Miracle-dz/UniFAR-FTUs huggingface dataset:
What can NMR spectroscopy of selenoureas and phosphinidenes teach us about the π-accepting abilities of N-heterocyclic carbenes?

The electronic nature of the interaction of NHCs with metal centres is of interest when exploring their properties, how these properties in ﬂ uence those of metal complexes, and how these properties might depend on ligand structure. Selenourea and phosphinidene complexes have been proposed to allow the measurement of the p -accepting ability of NHCs, independent of their s -donating ability, via the collection of 77 Se or 31 P NMR spectra, respectively. Herein, the synthesis and characterisation of selenoureas derived from a range of imidazol-2-ylidenes, 4,5-dihydroimidazol-2-ylidenes and triazol-2-ylidenes are documented. Computational studies are used to explore the link between the shielding of the selenium centre and the electronic properties of the NHCs. Results show that d Se is correlated to the energy gap between a ﬁ lled lone pair orbital on Se and the empty p * orbital corresponding to the Se – NHC bond. Bond energy decomposition analysis indicated no correlation between the orbital s -contribution to bonding and the chemical shielding, while a good correlation was found between the p -contribution to bonding and the chemical shielding, con ﬁ rming that this technique is indeed able to quantify the ability of NHCs to accept p -electron density. Calculations conducted on phosphinidene adducts yielded similar results. With the link between d Se and d P and p -back bonding ability clearly established, these compounds represent useful ways in which to fully understand and quantify this aspect of the electronic properties of NHCs.
Dendritic Computation for Neuromorphic Applications

In this paper, we highlight how computational properties of biological dendrites can be leveraged for neuromorphic applications. Specifically, we demonstrate analog silicon dendrites that support multiplication mediated by conductance-based input in an interception model inspired by the biological dragonfly. We also demonstrate spatiotemporal pattern recognition and direction selectivity using dendrites on the Loihi neuromorphic platform. These dendritic circuits can be assembled hierarchically as building blocks for classifying complex spatiotemporal patterns.
Patterns of song variation in a migratory population of pine warberls--behavioral implications in a changing climate.

As our climate continues to change, the range of suitable habitats for many species will be in flux, which along with changes in many biotic and abiotic factors will bring about changes in migratory behavior. This has already been seen for many species of birds, which have begun migrating shorter distances and even halting migration entirely as necessary resources become available year-round. Behavioral differences between migratory and non-migratory populations of birds have been observed for some species, particularly in song repertoire size and sharing. As a way to predict how vocal behavior and patterns will change as a result of climate change, comparisons can be made between populations of pine warblers, a wood-warbler unique for the presence of migratory behavioral plasticity, with migratory populations in the northern United States and Canada, and non-migratory populations in the southern United States. Due to the absence of previous studies on pine warbler song behavior, the patterns and variation across populations was assessed to provide good baseline data with which to make future comparisons. In the assessment of two migratory populations of pine warblers in northern Michigan, I found birds to possess relatively small repertoires, singing an average of three songs each. These songs could be categorized as “first” and “second” category songs, with characteristics similar to other wood-warblers. However, the use of these songs differed dramatically from what was expected, as birds sang both first and second category songs throughout the day, showing quite unique behavior for a wood-warbler. In an analysis of song variation across a population, I found that neighbors were not significantly more likely to share songs than non-neighbors. In a comparison of note repetition rates with frequency ranges, I found a very tightly clumped distribution, falling quite close to a theoretical vocal performance limit. Though the small repertoire size and low levels of song sharing observed in this population agree with predictions about migratory songbirds, the use of first and second category songs as well as vocal performance show interesting differences from other wood-warblers that would benefit from further study. The observations collected in this study will help greatly in the study of behavioral differences in migratory and non-migratory populations, and could give great insight into the potentially farreaching behavioral consequences of climate change.
Measuring the predictability of life outcomes with a scientific mass collaboration

Citation for published version: Salganik, MJ, Lundberg, I, Kindel, AT, Ahearn, CE, Al-ghoneim, K, Almaatouq, A, Altschul, DM, Brand, JE, Carnegie, NB, Compton, RJ, Datta, D, Davidson, T, Filippova, A, Gilroy, C, Goode, BJ, Jahani, E, Kashyap, R, Kirchner, A, Mckay, S, Morgan, AC, Pentland, A, Polimis, K, Raes, L, Rigobon, DE, Roberts, CV, Stanescu, DM, Suhara, Y, Usmani, A, Wang, EH, Adem, M, Alhajri, A, Alshebli, B, Amin, R, Amos, RB, Argyle, LP, Baer-bositis, L, Büchi, M, Chung, B, Eggert, W, Faletto, G, Fan, Z, Freese, J, Gadgil, T, Gagné, J, Gao, Y, Halpern-manners, A, Hashim, SP, Hausen, S, He, G, Higuera, K, Hogan, B, Horwitz, IM, Hummel, LM, Jain, N, Jin, K, Jurgens, D, Kaminski, P, Karapetyan, A, Kim, EH, Leizman, B, Liu, N, Möser, M, Mack, AE, Mahajan, M, Mandell, N, Marahrens, H, Mercado-garcia, D, Mocz, V, Mueller-gastell, K, Musse, A, Niu, Q, Nowak, W, Omidvar, H, Or, A, Ouyang, K, Pinto, KM, Porter, E, Porter, KE, Qian, C, Rauf, T, Sargsyan, A, Schaffner, T, Schnabel, L, Schonfeld, B, Sender, B, Tang, JD, Tsurkov, E, Van Loon, A, Varol, O, Wang, X, Wang, Z, Wang, J, Wang, F, Weissman, S, Whitaker, K, Wolters, MK, Woon, WL, Wu, J, Wu, C, Yang, K, Yin, J, Zhao, B, Zhu, C, Brooks-gunn, J, Engelhardt, BE, Hardt, M, Knox, D, Levy, K, Narayanan, A, Stewart, BM, Watts, DJ & Mclanahan, S 2020, 'Measuring the predictability of life outcomes with a scientific mass collaboration', Proceedings of the National Academy of Sciences, vol. 117, no. 15, pp. 8398-8403. https://doi.org/10.1073/pnas.1915006117
Neuromorphic luminance-edge contextual preprocessing of naturally obscured targets

Contextual grouping mechanisms in early visual cortex are thought to aid in perception of ambiguous textures, including partially obscured targets under real-world high dynamic range (HDR) luminance. Yet, deep neural networks struggle with naturalistic obscuration and illumination while requiring millions of neurons and power-hungry GPUs for processing. We hypothesized that contextual grouping mechanisms for edge and luminance processing may aid in localization of targets under natural obscuration and illumination. To address this issue, we developed a novel small (< 10,000 neurons) spiking neural network (SNN) that uses spike time correlations to leverage the combined luminance and orientation similarity of nearby image regions for image pre-processing, to support downstream deep neural network (DNN) target localization. The network has leaky integrate-and-fire neurons with current based (CuBa) synapses and is simulated using the Nengo LOIHI API, with potential application via Intel's LOIHI neuromorphic hardware. We collected 89 HDR images of a target dummy in a heavily wooded environment under varying occlusion and illumination. We used SNN preprocessing to adjust local image contrast based on the grouping mechanism, followed by a DNN classifier (Detectron2) to localize the target. Results show that a small SNN for image preprocessing can aid image segmentation and localization of occluded targets, marking an initial step towards more efficient and accurate target recognition under natural illumination and occlusion.
Enabling local learning for generative-replay-based continual learning with a recurrent model of the insect memory center

Continual learning without catastrophic forgetting of previous experiences is an open general challenge for artificial neural networks, but is especially under-explored for artificial neural networks suitable to implement on neuromorphic platforms. An algorithmic understanding of how continual learning occurs in biological neural networks can inform solutions for artificial neural networks, especially in neuromorphic platforms whose biomimetic computing architectures lend themselves to more biofidelic algorithms. In this work, we derive an approach for generative-replay-based continual learning with a three-factor local learning rule based on recurrent connectivity in the insect's memory center, and characterize the model with a CIFAR-100 class incremental continual learning task. First, we investigate the properties of the model's internal representations and find that the high dimensional sparse representations enable this form of generative replay, and that these representations can be binary as required on spiking neuromorphic platforms with little detriment to model performance. Next, we derive a three-factor local learning rule by introducing simplifying assumptions to network updates from error backpropagation optimization which makes the learning rule biologically plausible (i.e., without weight transport) and amenable to neuromorphic implementation. Finally, we find that these simplifications enhance performance during gradient-based optimization for continual learning and when implemented locally achieve this increased performance. Overall, the outcomes of this work can inform a more detailed understanding for continual learning in this biological circuit, as well as introduce general approaches for neuromorphic continual learning.
Age-dependent extinction and the neutral theory of biodiversity

Red Queen (RQ) theory states that adaptation does not protect species from extinction because their competitors are continually adapting alongside them. RQ was founded on the apparent independence of extinction risk and fossil taxon age, but analytical developments have since demonstrated that age-dependent extinction is widespread, usually most intense among young species. Here we develop ecological neutral theory as a general framework for modeling fossil species survivorship under incomplete sampling. We show that it provides excellent fit to a high-resolution dataset of species durations for Paleozoic zooplankton, and more broadly can account for age-dependent extinction seen throughout the fossil record. Unlike widely used alternative models, the neutral model has parameters with biological meaning, thereby generating testable hypotheses on changes in ancient ecosystems. The success of this approach suggests novel interpretations of mass extinctions and of scaling in eco-evolutionary systems. Intense extinction among young species does not necessarily refute RQ or require a special explanation, but can instead be parsimoniously explained by neutral dynamics operating across species regardless of age. Significance Statement Red Queen theory predicts that competition among species should cause extinction risk to be independent of species age, but recent analyses have refuted this central prediction. To fill the resulting theoretical vacuum, we used ecological neutral theory to build a model of the lifespans of incompletely sampled species evolving under zero-sum competition. This model predicts survivorship among fossil zooplankton with surprising accuracy and accounts for empirical deviations from the predictions of Red Queen more generally. A neutral model of background extinction allows for interpreting survivorship curves in terms of biological process, suggests a novel understanding of mass extinctions, and supports a role for competition in extinction.
A noise-robust acoustic method for recognizing foraging activities of grazing cattle

Farmers must continuously improve their livestock production systems to remain competitive in the growing dairy market. Precision livestock farming technologies provide individualized monitoring of animals on commercial farms, optimizing livestock production. Continuous acoustic monitoring is a widely accepted sensing technique used to estimate the daily rumination and grazing time budget of free-ranging cattle. However, typical environmental and natural noises on pastures noticeably affect the performance limiting the practical application of current acoustic methods. In this study, we present the operating principle and generalization capability of an acoustic method called Noise-Robust Foraging Activity Recognizer (NRFAR). The proposed method determines foraging activity bouts by analyzing fixed-length segments of identified jaw movement events produced during grazing and rumination. The additive noise robustness of the NRFAR was evaluated for several signal-to-noise ratios using stationary Gaussian white noise and four different nonstationary natural noise sources. In noiseless conditions, NRFAR reached an average balanced accuracy of 86.4%, outperforming two previous acoustic methods by more than 7.5%. Furthermore, NRFAR performed better than previous acoustic methods in 77 of 80 evaluated noisy scenarios (53 cases with p<0.05). NRFAR has been shown to be effective in harsh free-ranging environments and could be used as a reliable solution to improve pasture management and monitor the health and welfare of dairy cows. The instrumentation and computational algorithms presented in this publication are protected by a pending patent application: AR P20220100910. Web demo available at: https://sinc.unl. edu.ar/web-demo/nrfar
Ghrelin – Physiological Functions and Regulation

Ghrelin is an orexigenic peptide predominantly secreted from the stomach and stimulates appetite and growth hormone (GH) release. Studies have provided evidence that ghrelin exercises a wide range of functions, including regulation of food intake and energy metabolism, modulation of cardiovascular function, stimulation of osteoblast proliferation and bone formation and stimulation of neurogenesis and myogenesis. In the gastrointestinal system, ghrelin affects multiple functions, including secretion of gastric acid, gastric motility and pancreatic protein output. Most of these functions have been attributed to the actions of acylated ghrelin. The balance among its secretion rate, degradation rate and clearance rate determines the circulating level of ghrelin. This review explains what ghrelin is, its physiological functions and the factors that influence its level.
Protozoan predation enhances stress resistance and antibiotic tolerance in the opportunistic pathogen Burkholderia cenocepacia by triggering the SOS response

Bacterivorous protists are thought to serve as training grounds for bacterial pathogens by subjecting them to the same hostile conditions that they will encounter in the human host. Bacteria that survive intracellular digestion exhibit enhanced virulence and stress resistance after successful passage through protozoa but the underlying mechanisms remain to be clarified. Here we show that the opportunistic pathogen Burkholderia cenocepacia survives phagocytosis by ciliates found in domestic and hospital sink drains, and viable bacteria are expelled packaged in respirable membrane vesicles with enhanced resistance to oxidative stress, desiccation and antibiotics, thereby contributing to bacterial dissemination in the environment. By using diverse methodological approaches, we demonstrate that reactive oxygen species generated within the protozoan phagosome promote the formation of persisters tolerant to ciprofloxacin by activating the bacterial SOS response. Besides, we show that genes encoding antioxidant enzymes are upregulated during passage through ciliates increasing bacterial resistance to oxidative radicals. We prove that suppression of the SOS response impairs bacterial intracellular survival and persister formation within protists. This study highlights the significance of protozoan food vacuoles as niches that foster bacterial adaptation in natural and built environments and suggests that persister switch within phagosomes may be a widespread phenomenon in bacteria surviving intracellular digestion.
Intensive Versus Standard Blood Pressure Control in SPRINT-Eligible Participants of the ACCORD-BP Trial

This study was a post hoc, multivariate, subgroup analysis of ACCORD-BP (Action to Control Cardiovascular Risk in Diabetes Blood Pressure) participants. Participants were eligible for the analysis if theywere in the standard glucose control arm of ACCORD-BP and also had the additional CVD risk factors required for SPRINT (Systolic Blood Pressure Intervention Trial) eligibility. We used a Cox proportional hazards regression model to compare the effect of intensive versus standardBP control on CVDoutcomes. The “SPRINT-eligible”ACCORD-BP participantswere pooledwith SPRINT participants to determine whether the effects of intensive BP control interacted with T2DM.
FPT Approximation and Subexponential Algorithms for Covering Few or Many Edges

We study the \textsc{$\alpha$-Fixed Cardinality Graph Partitioning ($\alpha$-FCGP)} problem, the generic local graph partitioning problem introduced by Bonnet et al. [Algorithmica 2015]. In this problem, we are given a graph $G$, two numbers $k,p$ and $0\leq\alpha\leq 1$, the question is whether there is a set $S\subseteq V$ of size $k$ with a specified coverage function $cov_{\alpha}(S)$ at least $p$ (or at most $p$ for the minimization version). The coverage function $cov_{\alpha}(\cdot)$ counts edges with exactly one endpoint in $S$ with weight $\alpha$ and edges with both endpoints in $S$ with weight $1 - \alpha$. $\alpha$-FCGP generalizes a number of fundamental graph problems such as \textsc{Densest $k$-Subgraph}, \textsc{Max $k$-Vertex Cover}, and \textsc{Max $(k,n-k)$-Cut}. A natural question in the study of $\alpha$-FCGP is whether the algorithmic results known for its special cases, like \textsc{Max $k$-Vertex Cover}, could be extended to more general settings. One of the simple but powerful methods for obtaining parameterized approximation [Manurangsi, SOSA 2019] and subexponential algorithms [Fomin et al. IPL 2011] for \textsc{Max $k$-Vertex Cover} is based on the greedy vertex degree orderings. The main insight of our work is that the idea of greed vertex degree ordering could be used to design fixed-parameter approximation schemes (FPT-AS) for $\alpha>0$ and the subexponential-time algorithms for the problem on apex-minor free graphs for maximization with $\alpha>1/3$ and minimization with $\alpha<1/3$.
Protection of β2GPI Deficient Mice from Thrombosis Reflects a Defect in PAR3-facilitated Platelet Activation

Background Antibodies to β2-glycoprotein I (β2GPI) cause thrombosis in antiphospholipid syndrome, however the role of β2GPI itself in regulation of coagulation pathways in vivo is not well understood. Methods We developed β2GPI-deficient mice (Apoh-/-) by deleting exon 2 and 3 of Apoh using CRISPR/Cas9 and compared the propensity of wild-type (WT) and Apoh-/-mice to develop thrombosis using rose bengal and FeCl3-induced carotid thrombosis, laser-induced cremaster arteriolar injury, and inferior vena cava (IVC) stasis models. We also compared tail bleeding times and assessed platelet activation in WT and Apoh-/- mice in the absence and presence of exogenous β2GPI. Results Compared to WT littermates, Apoh-/- mice demonstrated a prolonged time to occlusion of the carotid artery after exposure to rose bengal or FeCl3, and reduced platelet and fibrin accumulation in cremasteric arterioles after laser injury. Similarly, significantly smaller thrombi were retrieved from the IVC of Apoh-/-mice 48 hours after IVC occlusion. The activated partial thromboplastin time (aPTT) and prothrombin time, as well as aPTT reagent- and tissue factor-induced thrombin generation times using plasma from Apoh-/- and WT mice revealed no differences. However, we observed significant prolongation of tail bleeding in Apoh-/- mice, and reduced P-selectin expression and binding of fibrinogen to the activated α2bβ3 integrin on platelets from these mice after stimulation with low thrombin concentrations; these changes were reversed by exogenous β2GPI. An antibody to PAR3 blocked thrombin-induced activation of WT, but not Apoh-/- platelets, as well as the ability of β2GPI to restore the activation response of Apoh-/- platelets to thrombin. β2GPI deficiency did not affect platelet activation by a PAR4-activator peptide, or ADP. Conclusions In mice, β2GPI may mediate procoagulant activity by enhancing the ability of PAR3 to present thrombin to PAR4, promoting platelet activation at low thrombin concentrations. Key Points β2GPI deficient mice are protected from experimental arterial, venous, and microvascular thrombosis. β2GPI deficient mice display prolonged tail bleeding times and reduced PAR3-facilitated platelet activation by low concentrations of thrombin.
ATG8 delipidation is dispensable for plant autophagy

Intracellular recycling via autophagy is governed by post-translational modifications of the autophagy related (ATG) proteins. One example is ATG4-dependent delipidation of ATG8, which assumes critical but distinct roles in autophagosome formation of yeast and mammals. Here, we discovered that ATG8 delipidation is dispensable for the maturation of autophagosomes, autophagic flux and related stress tolerance in Arabidopsis. In contrast, autophagy in an evolutionary distant Chlamydomonas strictly required ATG4-dependent ATG8 delipidation. Additionally, we uncovered distinct participation of Arabidopsis ATG8 orthologs in autophagosome biogenesis, especially prevalent under nitrogen depletion, thereby providing new insights into potential reasons behind ATG8 gene family expansion in vascular plants. Our findings point to evolutionary diversification of the molecular mechanism governing maturation of autophagosomes in eukaryotic lineages and highlight how this conserved pathway is tailored to diverse eukaryotic organisms.
The H3K27 acetyltransferase p300 is dispensable for thermogenic adipose tissue formation and function

Brown adipose tissue (BAT) is specialized for thermogenesis because it contains uncoupling protein (UCP)-1. BAT is also an endocrine organ, producing many signalling molecules important for regulating the metabolism of peripheral organs. Mounting evidence suggest that histone modifying enzymes are integral for the development, tissue maintenance, and postnatal functioning of brown and beige adipocytes. p300 and its functional homologue CREB-binding protein (CBP) are histone acetyltransferases that form the transcriptionally activating histone 3 acetyl-lysine 27 (H3K27ac) mark. Using Ucp1-Cre, we examined the requirement of p300 activity specifically within thermogenic adipocytes. We hypothesized that loss of p300 activity would impair gene programming integral for BAT development/function, rendering knockouts susceptible to metabolic dysfunction and unable to form beige adipocytes. Despite successful knockdown, brown fat was completely unaffected by p300 deletion. As such, knockout mice showed a comparable metabolic profile to littermate controls in response to diet-induced obesity. Furthermore, de novo beige adipogenesis within subcutaneous fat by a β3 adrenergic agonist remained intact in knockout mice. Although p300 and CBP have non-overlapping roles in other tissues, our results indicate p300 HAT activity is dispensable within thermogenic fats, likely due to functional compensation by CBP.