Miracle-dz/UniFAR-FTUs huggingface dataset:
The Alerting and Orienting Systems of Attention Are Modified by Cannabis Dependence

Abstract Attention allows us to select relevant information from the background. Although several studies have described that cannabis use induces deleterious effects on attention, it remains unclear if cannabis dependence affects the attention network systems differently. Objectives: To evaluate whether customary consumption of cannabis or cannabis dependence impacts the alerting, orienting, and executive control systems in young adults; to find out whether it is related to tobacco or alcohol dependence and if cannabis use characteristics are associated with the attention network systems. Method: One-hundred and fifty-four healthy adults and 102 cannabis users performed the Attention Network Test (ANT) to evaluate the alerting, orienting, and executive control systems. Results: Cannabis use enhanced the alerting system but decreased the orienting system. Moreover, those effects seem to be associated with cannabis dependence. Out of all the cannabis-using variables, only the age of onset of cannabis use significantly predicted the efficiency of the orienting and executive control systems. Conclusion: Cannabis dependence favors tonic alertness but reduces selective attention ability; earlier use of cannabis worsens the efficiency of selective attention and resolution of conflicts.
Residual Effects of Cannabis Use on Effort-Based Decision-Making

Abstract Objective: Acute Δ9-tetrahydrocannabinol (THC) administration in humans (Lawn etal., 2016) and rats (Silveira, Adams, Morena, Hill, & Winstanley, 2016) has been associated with decreased effort allocation that may explain amotivation during acute cannabis intoxication. To date, however, whether residual effects of cannabis use on effort-based decision-making are present and observable in humans have not yet been determined. The goal of this study was to test whether prolonged cannabis use has residual effects on effort-based decision-making in 24-hr abstinent cannabis using adults. Method: We evaluated performance on the Effort Expenditure for Reward Task (EEfRT) in 41 adult cannabis users (mean age = 24.63 years, 21 males) and 45 nonusers (mean age = 23.90 years, 19 males). A mixed 2x3x3 ANOVA with age as a covariate was performed to examine the effect of group, probability of winning, and reward amount on EEfRT performance. EEfRT performance was operationalized as % of trials for which the hard (vs. easy) condition was chosen. Pearson’s correlations were conducted to test the relationship between EEfRT performance and measures of cannabis use, anhedonia and motivation. Results: We found that cannabis users selected hard trials significantly more than nonusers regardless of win probability or reward level. Frequency of cannabis use was positively correlated with amount of % hard trials chosen. There were no significant correlations between % hard trials chosen, self-reported anhedonia, or motivation. Conclusions: These results suggest that unlike acute effects, residual effects of cannabis following 24 hrs of abstinence are associated with greater effort allocation during effort-based decision-making.
Guanidinium Methods for Total RNA Preparation

Cells are washed free of media and are then lysed by placing them in a 4 M guanidinium solution. The viscosity of the solution is reduced by drawing the lysate through a 20~G needle. The RNA is then pelleted through a CsCI step gradient. The supernatant fluid from this gradient is then carefully removed to allow complete separation of RNA, found in the pellet, from contaminating DNA and protein. The RNA in the pellet is then dissolved, ethanol precipitated, and quantitated spectrophotometrically at A26o' Materials Phosphate-buffered saline (pBS; APPENDIX 2) Guanidinium solution 5.7 M cesium chloride (CsCI) TES solution 3 M sodium acetate, pH 5.2 (APPENDIX 2) 100% ethanol
Deep Compositional Denoising for High‐quality Monte Carlo Rendering

We propose a deep‐learning method for automatically decomposing noisy Monte Carlo renderings into components that kernel‐predicting denoisers can denoise more effectively. In our model, a neural decomposition module learns to predict noisy components and corresponding feature maps, which are consecutively reconstructed by a denoising module. The components are predicted based on statistics aggregated at the pixel level by the renderer. Denoising these components individually allows the use of per‐component kernels that adapt to each component's noisy signal characteristics. Experimentally, we show that the proposed decomposition module consistently improves the denoising quality of current state‐of‐the‐art kernel‐predicting denoisers on large‐scale academic and production datasets.
Selection of an Immunogenic Peptide

Until recently the complete amino acid sequence was known for just a few proteins, obtained after years of laborious effort. Thday investigators are able to deduce a complete protein sequence from the corresponding cDNA sequence without purifying the protein (see Chapter 5). Based on an amino-terminal protein sequence or a variety of predictive methods, it is now possible to deduce a specific peptide sequence to be used, which then will cross-react with the intact native protein (UNIT11.15). Figure 11.14. 1 illustrates the steps involved in selecting an immunogenic peptide and its carrier and in producing an antipeptide antibody used to detect the protein from which the peptide sequence was derived.
Real‐time Monte Carlo Denoising with Weight Sharing Kernel Prediction Network

Real‐time Monte Carlo denoising aims at removing severe noise under low samples per pixel (spp) in a strict time budget. Recently, kernel‐prediction methods use a neural network to predict each pixel's filtering kernel and have shown a great potential to remove Monte Carlo noise. However, the heavy computation overhead blocks these methods from real‐time applications. This paper expands the kernel‐prediction method and proposes a novel approach to denoise very low spp (e.g., 1‐spp) Monte Carlo path traced images at real‐time frame rates. Instead of using the neural network to directly predict the kernel map, i.e., the complete weights of each per‐pixel filtering kernel, we predict an encoding of the kernel map, followed by a high‐efficiency decoder with unfolding operations for a high‐quality reconstruction of the filtering kernels. The kernel map encoding yields a compact single‐channel representation of the kernel map, which can significantly reduce the kernel‐prediction network's throughput. In addition, we adopt a scalable kernel fusion module to improve denoising quality. The proposed approach preserves kernel prediction methods’ denoising quality while roughly halving its denoising time for 1‐spp noisy inputs. In addition, compared with the recent neural bilateral grid‐based real‐time denoiser, our approach benefits from the high parallelism of kernel‐based reconstruction and produces better denoising results at equal time.
Anaemia and its associated factors among diabetes mellitus patients in Ethiopia: A systematic review and meta‐analysis

Anaemia is common but often overlooked in diabetes mellitus (DM) patients. There is also no official nationwide survey registry that estimated the prevalence of anaemia in DM patients in Ethiopia. Therefore, the main aim of this study is to determine the countrywide pooled prevalence and associated factors of anaemia in DM patients.
Mobility Shift DNA‐Binding Assay Using Gel Electrophoresis

The DNA-binding assay using mobility shift polyacrylamide gel electrophoresis (pAGE) is a simple. rapid, and extremely sensitive method for the detection of sequence-specific DNA-binding proteins in crude extracts. This assay also permits the quantitative determination of the affinity, abundance, association rate constants, dissociation rate constants, and binding specificity of DNA-binding proteins. Proteins that bind specifically to an end-labeled DNA fragment retard the mobility of the fragment during electrophoresis, resulting in discrete bands corresponding to the individual protein-DNA complexes.
Custom‐made design of metabolite composition in N. benthamiana leaves using CRISPR activators

Transcriptional regulators based on CRISPR architecture expand our ability of reprogramming endogenous gene expression in plants. One of their potential applications is the customization of plant metabolome through the activation of selected enzymes in a given metabolic pathway. Using the previously described multiplexable CRISPR activator dCasEV2.1, we assayed the selective enrichment in Nicotiana benthamiana leaves of four different flavonoids, namely naringenin, eriodictyol, kaempferol and quercetin. After careful selection of target genes and guide RNAs combinations, we created successful activation programs for each of the four metabolites, each program activating between three and seven genes, and with individual gene activation levels ranging from 4- to 1500-fold. Metabolic analysis of the flavonoid profiles of each multigene activation program showed a sharp and selective enrichment of the intended metabolites and their glycosylated derivatives. Remarkably, principal component analysis of untargeted metabolic profiles clearly separated samples according to their activation treatment, and hierarchical clustering separated the samples in five groups, corresponding to the expected four highly enriched metabolite groups, plus an un-activated control. These results demonstrate that dCasEV2.1 is a powerful tool for re-routing metabolic fluxes towards the accumulation of metabolites of interest, opening the door for custom-made design of metabolic contents in plants.
A multiple hypotheses framework to study movement ecology and diet in a migratory songbird

Whether and how migratory organisms exhibit inter-individual behavioral and/or physiological variation across movement strategies remains an open question. The Dark-eyed Junco (Junco hyemalis) is a migratory songbird known for its intra-species variation displayed in relation to morphology, song repertoires, and migration. Thus, studies focusing on juncos can reveal how migratory strategy may covary with other individual-scale factors and, therefore, identify the selective forces driving intra-species variations throughout its distribution. We used Dark-eyed Junco hydrogen stable isotope feather values (δ2H) and implemented a Bayesian framework to infer the breeding and molting origin of migratory juncos captured on their winter grounds in Oklahoma, United States (U.S.). We modeled the distribution of feather hydrogen stable isotope values as a function of five morphological variables including body mass and fat deposition measured in Oklahoma during the winter. We then investigated the trade-off between longer and more energetically costly migration strategies in relation to diet preferences through carbon (δ13C) and nitrogen (δ15N) stable isotope analysis from feather values. Dark-eyed Juncos wintering in south central U.S. likely originate from multiple breeding populations in northern U.S. and Canada. Body condition at the wintering ground (e.g., mass) had no effect on feather hydrogen stable isotope abundance. However, we found a positive correlation between nitrogen and hydrogen stable isotopes, suggesting that a trophic level shift towards insect consumption might occur in individuals migrating from southern latitudes. Increased insect-derived protein consumption might be explained by reduced fatty-acid reserves necessary to complete a shorter migratory journey.
Creating a bottleneck: Robust LC3B lipidation analysis by adjusting autophagic flux with low concentrations of Bafilomycin A1

Autophagic flux can be quantified based on the accumulation of lipidated LC3B in the presence of late-stage autophagy inhibitors. This method has been widely applied to identify novel compounds that activate autophagy. Here we scrutinize this approach and show that bafilomycin A1 (BafA) but not chloroquine is suitable for flux quantification due to the stimulating effect of chloroquine on non-canonical LC3B-lipidation. Significant autophagic flux increase by rapamycin could only be observed when combining it with BafA concentrations not affecting basal flux, a condition which created a bottleneck, rather than fully blocking autophagosome-lysosome fusion, concomitant with autophagy stimulation. When rapamycin was combined with saturating concentrations of BafA, no significant further increase of LC3B lipidation could be detected over the levels induced by the late-stage inhibitor. The large assay window obtained by this approach enables an effective discrimination of autophagy activators based on their cellular potency. To demonstrate the validity of this approach, we show that a novel inhibitor of the acetyltransferase EP300 activates autophagy in a mTORC1-dependent manner. We propose that the creation of a sensitized background rather than a full block of autophagosome progression is required to quantitatively capture changes in autophagic flux.
Consistent differences among individuals more influential than energetic trade-offs in life history variation in grey seals (Halichoerus grypus)

Life history variation is thought to be mainly a result of energetic trade-offs among fitness components; however, detecting these trade-offs in natural populations has yielded mixed results. Individual quality and environmental variation may mask expected relationships among fitness components because some higher quality individuals may be able to acquire more resources and invest more in all functions. Thus, life history variation may be more affected by variation in individual quality than varying strategies to resolve energetic trade-offs, e.g. costs of reproduction. Here, we investigated whether variation in female quality or costs of reproduction is a larger factor in shaping differences in life history trajectories by assessing the relationship between survival and individual reproductive performance using a 32-year longitudinal data set of repeated reproductive measurements from 273 individually marked, known-aged female grey seals (Halichoerus grypus) from the Sable Island breeding colony. We defined individual reproductive performance using two traits: reproductive frequency (a female’s probability of breeding) and provisioning performance (provisions given to young measured by offspring mass), computed using mixed effects models separately for (1) all reproductive events, and (2) an age-class specific reproductive investment. Individual differences contributed a large portion of the variance in reproductive traits, with individuals displaying a range in individual reproductive frequencies from 0.45 to 0.94, and a range of average pup weaning masses from 34.9 kg to 61.8 kg across their lifetime. We used a Cormack-Jolly-Seber open-population model to estimate the effect of these reproductive performance traits on adult survival probability. Our approach estimated a positive relationship between reproductive performance and survival, where individuals that consistently invest well in their offspring survive longer. The best supported model estimated survival as a function of age-class specific provisioning performance, where late-life performance was quite variable and had the greatest impact on survival, possibly indicating individual variation in senescence. There was no evidence to support a trade-off in reproductive performance and survival at the individual level. These results suggest that in grey seals, individual quality is a stronger driver in life history variation than varying strategies to mitigate trade-offs among fitness components.
Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution

Significance Gene duplication is a major source of evolutionary innovation and is associated with the increases in biological complexity and adaptive radiation. Termites are model social organisms characterized by a sophisticated caste system. We analyzed the genome of the Japanese subterranean termite, an ecologically and economically important insect acting as a destructive pest. The analyses revealed the significance of gene duplication in social evolution. Gene duplication associated with caste-biased gene expression was prevalent in the termite genome. Many of the duplicated genes were related to social functions, such as chemical communication, social immunity, and defense, and they were often expressed in caste-specific organs. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and functional specialization. Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing a transitional taxon between the higher (Termitidae) and lower (other families) termites. Here, we report the genome, transcriptome, and methylome of the Japanese subterranean termite Reticulitermes speratus. Our analyses highlight the significance of gene duplication in social evolution in this termite. Gene duplication associated with caste-biased gene expression was prevalent in the R. speratus genome. The duplicated genes comprised diverse categories related to social functions, including lipocalins (chemical communication), cellulases (wood digestion and social interaction), lysozymes (social immunity), geranylgeranyl diphosphate synthase (social defense), and a novel class of termite lineage–specific genes with unknown functions. Paralogous genes were often observed in tandem in the genome, but their expression patterns were highly variable, exhibiting caste biases. Some of the assayed duplicated genes were expressed in caste-specific organs, such as the accessory glands of the queen ovary and the frontal glands of soldier heads. We propose that gene duplication facilitates social evolution through regulatory diversification, leading to caste-biased expression and subfunctionalization and/or neofunctionalization conferring caste-specialized functions.
Cultural behaviours can be experimentally induced in wild baboons despite constraints on social information transmission

The formation of culture in animal societies, including humans, relies on the social transmission of information amongst individuals. This spread depends upon the transmission of social information, or social learning, between individuals. However, not all information spreads. To better understand how constraints at the individual-, dyad- and group-level might influence the formation of culture, we experimentally introduced four innovations (novel behaviours) across three troops of wild chacma baboons (Papio ursinus). At the individual-level, different phenotypic traits constrained individuals’ use of social information about the innovations. At the dyad-level, we found evidence for social reinforcement and directed social learning affecting who learnt and from whom. Group-level characteristics also limited the diffusion of information, which spread more slowly through social networks that showed less mixing across age classes. Nevertheless, despite these multi-level limitations, the four innovations quickly spread through all the social groups in which they were tested, suggesting that the formation of animal cultures can be surprisingly resilient to constraints on information transmission.
Human engineered skeletal muscle of hypaxial origin from pluripotent stem cells with advanced function and regenerative capacity

Human pluripotent stem cell derived muscle models show great potential for translational research. Here, we describe developmentally inspired methods for derivation of skeletal muscle cells and their utility in three-dimensional skeletal muscle organoid formation as well as skeletal muscle tissue engineering. Key steps include the directed differentiation of human pluripotent stem cells to embryonic muscle progenitors of hypaxial origin followed by primary and secondary fetal myogenesis into hypaxial muscle with development of a satellite cell pool and evidence for innervation in vitro. Skeletal muscle organoids faithfully recapitulate all steps of embryonic myogenesis in 3D Tissue engineered muscle exhibits organotypic maturation and function, advanced by thyroid hormone. Regenerative competence was demonstrated in a cardiotoxin injury model with evidence of satellite cell activation as underlying mechanism. Collectively, we introduce a hypaxial muscle model with canonical properties of bona fide skeletal muscle in vivo to study muscle development, maturation, disease, and repair.
We are not ready yet: limitations of transfer learning for Disease Named Entity Recognition

Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer learning-based methods, BERT models are used in a variety of biomedical and clinical applications. For the available data sets, these models show excellent results – partly exceeding the inter-annotator agreements. However, biomedical named entity recognition applied on COVID-19 preprints shows a performance drop compared to the results on available test data. The question arises how well trained models are able to predict on completely new data, i.e. to generalize. Based on the example of disease named entity recognition, we investigate the robustness of different machine learning-based methods – thereof transfer learning – and show that current state-of-the-art methods work well for a given training and the corresponding test set but experience a significant lack of generalization when applying to new data. We therefore argue that there is a need for larger annotated data sets for training and testing.
The presence of corticomuscular coherence during unipedal stance

Objective To elucidate cortical involvement in postural control during unipedal stance by observing corticomuscular coherence (CMC) between the sensorimotor cortex and ankle joint muscles. Methods Twenty-one participants performed three tasks: bipedal stance, unipedal stance, and isometric contraction. We measured the maximal peak of CMC (CMCmax) between electroencephalograms overlying the foot representation area and surface electromyograms from the tibialis anterior (TA), medial gastrocnemius (MG), lateral gastrocnemius (LG), and soleus (SOL), respectively, for each task. We measured the center of pressure (COP) during both stance tasks. Results Although there was no significant CMC during bipedal stance, significant CMC was observed for all muscles during unipedal stance, with larger COP fluctuation. The results revealed significant differences in CMCmax between unipedal and bipedal stance tasks (TA, p = 0.002; MG, p = 0.016; LG, p = 0.003; SOL, p = 0.009). Additionally, CMCmax was obtained in higher frequency bands during the unipedal stance task than during the isometric contraction task. Conclusions Significant CMC indicates direct involvement of the sensorimotor cortex in postural control during unipedal stance. Significance Greater postural demands due to narrow base-of-support during unipedal stance requires voluntary control of muscle activity by the sensorimotor cortex. Highlights Corticomuscular coherence (CMC) was measured in ankle muscles during bipedal stance, unipedal stance and isometric contraction. Significant CMC was observed during unipedal stance but not during bipedal stance. The peak frequency of CMC was higher during unipedal stance than during isometric contraction.