. Proposed changes to the CAP under Agenda 2000 include the reduction of the obligatory set-aside rate to zero. These results sugges.
PARAMETERS FOR IDENTIFYING FAILURE OF PASSIVE TRANSFER IN SITATUNGA (TRAGELAPHUS SPEKII )

Abstract: Failure of passive transfer of immunity (FPT) leads to increased calf morbidity and mortality and requires intensive, time-sensitive, and often expensive management for nondomestic ruminants. Without species-specific information with which to make informed decisions, neonatal data from domestic ruminants are often extrapolated to nondomestic zoo-housed species. To date, there have been no studies evaluating FPT in sitatunga (Tragelaphus spekii). The goal of the present study was to establish parameters to characterize adequate passive transfer in sitatunga calves and compare them to published reference intervals in other species. Medical records of 22 sitatunga calves (12 female, 10 male) were reviewed. Seventeen of these calves were defined as “healthy,” having survived at least 60 days without colostrum administration or a plasma transfusion. Calf weight, serum glucose, serum gamma-glutamyl transferase (GGT), total protein (TP), globulin concentrations, and results of a zinc sulfate turbidity test (ZSTT) were noted where possible. Mean birth weight of healthy calves at 24 hr was 4.5 kg (range: 3.76.5 kg, n = 12). The mean blood glucose in healthy calves was 152 mg/dl (range: 80–182, n = 16), mean serum TP concentration was 5.9 g/dl (range: 4.9–7.5, n = 16), mean serum globulin concentration was 3.3 g/dl (range: 1.7–4.7, n = 17), and mean serum GGT concentration was 466 U/L (range: 91–1901, n = 16). A ZSTT was performed for 10 healthy calves, resulting in four negative ZSTT results despite having no clinical signs of FPT and the calves having been observed nursing before testing. Sitatunga appear to have lower values for normal FPT parameters than those developed for domestic cattle. This study illustrates the difficulty of cross-species comparisons, as even closely related species can vary greatly in biologic parameters.
THORACIC RADIOGRAPHY AND TRANSTHORACIC ECHOCARDIOGRAPHY IN CLINICALLY HEALTHY RING-TAILED LEMURS (LEMUR CATTA)

Abstract: Cardiac disease has been recognized as a major cause of death in captive nonhuman primates, which necessitates diagnostic (imaging) techniques to screen for and diagnose preclinical and clinical stages of possible cardiac conditions. Echocardiography is currently the most commonly used diagnostic tool for evaluation of cardiac anatomy and function. Complete with thoracic radiography and blood levels of two cardiac biomarkers, N-terminal probrain natriuretic peptide (NT-proBNP) and cardiac troponin T (cTnT), it gives an extensive examination of the cardiorespiratory system. The purpose of this cross-sectional cohort study is to describe normal thoracic anatomy using thoracic radiography, and to provide normal values for echocardiographic measurements in 20 ring-tailed lemurs (Lemur catta). Additionally, cardiac biomarkers were determined. Three radiographic projections of the thoracic cavity and a complete transthoracic echocardiography were performed in 20 clinically healthy ring-tailed lemurs during their annual health examinations. Similar standard right parasternal and left apical echocardiographic images were obtained as described in dogs and cats and normal values for routine two-dimensional (2D-), time-motion (M-) and Doppler mode measurements were generated. Furthermore, a noninvasive smartphone base ECG recording and blood concentrations of cardiac biomarkers were obtained. Other radiographic measurements are provided for the skeletal and respiratory systems such as the trachea to inlet ratio and tracheal inclination. Knowledge of the normal radiographic thoracic and echocardiographic anatomy and function are fundamental for the diagnosis and follow-up of cardiac disease in affected individuals and for species screening, and will be of added value in future research in and conservation of this endangered species.
Analysis of Energy Transport Behavior and Geometric Effects in Graphene

Graphene is an excellent heat conductor, with the potential to be used as a heat spreader for applications where there are fast, transient heat pulses. In this study we analyze and describe energy transport in graphene subject to an initial pulse of energy. We analyze the effects of using harmonic, anharmonic, and a non-linear (Tersoff) potentials to describe the transient energy transport and compare these to classical continuum descriptions. The energy pulse produces pure wave-like behavior and a spatial energy distribution that has geometric features similar to the graphene geometry itself. Depending on the potential used, the energy travels outward from the impulse location following a similar pattern as the hexagonal shape of graphene. This pattern is clearly identified when the transport is treated with a harmonic potential. Increasing the anharmonicity and non-linearity dampens this effect and results in thermal transport that does not follow the geometry of graphene.