Miracle-dz/UniFAR-FTUs huggingface dataset:
Corollary discharge prevents signal distortion and enhances sensing during locomotion

Sensory feedback during movement entails sensing a mix of externally- and self-generated stimuli (respectively, exafference and reafference). In many peripheral sensory systems, a parallel copy of the motor command, a corollary discharge, is thought to eliminate sensory feedback during behaviors. However, reafference has important roles in motor control, because it provides real-time feedback on the animal’s motions through the environment. In this case, the corollary discharge must be calibrated to enable feedback while avoiding negative consequences like sensor fatigue. The undulatory motions of fishes’ bodies generate induced flows that are sensed by the lateral line sensory organ, and prior work has shown these reafferent signals contribute to the regulation of swimming kinematics. Corollary discharge to the lateral line reduces the gain for reafference, but cannot eliminate it altogether. We develop a data-driven model integrating swimming biomechanics, hair cell physiology, and corollary discharge to understand how sensory modulation is calibrated during locomotion in larval zebrafish. In the absence of corollary discharge, lateral line afferent units exhibit the highly heterogeneous habituation rates characteristic of hair cell systems, typified by decaying sensitivity and phase distortions with respect to an input stimulus. Activation of the corollary discharge prevents habituation, reduces response heterogeneity, and regulates response phases in a narrow interval around the time of the peak stimulus. This suggests a synergistic interaction between the corollary discharge and the polarization of lateral line sensors, which sharpens sensitivity along their preferred axes. Our integrative model reveals a vital role of corollary discharge for ensuring precise feedback, including proprioception, during undulatory locomotion.
Gene Expression Profiling of Skeletal Muscles

Soleus and tibialis anterior are two well-characterized skeletal muscles commonly utilized in skeletal muscle-related studies. Next-generation sequencing provides an opportunity for an in-depth biocomputational analysis to identify the gene expression patterns between soleus and tibialis anterior and analyze those genes’ functions based on past literature. This study acquired the gene expression profiles from soleus and tibialis anterior murine skeletal muscle biopsies via RNA-sequencing. Read counts were processed through edgeR’s differential gene expression analysis. Differentially expressed genes were filtered down using a false discovery rate less than 0.05c, a fold-change value larger than twenty, and an association with overrepresented pathways based on the Reactome pathway over-representation analysis tool. Most of the differentially expressed genes associated with soleus encoded for components of lipid metabolism and unique contractile elements. Differentially expressed genes associated with tibialis anterior encoded mostly for glucose and glycogen metabolic pathways’ regulatory enzymes and calcium-sensitive contractile components. These gene expression distinctions partly explain the genetic basis for muscle specialization and may help to explain skeletal muscle susceptibility to disease and drugs and refine tissue engineering approaches.
Stress diminishes outcome but enhances response representations during instrumental learning

Stress may shift behavioural control from a goal-directed system that encodes action-outcome relationships to a habit system that learns stimulus-response associations. Although this shift to habits is highly relevant for stress-related psychopathologies, limitations of existing behavioural paradigms hindered previous research to answer the fundamental question of whether the stress-induced bias to habits is due to impaired goal-directed or enhanced habitual processing (or both). Here, we leveraged EEG-based multivariate pattern analysis to decode neural outcome representations, crucial for goal-directed control, and response representations, essential for habitual responding, during instrumental learning. We show that stress reduces outcome representations but enhances response representations, both of which were directly associated with a behavioural index of habitual responding. Further, changes in outcome and response representations were uncorrelated, suggesting that these may reflect distinct processes. Our findings indicate that habit behaviour under stress is the result of both enhanced habitual and diminished goal-directed processing.
Effect of ozone exposure on Amyotrophic Lateral Sclerosis (ALS) pathology using a mice model of TDP-43 proteinopathy

Background Ozone (O3), one of the main photochemical pollutants in the atmosphere today, is a serious health risk factor. Although the effects of O3 exposure have been documented on many diseases, they have not yet been examined on Amyotrophic Lateral Sclerosis (ALS)- a fatal progressive and neurodegenerative disease. Objectives To investigate the effect of the O3 exposure in a mice model of TDP-43 proteinopathy, exploring a possible association between the O3 exposure and the ALS pathogenesis. Methods TDP-43A315T and wild-type (WT) mice were exposed to O3 (0.25 ppm) or filtered air (FA) for 15 days (4 hours/day). We assessed (1) weight loss (2) motor performance (3) plasma glucose content and (4) metabolic markers from plasma samples of the animals. Results Throughout the experiment, we observed a progressive decline in body weight and the motor coordination in TDP-43A315T mice compared to WT controls. Although there was a trend, there were no significant differences in the decline of body weight of TDP-43A315T mice when exposed to either FA or O3. In O3-TDP-43A315T mice, the disease duration lasted longer. In addition, O3-TDP-43A315T mice showed improvements in motor performance as well TDP-43A315T mice were hypoglycemic compared to WT mice. However, FA-TDP-43A315T mice showed lower plasma glucose levels at the disease end-stage. We found altered levels of adipokines and metabolic proteins in TDP-43A315T mice compared to WT controls. A positive correlation was found among GIP and glucagon compared to insulin concentrations in control mice. Interestingly, resistin, Gastric Inhibitory Peptide (GIP), Glucagon Like Peptide 1 (GIP-1) and insulin levels were higher in O3-TDP-43A315T mice. Discussion We provide new evidence about a mechanistic link between O3 exposure and the improvement of the metabolic disturbances present in TDP-43A315T mice. Further studies are needed to corroborate the obtained results as they warrant to understanding the underlying mechanisms.
Coexistence of Neutral and Ion-Pair Clusters of Hydrated Sulfuric Acid H2SO4(H2O)n (n = 1−5)A Molecular Orbital Study

Various isomeric structures of the hydrated clusters of sulfuric acid, H2SO4(H2O)n (n = 1−5), are examined using a density functional molecular orbital method. Due to the small energy difference between trans and cis conformations about two OH groups of sulfuric acid, there are three types of isomeric forms of the hydrated clusters of sulfuric acid which involve the proton nontransferred trans conformer, the proton transferred trans conformer, and the proton nontransferred cis conformer of sulfuric acid. In the case of transoid H2SO4, the proton transferred ion-pair structures become more stable than the proton nontransferred structures as the number of water molecules increases. The hydrated clusters of the cis conformation remain neutral hydrogen-bonded structures even if the number of water molecules increases. All stable clusters tend to form multi-cyclic structures. While both protons of sulfuric acid participate in cyclic hydrogen bonding in the neutral structures, the OH group of HSO4- in the ion-p.
Conservation and Convergence of Genetic Architecture in the Adaptive Radiation of Anolis Lizards

The G matrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However, G can evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution of G in similar environments would suggest that G evolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation of Anolis lizards to ask whether convergence of G accompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measured G in seven species representing three ecomorphs (trunk-crown, trunk- ground, and grass-bush). We found that the overall structure of G does not converge. Instead, the structure of G is well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements of G showed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution of G, even as its overall structure remains conserved.
Plant responses to multiple antagonists are mediated by order of attack and phytohormone crosstalk

Plants are often attacked by multiple antagonists, and traits of the attacking organisms, and their order of arrival onto hosts, may affect plant defenses. However, few studies have assessed how multiple antagonists, and varying attack order, affect plant defense or nutrition. To address this, we assessed defensive and nutritional responses of Pisum sativum plants after attack by a vector herbivore (Acrythosiphon pisum), a non-vector herbivore (Sitona lineatus), and a pathogen (Pea enation mosaic virus, PEMV). We show PEMV-infectious A. pisum induced several pathogen-specific plant defense signals, but these defenses were inhibited when S. lineatus was present in peas infected with PEMV. In contrast, feeding by S. lineatus induced anti-herbivore defense signals, but these defenses were enhanced by PEMV. Sitona lineatus also increased abundance of plant amino acids, but only when they attacked after PEMV-infectious A. pisum. Our results suggest that diverse communities of biotic antagonists alter defense and nutritional traits of plants through complex pathways that depend on the identity of attackers and their order of arrival onto hosts. Moreover, we show interactions among a group of biotic stressors can vary along a spectrum from antagonism to enhancement/synergism based on the identity and order of attackers, and these interactions are mediated by a multitude of phytohormone pathways.
BET Inhibition Enhances TNF-Mediated Antitumor Immunity

Small molecules that target epigenetic regulators, such as BET inhibitors, can alter tumor cell responses to pro-inflammatory cytokines via modulation of prosurvival signaling pathways. Use of small-molecule agents in combination with immunotherapy increases tumor susceptibility to CTL killing. Targeting chromatin binding proteins and modifying enzymes can concomitantly affect tumor cell proliferation and survival, as well as enhance antitumor immunity and augment cancer immunotherapies. By screening a small-molecule library of epigenetics-based therapeutics, BET (bromo- and extra-terminal domain) inhibitors (BETi) were identified as agents that sensitize tumor cells to the antitumor activity of CD8+ T cells. BETi modulated tumor cells to be sensitized to the cytotoxic effects of the proinflammatory cytokine TNF. By preventing the recruitment of BRD4 to p65-bound cis-regulatory elements, BETi suppressed the induction of inflammatory gene expression, including the key NF-κB target genes BIRC2 (cIAP1) and BIRC3 (cIAP2). Disruption of prosurvival NF-κB signaling by BETi led to unrestrained TNF-mediated activation of the extrinsic apoptotic cascade and tumor cell death. Administration of BETi in combination with T-cell bispecific antibodies (TCB) or immune-checkpoint blockade increased bystander killing of tumor cells and enhanced tumor growth inhibition in vivo in a TNF-dependent manner. This novel epigenetic mechanism of immunomodulation may guide future use of BETi as adjuvants for immune-oncology agents.
Coordination between nucleotide excision repair and specialized polymerase DnaE2 action enables DNA damage survival in non-replicating bacteria

Translesion synthesis (TLS) is a highly conserved mutagenic DNA lesion tolerance pathway, which employs specialized, low-fidelity DNA polymerases to synthesize across lesions. Current models suggest that activity of these polymerases is predominantly associated with ongoing replication, functioning either at or behind the replication fork. Here we provide evidence for DNA damage-dependent function of a specialized polymerase, DnaE2, in replication-independent conditions. We develop an assay to follow lesion repair in non-replicating Caulobacter and observe that components of the replication machinery localize on DNA in response to damage. These localizations persist in the absence of DnaE2 or if catalytic activity of the polymerase is mutated. Single-stranded DNA gaps for SSB binding and low-fidelity polymerase-mediated synthesis are generated by nucleotide excision repair, as replisome components fail to localize in its absence. This mechanism of gap-filling facilitates cell cycle restoration when cells are released into replication-permissive conditions. Thus, such cross-talk (between activity of NER and specialized polymerases in subsequent gap-filling) helps preserve genome integrity and enhances survival in a replication-independent manner.
Developmental change in prefrontal cortex recruitment supports the emergence of value-guided memory

Prioritizing memory for valuable information can promote adaptive behavior across the lifespan, but it is unclear how the neurocognitive mechanisms that enable the selective acquisition of useful knowledge develop. Here, using a novel task coupled with functional magnetic resonance imaging, we examined how children, adolescents, and adults (N = 90) learn from experience what information is likely to be rewarding, and modulate encoding and retrieval processes accordingly. We found that the ability to use learned value signals to selectively enhance memory for useful information strengthened throughout childhood and into adolescence. Encoding and retrieval of high- vs. low-value information was associated with increased activation in striatal and prefrontal regions implicated in value processing and cognitive control. Age-related increases in value-based lateral prefrontal cortex modulation mediated the relation between age and memory selectivity. Our findings demonstrate that developmental increases in the strategic engagement of the prefrontal cortex support the emergence of adaptive memory.
Impact of an oral amino acid provision on Achilles peritendinous amino acid concentrations in young and older adults

Recent studies have indicated that consumption of amino acid-rich compounds can increase tendon collagen content and enhance biomechanical function. Still, it is not clear as to what extent oral consumption of amino acids alters peritendinous amino acid concentrations. Whether aging alters the delivery of amino acids to tendon tissue after oral consumption is also not known. Using microdialysis, we determined the impact of a single oral essential amino acid bolus on Achilles peritendinous amino acid concentrations in younger (n=7; 27±1 yr.) and older adults (n=6; 68±2 yrs.) over four hours. The peritendinous concentration of all amino acids in the beverage except methionine (p=0.136) and glycine (p=0.087) increased with time (p<0.05). Additionally, the concentrations of glycine and arginine were greater in older adults (p≤0.05). We also accessed the impact of amino acid consumption on peritendinous concentrations of pro-collagen Iα1, a marker of collagen synthesis. Pro-collagen Iα1 tended to change with time (p=0.071) but was not altered age (p=0.226). We demonstrate that an oral amino acid bolus leads to modest increases in Achilles peritendinous amino acid concentrations in young and older adults. The concentration of some amino acids was also greater in older adults. However, the amino acid bolus did not significantly impact peritendinous pro-collagen concentrations.
DLAB: deep learning methods for structure-based virtual screening of antibodies

Antibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time-and cost-intensive and heavily reliant on in-vivo and in-vitro high throughput screens. Here, we introduce a framework for structure-based deep learning for antibodies (DLAB) which can virtually screen putative binding antibodies against antigen targets of interest. DLAB is built to be able to predict antibody-antigen binding for antigens with no known antibody binders. We demonstrate that DLAB can be used both to improve antibody-antigen docking and structure-based virtual screening of antibody drug candidates. DLAB enables improved pose ranking for antibody docking experiments as well as selection of antibody-antigen pairings for which accurate poses are generated and correctly ranked. We also show that DLAB can identify binding antibodies against specific antigens in a case study. Our results demonstrate the promise of deep learning methods for structure-based virtual screening of antibodies.
Spatial model of water quality in Southeast Asian urban lake based on HBI using macrozoobenthos diversity as a proxy

Urban lake is one of ecosystem that has experienced anthropogenic pressures and this can affect its water quality. One of a robust approach to assess the water quality is by using Hilsenhoff Biotic Index (HBI). This tool is quite versatile since it can be applied by using any aquatic organism as proxy including macrozoobenthos. This invertebrate group also has an advantage since it is common and easy to collect. Here this study is first, aiming to provide HBI based water quality spatial model using macrozoobenthos as a proxy applied in urban lake in West Java in Southeast Asia and second to seek the best model that can represent the water quality variables in particular dissolved oxygen (DO), pH, and temperature. Based on the spatial model and HBI, either inlet or outlet parts of the lake, it has better water quality in comparison to central parts. Based on HBI values, water quality in inlet and outlet parts (HBI = 6.7) is categorized as fair and poor (HBI = 6.9) for the central parts of the lake. The increase in HBI and decrease in water quality are positively correlated with the increase in water temperature variable in comparison to water DO and pH variables. Akaike model selection confirms that the macrozoobenthos diversity can be used as a proxy for increase in water temperature (Ψ)HBI (~temp)(AIC = −10.264) followed by combination of water temperature increase and decrease in DO(Ψ)HBI (~temp+DO)(AIC = −9.042398).
Time trend, social vulnerability, and identification of risk areas for tuberculosis in Brazil: An ecological study

INTRODUCTION Tuberculosis is one of the ten leading causes of death and the leading infectious cause worldwide. The disease represents a challenge to health systems around the world. In 2018, it is estimated that 10 million people were affected by tuberculosis, and approximately 1.5 million people died due to the disease worldwide, including 251,000 patients coinfected with HIV. In Brazil, the disease caused 4,490 deaths, with rate of 2.2 deaths per 100,000 inhabitants. The objective of this study was to analyze the time behavior, spatial distribution, and the effects of social vulnerability on the incidence of TB in Brazil during the period from 2001 to 2017. METHODS A spatial-temporal ecological study was conducted, including all new cases of tuberculosis registered in Brazil during the period from 2001 to 2017. The following variables were analyzed: incidence rate of tuberculosis, the Social Vulnerability Index, its subindices, its 16 indicators, and an additional 14 variables available on the Atlas of Social Vulnerability. The statistical treatment of the data consisted of the following three stages: a) time trend analysis with a joinpoint regression model; b) spatial analysis and identification of risk areas based on smoothing of the incidence rate by local empirical Bayesian model, application of global and local Moran statistics, and, finally, spatial-temporal scan statistics; and c) analysis of association between the incidence rate and the indicators of social vulnerability. RESULTS Brazil reduced the incidence of tuberculosis from 42.8 per 100,000 to 35.2 per 100,000 between 2001 and 2017. Only the state of Minas Gerais showed an increasing trend, whereas nine other states showed a stationary trend. A total of 326 Brazilian municipalities were classified as high priority, and 22 high-risk spatial clusters were identified. The overall Social Vulnerability Index and the subindices of Human Capital and Income and Work were associated with the incidence of tuberculosis. It was also observed that the incidence rates were greater in municipalities with greater social vulnerability. CONCLUSIONS This study identified spatial clusters with high risk of TB in Brazil. A significant association was observed between the incidence rate of TB and the indices of social vulnerability.
Leptin regulates glucose homeostasis via the canonical WNT pathway

Leptin is a body weight regulatory hormone, but it is arguably even more potent at regulating blood glucose levels. To further our understanding of the molecular mechanisms by which leptin controls glucose homeostasis, we have used transgenic zebrafish models and conditional deletion of beta catenin in the mediobasal hypothalamus of adult mice to show that Wnt signalling in the brain mediates glucoregulatory effects of leptin. In zebrafish, under normal feeding conditions, leptin regulates glucose homeostasis but not adipostasis. In times of nutrient excess, we found that leptin also regulates body weight and size in this species. Using a Wnt signalling reporter fish, we show that leptin directly activates the canonical Wnt pathway in vivo. Pharmacological inhibition of this pathway prevented the leptin-induced improvement in glucose tolerance. In adult mice, conditional deletion of the key Wnt effector molecule, β-catenin, in the mediobasal hypothalamus of male mice confirmed the essential role of the Wnt pathway in mediating leptin action and the neuroendocrine regulation of glucose homeostasis. Adult-onset β-catenin deletion in the mediobasal hypothalamus led to glucose intolerance, exacerbation of caloric intake and body weight gain under high fat diet, as well as resistance to exogenous leptin.