Miracle-dz/UniFAR-FTUs huggingface dataset:
High conservation priority of range-edge plant populations not matched by habitat protection or research effort

High-latitude countries tend to contain the polar range-edge of many species that are nationally rare but globally common. This can focus national conservation efforts toward range-edge populations, whose conservation needs and value are disputed. Using plants in Canada as a case study, we ask whether national species-conservation rankings prioritize range-edge populations, and whether conservation priority is matched by habitat protection and research effort. We found that >75% of federally-protected plants only occur in Canada peripherally, at the northernmost 20% or less of their total range, and that the most imperilled taxa had the smallest percentage of their range in Canada (endangered plants: median=1.0%). Occurring peripherally in Canada was associated with higher threat even after accounting for range area, potentially because range-edge taxa experienced 85% higher human population densities in their Canadian range than non-peripheral taxa. High conservation priority was not matched by habitat protection, as more imperilled and more peripheral taxa had smaller fractions of their Canadian range in protected areas. Finally, peer-reviewed research on plants at-risk in Canada was low. Only 42% of plants considered at-risk in Canada had been studied in Canada, and only 11% of species with large distributions outside Canada had been studied in the context of their wider geographic range—information that is critical to establishing their relative conservation value. Our results illustrate that plant conservation in Canada is fundamentally linked to conserving range-edge populations, yet edge populations themselves are understudied, a research gap we must close to improve evidence-based conservation.
Knowledge-Aware Interpretable Recommender Systems

Recommender systems are everywhere, from e-commerce to streaming platforms. They help users lost in the maze of available information, items and services to ﬁnd their way. Among them, over the years, approaches based on machine learning techniques have shown particularly good performance for top-N recommendations engines. Unfortunately, they mostly behave as black-boxes and, even when they embed some form of description about the items to recommend, after the training phase they move such descriptions in a latent space thus loosing the actual explicit semantics of recommended items. As a consequence, the system designers struggle at providing satisfying explanations to the recommendation list provided to the end user. In this chapter, we describe two approaches to recommendation which make use of the semantics encoded in a knowledge graph to train interpretable models which keep the original semantics of the items description thus providing a powerful tool to automatically compute explainable results. The two methods relies on two completely different machine learning algorithms, namely, factorization machines and autoencoder neural networks. We also show how to measure the interpretability of the model through the introduction of two metrics: semantic accuracy and robustness.
Animal-related attitudes and activities in an urban population

Abstract We surveyed residents' attitudes toward common urban animals and their participation in animal-oriented activities in the city of Trondheim, Norway. The results show that people most like small birds, squirrels, butterflies, hedgehogs, ducks, geese and dogs, and dislike bats, snails, invertebrate species, mice and rats. Birds of prey, foxes, cats, bumblebees, magpies, pigeons, badgers, gulls, grasshoppers and crows received a neutral ranking. Generally, females more than males liked the popular and neutral species, while males more than females liked the less-preferred animals. A negative association was found between age of respondents and preferences for birds of prey, dogs, cats, badgers, bats, mice and rats. This relation was positive for some invertebrate species, and small and medium-sized birds. A positive correlation was found between educational level of the respondents and preference scores for most of the species listed. Watching television programs about nature (59% often/very often) and watching/feeding birds (41%) were the most frequently reported animal-related activities. When walking in the neighborhood, important animal-related motives for doing this were to observe birds (42%) and to observe mammals (34%). Interest in bird observation and television programs about nature increased with increasing age. Few respondents reported experiencing problems with wildlife, but dogs and cats were more often (36%) considered to create problems. These results indicate that wildlife plays an important role in shaping urban residents' daily experiences, and that both animals and their habitats should have a higher priority in urban planning and management.
Non-Rigid Musical Interfaces: Exploring Practices, Takes, and Future Perspective

Non-rigid interfaces allow for exploring new interactive paradigms that rely on deformable input and shape change, and whose possible applications span several branches of human-computer interaction (HCI). While extensively explored as deformable game controllers, bendable smartphones, and shape-changing displays, non-rigid interfaces are rarely framed in a musical context, and their use for composition and performance is rather sparse and unsys-tematic. With this work, we start a systematic exploration of this relatively uncharted research area, by means of (1) brieﬂy review-ing existing musical interfaces that capitalize on deformable input, and (2) surveying 11 among experts and pioneers in the ﬁeld about their experience with and vision on non-rigid musical interfaces. Based on experts’ input, we suggest possible next steps of musical appropriation with deformable and shape-changing technologies. We conclude by discussing how cross-overs between NIME and HCI research will beneﬁt non-rigid interfaces.
The Biology of the Dermestid Beetles, Trogoderma granarium Everts and Trogoderma versicolor (Creutz.)

Two Dermestid beetles, Trogoderma granarium Everts and T. versicolor (Creutz.) have been recorded on a variety of stored products. In England, T. granarium is a serious pest only in maltings. The life-history is described. The larvae are responsible for the damage to stored products, and their hairy nature facilitates the spread of infestations on sacking and clothing. All stages in the life-cycle are resistant to heat and dryness.
Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide

Ethanol production from carbon monoxide (CO) as a carbon and energy source by Clostridium ljungdahlii and “Clostridium autoethanogenum” is currently being commercialized. During gas fermentation, ethanol synthesis is NADH-dependent. However, ethanol oxidation and its regulatory mechanism remain incompletely understood. Energy metabolism analysis demonstrated that reduced ferredoxin is the sole source of NADH formation by the Rnf-ATPase system, which provides ATP for cell growth during CO fermentation. Therefore, ethanol production is tightly linked to biomass production (ATP production). Clarification of the mechanism of ethanol oxidation and biosynthesis can provide an important reference for generating high-ethanol-yield strains of C. ljungdahlii in the future. ABSTRACT Bioethanol production from syngas using acetogenic bacteria has attracted considerable attention in recent years. However, low ethanol yield is the biggest challenge that prevents the commercialization of syngas fermentation into biofuels using microbial catalysts. The present study demonstrated that ethanol metabolism plays an important role in recycling NADH/NAD+ during autotrophic growth. Deletion of bifunctional aldehyde/alcohol dehydrogenase (adhE) genes leads to significant growth deficiencies in gas fermentation. Using specific fermentation technology in which the gas pressure and pH were constantly controlled at 0.1 MPa and 6.0, respectively, we revealed that ethanol was formed during the exponential phase, closely accompanied by biomass production. Then, ethanol was oxidized to acetate via the aldehyde ferredoxin oxidoreductase pathway in Clostridium ljungdahlii. A metabolic experiment using 13C-labeled ethanol and acetate, redox balance analysis, and comparative transcriptomic analysis demonstrated that ethanol production and reuse shared the metabolic pathway but occurred at different growth phases. IMPORTANCE Ethanol production from carbon monoxide (CO) as a carbon and energy source by Clostridium ljungdahlii and “Clostridium autoethanogenum” is currently being commercialized. During gas fermentation, ethanol synthesis is NADH-dependent. However, ethanol oxidation and its regulatory mechanism remain incompletely understood. Energy metabolism analysis demonstrated that reduced ferredoxin is the sole source of NADH formation by the Rnf-ATPase system, which provides ATP for cell growth during CO fermentation. Therefore, ethanol production is tightly linked to biomass production (ATP production). Clarification of the mechanism of ethanol oxidation and biosynthesis can provide an important reference for generating high-ethanol-yield strains of C. ljungdahlii in the future.
The Affective Ising Model: A computational account of human affect dynamics

The human affect system is responsible for producing the positive and negative feelings that color and guide our lives. At the same time, when disrupted, its workings lie at the basis of the occurrence of mood disorder. Understanding the functioning and dynamics of the affect system is therefore crucial to understand the feelings that people experience on a daily basis, their dynamics across time, and how they can become dysregulated in mood disorder. In this paper, a nonlinear stochastic model for the dynamics of positive and negative affect is proposed called the Affective Ising Model (AIM). It incorporates principles of statistical mechanics, is inspired by neurophysiological and behavioral evidence about auto-excitation and mutual inhibition of the positive and negative affect dimensions, and is intended to better explain empirical phenomena such as skewness, multimodality, and non-linear relations of positive and negative affect. The AIM is applied to two large experience sampling studies on the occurrence of positive and negative affect in daily life in both normality and mood disorder. It is examined to what extent the model is able to reproduce the aforementioned non-Gaussian features observed in the data, using two sightly different continuous-time vector autoregressive (VAR) models as benchmarks. The predictive performance of the models is also compared by means of leave-one-out cross-validation. The results indicate that the AIM is better at reproducing non-Gaussian features while their performance is comparable for strictly Gaussian features. The predictive performance of the AIM is also shown to be better for the majority of the affect time series. The potential and limitations of the AIM as a computational model approximating the workings of the human affect system are discussed.
RNAi in Spodoptera frugiperda Sf9 Cells via Nanomaterial Mediated Delivery of dsRNA: a Comparison of Poly-L-Arginine Polyplex Nanoparticles and Poly-L-Arginine-Functionalized Au Nanoparticles.

This work focused on the delivery of dsRNA either complexed with poly-L-arginine (PLR-polyplex) or loaded onto poly-L-arginine functionalized 20 nm Au nanoparticles (PLR/Au NPs). RNA interference (RNAi) of a luciferase gene expressed in Spodopteria frugiperdi Sf9 stable cell line (Sf9_LUC) was used as a model system. The binding affinity of dsRNA with two modes of functionalization of Au NP was investigated: the electrostatic binding of PLR on citrate stabilized Au NP (e-PLR/Au NPs) via the layer-by-layer method or the covalent-linking reaction of the polymer with NHS groups on the Au NP surfaces (c-PLR/Au NPs) with excess groups quenched with either hydroxylamine (c-PLR/Au/Hyd NPs) or bovine serum albumin (c-PLR/Au/BSA NPs). The formation of PLR-polyplex particles resulting from the complexation of PLR and dsRNA were revealed by transmission electron microscope (TEM), scanning transmission electron microscope (STEM), and elemental mapping by energy dispersive X-ray spectroscopy (EDS). Luciferase gene knockdown was evaluated after exposure of Sf9 cells for 72h to 600 ng of dsRNA. Gene knockdown (GK) was found to be more efficient by exposing Sf9 cells to nanoscaled (size < 100 nm) PLR-polyplex (58% GK), in contrast to microscaled (size > 1 µm) PLR-polyplex (20% GK) or covalent PLR/Au/Hyd (7% GK) particles. The replacement of hydroxylamine by bovine serum albumin as ligand has significantly enhanced the efficiency of GK (31% GK). Investigation of endosomal escape, a key physiological barrier for dsRNA delivery, with CypHer-5E labeled dsRNA showed the good ability for the dsRNA conjugated to the different nanosystems to enter the cells compared to the unconjugated one. This study provides valuable information concerning the required properties of materials used for dsRNA delivery in lepidopteran cells such as nanoparticle size, stability in the cell culture media, the polymer molecular weight and binding strength to the nanoparticle, and the nature of ligands on surface.
Pharmacokinetics and subjective effects of 1P-LSD in humans after oral and intravenous administration.

1-Propanoyl-lysergic acid diethylamide (1P-LSD) appeared as a non-controlled alternative to LSD a few years ago. Although evidence is beginning to emerge from in vitro and animal studies that 1P-LSD might serve as a prodrug for LSD, an equivalent evaluation in humans is unavailable. Controlled oral and intravenous self-administrations of 100 μg 1P-LSD hemitartrate are reported in two human volunteers followed by analyses of urine and serum samples using a fully validated LC-MS/MS method. Psychometric evaluations included assessment of selected subjective drug effects and administration of the Five-Dimensions of Altered States of Consciousness rating scale (5D-ASC). In serum and urine, oral administrations of 1P-LSD only led to the detection of LSD reflecting biphasic elimination with a terminal elimination half-life of approx. t1/2 =6.4 h. 1P-LSD could be detected for only up to 4.16 h in serum and 2.7 h in urine following intravenous administration whereas LSD was detected in all serum samples (last sampling after approx. 24 h) and up to 80 h in urine. LSD showed first order elimination kinetics with an approx. t1/2 =5.7 h, whereas 1P-LSD showed a rapid decrease in concentration within the first hour followed by a slower decrease, most probably due to hydrolysis. Bioavailability of LSD after oral ingestion of 1P-LSD was close to 100%. The psychosensory effects of 1P-LSD and their time course were comparable to those seen after uptake of LSD in other studies which further supports the prodrug hypothesis. The 5D-ASC scores were higher after oral compared with intravenous administration of 1P-LSD.
Epigenetic conversion of conventional T cells into regulatory T cells by CD28 signal deprivation

Significance Regulatory T cells (Tregs) expressing the Treg-specific transcription factor Foxp3 are indispensable for suppressing hazardous immune responses such as autoimmune disease and allergy. Their stable function requires DNA hypomethylation at specific regions of Treg function-associated genes such as Foxp3. This report shows that, in the course of in vitro Treg generation from conventional T cells by antigenic stimulation in the presence of TGF-β and IL-2, deprivation of CD28 costimulatory signal can induce Treg-specific DNA hypomethylation in developing Tregs. Additional in vitro culture with IL-2 alone further stabilizes their Treg-type hypomethylation status, enabling their in vivo transfer to effectively suppress immune responses. These findings would help in producing functionally stable Tregs from disease-mediating T cells for treatment of various immunological diseases. Foxp3-expressing regulatory T cells (Tregs) can be generated in vitro by antigenic stimulation of conventional T cells (Tconvs) in the presence of TGF-β and IL-2. However, unlike Foxp3+ naturally occurring Tregs, such in vitro induced Tregs (iTregs) are functionally unstable mainly because of incomplete Treg-type epigenetic changes at Treg signature genes such as Foxp3. Here we show that deprivation of CD28 costimulatory signal at an early stage of iTreg generation is able to establish Treg-specific DNA hypomethylation at Treg signature genes. It was achieved, for example, by TCR/TGF-β/IL-2 stimulation of CD28-deficient Tconvs or CD28-intact Tconvs without anti-CD28 agonistic mAb or with CD80/CD86-blocked or -deficient antigen-presenting cells. The signal abrogation could induce Treg-type hypomethylation in memory/effector as well as naive Tconvs, while hindering Tconv differentiation into effector T cells. Among various cytokines and signal activators/inhibitors, TNF-α and PKC agonists inhibited the hypomethylation. Furthermore, CD28 signal deprivation significantly reduced c-Rel expression in iTregs; and the specific genomic perturbation of a NF-κB binding motif at the Foxp3 CNS2 locus enhanced the locus-specific DNA hypomethylation even in CD28 signaling-intact iTregs. In addition, in vitro maintenance of such epigenome-installed iTregs with IL-2 alone, without additional TGF-β or antigenic stimulation, enabled their expansion and stabilization of Treg-specific DNA hypomethylation. These iTregs indeed stably expressed Foxp3 after in vivo transfer and effectively suppressed antigen-specific immune responses. Taken together, inhibition of the CD28-PKC-NF-κB signaling pathway in iTreg generation enables de novo acquisition of Treg-specific DNA hypomethylation at Treg signature genes and abundant production of functionally stable antigen-specific iTregs for therapeutic purposes.
A rat model of valproate teratogenicity from chronic oral treatment during pregnancy

Sodium valproate (VPA), the most effective antiepileptic drug for patients with genetic generalized epilepsy (GGE), is a potent human teratogen that increases the risk of a range of congenital malformations, including spina bifida. The mechanisms underlying this teratogenicity are not known, but may involve genetic risk factors. This study aimed to develop an animal model of VPA‐induced birth defects.
A Novel Rapid-Flooding Approach With Real-Time Delay Compensation for Wireless-Sensor Network Time Synchronization

One-way-broadcast-based flooding time synchronization algorithms are commonly used in wireless-sensor networks (WSNs). However, the packet delay and clock drift pose a challenge to accuracy, as they entail serious by-hop error accumulation problems in the WSNs. To overcome this, a rapid-flooding multibroadcast time synchronization with real-time delay compensation (RDC-RMTS) is proposed in this article. By using a rapid-flooding protocol, flooding latency of the referenced time information is significantly reduced in the RDC-RMTS. In addition, a new joint clock skew-offset maximum-likelihood estimation (MLE) is developed to obtain the accurate clock parameter estimations and the real-time packet delay estimation. Moreover, an innovative implementation of the RDC-RMTS is designed with an adaptive clock offset estimation. The experimental results indicate that the RDC-RMTS can easily reduce the variable delay and significantly slow the growth of by-hop error accumulation. Thus, the proposed RDC-RMTS can achieve accurate time synchronization in large-scale complex WSNs.
Selective Autophagy Maintains the Aryl Hydrocarbon Receptor Levels in HeLa Cells: A Mechanism That Is Dependent on the p23 Co-Chaperone

The aryl hydrocarbon receptor (AHR) is an environmental sensing molecule which impacts diverse cellular functions such as immune responses, cell growth, respiratory function, and hematopoietic stem cell differentiation. It is widely accepted that the degradation of AHR by 26S proteasome occurs after ligand activation. Recently, we discovered that HeLa cells can modulate the AHR levels via protein degradation without exogenous treatment of a ligand, and this degradation is particularly apparent when the p23 content is down-regulated. Inhibition of autophagy by a chemical agent (such as chloroquine, bafilomycin A1, or 3-methyladenine) increases the AHR protein levels in HeLa cells whereas activation of autophagy by short-term nutrition deprivation reduces its levels. Treatment of chloroquine retards the degradation of AHR and triggers physical interaction between AHR and LC3B. Knockdown of LC3B suppresses the chloroquine-mediated increase of AHR. Down-regulation of p23 promotes AHR degradation via autophagy with no change of the autophagy-related gene expression. Although most data in this study were derived from HeLa cells, human lung (A549), liver (Hep3B), and breast (T-47D and MDA-MB-468) cells also exhibit AHR levels sensitive to chloroquine treatment and AHR–p62/LC3 interactions. Here we provide evidence supporting that AHR undergoes the p62/LC3-mediated selective autophagy in HeLa cells.
Neural networks for open and closed Literature-based Discovery

Literature-based Discovery (LBD) aims to discover new knowledge automatically from large collections of literature. Scientific literature is growing at an exponential rate, making it difficult for researchers to stay current in their discipline and easy to miss knowledge necessary to advance their research. LBD can facilitate hypothesis testing and generation and thus accelerate scientific progress. Neural networks have demonstrated improved performance on LBD-related tasks but are yet to be applied to it. We propose four graph-based, neural network methods to perform open and closed LBD. We compared our methods with those used by the state-of-the-art LION LBD system on the same evaluations to replicate recently published findings in cancer biology. We also applied them to a time-sliced dataset of human-curated peer-reviewed biological interactions. These evaluations and the metrics they employ represent performance on real-world knowledge advances and are thus robust indicators of approach efficacy. In the first experiments, our best methods performed 2-4 times better than the baselines in closed discovery and 2-3 times better in open discovery. In the second, our best methods performed almost 2 times better than the baselines in open discovery. These results are strong indications that neural LBD is potentially a very effective approach for generating new scientific discoveries from existing literature. The code for our models and other information can be found at: https://github.com/cambridgeltl/nn_for_LBD.