Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering how specialized interneuron-specific cell types contribute to circuit function

The wide diversity of inhibitory cells across the brain makes them fit to contribute to network dynamics in specialized fashions. However, the contributions of a particular inhibitory cell type in a behaving animal is challenging to decipher as one needs to both record cellular activities and identify the cell type being recorded. Thus, using computational modeling to explore cell-specific contributions so as to predict and hypothesize functional contributions is desirable. Here we examine potential contributions of interneuron-specific 3 (I-S3) cells - a type of inhibitory interneuron found in CA1 hippocampus that only targets other inhibitory interneurons - during simulated theta rhythms. We use previously developed multi-compartment models of oriens lacunosum-moleculare (OLM) cells, the main target of I-S3 cells, and explore how I-S3 cell inputs during in vitro and in vivo scenarios contribute to theta. We find that I-S3 cells suppress OLM cell spiking, rather than engender its spiking via post-inhibitory rebound mechanisms. To elicit recruitment similar to experiment, the inclusion of disinhibited pyramidal cell inputs is necessary, suggesting that I-S3 cell firing can broaden the window for disinhibiting pyramidal cells. Using in vivo virtual networks, we show that I-S3 cells can contribute to a sharpening of OLM cell recruitment at theta frequencies. Further, a shifting of the timing of I-S3 cell spiking due to external modulation can shift the timing of the OLM cell firing and thus disinhibitory windows. We thus propose a specialized contribution of I-S3 cells to create temporally precise coordination of modulation pathways. Significance Statement How information is processed across different brain structures is an important question that relates to the different functions that the brain performs. In this work we use computational models that focus on a particular inhibitory cell type that only inhibits other inhibitory cell types – the I-S3 cell in the hippocampus. We show that this cell type is able to broaden the window for disinhibition of excitatory cells. We further illustrate that this broadening presents itself as a mechanism for input pathway switching and modulation over the timing of inhibitory cell spiking. Overall, this work contributes to our knowledge of how coordination between sensory and memory consolidation information is attained in a brain area that is involved in memory formation.
Exact and asymptotic identification-robust inference for dynamic structural equations with an application to New Keynesian Phillips Curves

Abstract Many models in econometrics involve endogeneity and lagged dependent variables. We start by observing that usual identification-robust (IR) tests are unreliable when model variables are nonstationary or nearly nonstationary. We propose IR methods which are also robust to nonstationarity: one Anderson-Rubin type procedure and two split-sample procedures. Our procedures are also robust to missing instruments. For distributional theory, three different sets of assumptions are considered. First, on assuming Gaussian structural errors, we show that two of the proposed statistics follow the standard F distribution. Second, for more general cases, we assume that the distribution of errors is completely specified up to an unknown scale factor, allowing the Monte Carlo test method to be applied. This assumption enables one to deal with non-Gaussian error distributions. For example, even when errors follow heavy-tailed distribution, such as the Cauchy distribution or more generally the family of stable distributions—which may not have moments and thus make inference difficult—our procedures provide simple and exact solutions. Third, we establish the asymptotic validity of our procedures under quite general distributional assumptions. We present simulation results showing that our procedures control their level correctly and have good power properties. The methods are applied to an empirical example, the New Keynesian Phillips curve, in which both weak identification and nonstationarity present challenges. The results of this empirical study suggest forward-looking behavior of U.S. inflation.
Estimation of average treatment effect based on a semiparametric propensity score

Abstract This paper considers the estimation of average treatment effect using propensity score method. We propose to use a semiparametric single-index model to estimate the propensity score. This avoids the curse of dimensionality problem with the nonparametric method based propensity score estimator. We establish the asymptotic distribution of the average treatment effect estimator. Monte Carlo simulation results show that the proposed method works well in finite samples and outperforms the conventional nonparametric kernel approach. We apply the proposed method to an empirical data examining the efficacy of right heart catheterization on medical outcomes.
Procedural Control Versus Resources as Potential Origins of Human Hyper Selectivity

In the current review, we argue that experimental results usually interpreted as evidence for cognitive resource limitations could also reflect functional necessities of human information processing. First, we point out that selective processing of only specific features, objects, or locations at each moment in time allows humans to monitor the success and failure of their own overt actions and covert cognitive procedures. We then proceed to show how certain instances of selectivity are at odds with commonly assumed resource limitations. Next, we discuss examples of seemingly automatic, resource-free processing that challenge the resource view but can be easily understood from the functional perspective of monitoring cognitive procedures. Finally, we suggest that neurophysiological data supporting resource limitations might actually reflect mechanisms of how procedural control is implemented in the brain.
Optical Mapping of Brain Activity Underlying Directionality and Its Modulation by Expertise in Mandarin/English Interpreting

Recent neuroimaging research has suggested that unequal cognitive efforts exist between interpreting from language 1 (L1) to language 2 (L2) compared with interpreting from L2 to L1. However, the neural substrates that underlie this directionality effect are not yet well understood. Whether directionality is modulated by interpreting expertise also remains unknown. In this study, we recruited two groups of Mandarin (L1)/English (L2) bilingual speakers with varying levels of interpreting expertise and asked them to perform interpreting and reading tasks. Functional near-infrared spectroscopy (fNIRS) was used to collect cortical brain data for participants during each task, using 68 channels that covered the prefrontal cortex and the bilateral perisylvian regions. The interpreting-related neuroimaging data was normalized by using both L1 and L2 reading tasks, to control the function of reading and vocalization respectively. Our findings revealed the directionality effect in both groups, with forward interpreting (from L1 to L2) produced more pronounced brain activity, when normalized for reading. We also found that directionality was modulated by interpreting expertise in both normalizations. For the group with relatively high expertise, the activated brain regions included the right Broca’s area and the left premotor and supplementary motor cortex; whereas for the group with relatively low expertise, the activated brain areas covered the superior temporal gyrus, the dorsolateral prefrontal cortex (DLPFC), the Broca’s area, and visual area 3 in the right hemisphere. These findings indicated that interpreting expertise modulated brain activation, possibly because of more developed cognitive skills associated with executive functions in experienced interpreters.
A New Species-Specific Typing Method for Salivarius Group Streptococci Based on the Dephospho-Coenzyme A Kinase (coaE) Gene Sequencing

Viridans streptococci are a group of α-hemolytic streptococcal species. They are mainly commensals, most abundant in the mouth supporting oral health. But they also include important human pathogens such as Streptococcus pneumoniae. Identification and molecular typing of viridans group streptococci are challenging, especially for members of the salivarius group. In this study, we developed a single-locus molecular typing method that is able to differentiate among the highly phylogenetically related members of the salivarius group (S. salivarius, S. vestibularis and S. thermophilus) and might support differentiation in other groups as well. This typing approach is based on the amplification and sequence analysis of the housekeeping gene dephospho-coenzyme A kinase (coaE), a gene with unrecognized taxonomic potential to date. Here, we analysed coaE gene sequences of 154 publicly available genomes and of 30 salivarius group isolates of our own collection that together belong to 20 different gram-positive bacterial (sub) species. Our results revealed that the coaE phylogeny distinguished between streptococcal and non-streptococcal genomes and that coaE gene sequences were species-specific. In contrast to MALDI-TOF MS performance, the coaE typing was able to precisely identify the phylogenetically very closely related members of the salivarius group.
The Indispensable Dog

Dogs’ remarkable success in living in a human-dominated world rests on a set of adaptations to cohabitation with humans. In this paper, I review the nature of these adaptations. They include changes in reproductive and foraging behavior from their ancestor species, wolves, which can be understood as adaptations to the change from hunting live prey to feeding on human food residues. Dogs also show several changes in social behavior which are more controversial and even somewhat paradoxical. Contrary to theories of canine domestication which view dogs as less aggressive and more cooperative than wolves, several studies show that dogs’ social interactions with conspecifics are more hierarchical and competitive than are wolves’. As scavengers rather than hunters, dogs do not need to cooperate with conspecifics the way that wolves do. But how then can we understand dogs’ willingness to cooperate with humans? I propose an integrated account of dogs’ social behavior that does not assume that dogs need to recognize the species-identity of the individuals with whom they interact. Because of the overlap in formal signals of dominance and submission between dog and human and people’s complete control over the resources dogs need, I propose that people occupy a status of “super-dominance” over dogs. This conception suggests several new lines of research which could shed light on the human-dog relationship to the benefit of both partners.
Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.
Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA

Uracil-DNA glycosylase (UDG) is one of the most important base excision repair (BER) enzymes involved in the repair of uracil-induced DNA lesion by removing uracil from the damaged DNA. Uracil in DNA may occur due to cytosine deamination or deoxy uridine monophosphate (dUMP) residue misincorporation during DNA synthesis. Medical evidences show that an abnormal expression of UDG is related to different types of cancer, including colorectal cancer, lung cancer, and liver cancer. Therefore, the research of UDG is crucial in cancer treatment and prevention as well as other clinical activities. Here we applied multiple computational methods to study UDG in several perspectives: Understanding the stability of the UDG enzyme in different pH conditions; studying the differences in charge distribution between the pocket side and non-pocket side of UDG; analyzing the field line distribution at the interfacial area between UDG and DNA; and performing electrostatic binding force analyses of the special region of UDG (pocket area) and the target DNA base (uracil) as well as investigating the charged residues on the UDG binding pocket and binding interface. Our results show that the whole UDG binding interface, and not the UDG binding pocket area alone, provides the binding attractive force to the damaged DNA at the uracil base.
Taxonomic and Functional Diversity of Aquatic Macroinvertebrate Assemblages and Water Quality in Rivers of the Dry Tropics of Costa Rica

One of Costa Rica’s driest areas is the province of Guanacaste, in the Pacific Northwest, with almost no rain during the dry season from November to April. Due to this marked seasonality, the area is covered by dry tropical deciduous forest, considered the most threatened and least known tropical ecosystem in this area. This study analyzes and characterizes the assemblages of aquatic macroinvertebrates in water bodies within the Tempisque basin. Biological water quality was measured using the BMWP′-CR index. Macroinvertebrate assemblages were analyzed using abundance, richness, and functional feeding group approaches (FFG). Partial least square (PLS) analyses were performed, and the relationships between environmental factors and macroinvertebrate assemblages are also discussed. Macroinvertebrate assemblages were dominated numerically by mayflies, caddisflies, flies, and beetles. The BWMP′-CR index showed varying biological water quality, ranging from “very bad” to “excellent,” depending on rainfall and site management. Results suggest that tropical Mesoamerican rivers contradict the “river continuum concept” because predators and scrapers displace shredders in numbers. On the other hand, the study area shows a notable high richness of the Coleoptera genera. The class Rhynchocoela (Nemertea) is reported for the first time in Central America. The results indicate that the dry forest river ecosystem shows staggering biodiversity despite the surrounding agricultural land use, probably because of their older origin concerning tropical rain forests in Central America.
Physical Activity in Adolescents Living in Rural and Urban New Caledonia: The Role of Socioenvironmental Factors and the Association With Weight Status

Physical activity (PA) is an important factor for the prevention of overweight and obesity, particularly during adolescence. This study focuses on the understudied adolescent population of New Caledonia with the aim to (1) determine the daily PA levels and estimate the sedentary time through out-of-school sitting time; (2) highlight the influence of sociodemographic and environmental factors, and (3) assess the associations of PA and sitting time with overweight and obesity. A sample of 508 school-going adolescents living in New Caledonia was surveyed about their PA habits using the International Physical Activity Questionnaire–Short Form, as well as about the context in which they usually engage in PA. The influences of the place of living and ethnic community were also investigated. Results indicated that about 66% of the adolescents performed an average of at least 60 min of PA daily. Both Melanesian adolescent boys and girls were more active than Caucasian adolescents but only when they lived in rural areas (females: 115 vs. 93 min/day, p = 0.018; males: 133 vs. 97 min/day, p = 0.018). Indeed, PA was reduced in an urban environment (females: 88 min/day; males: 95 min/day, p = 0.028; rural vs. urban in Melanesian adolescents). Melanesian adolescents also spent less time in out-of-school sitting than Caucasian adolescents independently of where they lived (females: 164 vs. 295 min/day, p < 0.001; males: 167 vs. 239 min/day, p = 0.001). Feeling safe was positively associated with PA levels (females: ORadj = 2.85, p < 0.001; males: ORadj = 4.45, p < 0.001). In the adolescent boys, accessibility to a suitable place was also an important factor (ORadj = 2.94, p = 0.002). Finally, while PA and sitting time were negatively associated with overweight in male adolescents (ORadj = 0.28, p = 0.044 and ORadj = 0.39, p = 0.004), they were not in females. Living in a rural area allowed the Melanesian adolescents to maintain a more active lifestyle with more physical activities and less sitting time. Our results also indicated that safety was an important driver for engagement in PA. The urban environment in New Caledonia appears to be a contributor of a less active lifestyle in adolescents.
Effects of Ayahuasca on Personality: Results of Two Randomized, Placebo-Controlled Trials in Healthy Volunteers

Rationale: Previous studies with the serotonergic hallucinogens LSD and psilocybin showed that these drugs induced changes in personality traits, such as increases in Openness. However, results are inconsistent, and the effects of ayahuasca on personality were never investigated in a controlled trial. Objectives: To assess the effects of ayahuasca on personality in two randomized, placebo-controlled trials in healthy volunteers. Methods: Data from two parallel-group, randomized, placebo-controlled trials in healthy volunteers were included. In the first trial, 15 volunteers ingested ayahuasca or placebo, while in the second trial 15 volunteers received placebo+ayahuasca or cannabidiol (CBD)+ayahuasca. Personality was assessed with the NEO-Five Factor Inventory (NEO-FFI) at baseline and 21 days post-treatment. Results: There were significant differences between groups in baseline Openness scores, but not on day 21. A significant increase in Openness scores was observed in the placebo + ayahuasca group in study 2. No other within-group differences were observed for any other domain. Conclusions: Ayahuasca produced inconsistent effects on personality since it induced significant increase in Openness 21 days post-drug intake only in one of the trials. The absence of significant differences in the other ayahuasca groups could be due to small sample sizes and baseline differences among groups. The effects of ayahuasca and other serotonergic hallucinogens on personality should be further investigated in clinical samples.
COVID-19-Fear Affects Current Safety Behavior Mediated by Neuroticism—Results of a Large Cross-Sectional Study in Germany

Objectives: Although many research studies concerning changes in personality and behavior in time of COVID-19 pandemic emerged, important questions still have not been answered. This study with a large sample aimed to give insights into the impact of personality on pandemic fear and behavior by investigating the Big Five traits, COVID-19-fear, and associated behavioral changes in a large German-speaking sample. Methods: About 14,048 healthy respondents (65.5% female, 34.2% male, and 0.32% other gender/gender queer; range = 18–85 years, median age 35–44 years) participated in the survey during the COVID-19 pandemic. Two scales, “adherent” safety behavior (ASB, α = 0.857) and “dysfunctional” safety behavior (DSB, α = 0.876), three items each, measured pandemic-associated behavior. The Big Five Inventory-10 (BFI-10) tested personality traits. Results: While ASB correlated negatively with extraversion (rho = −0.053, ≤ 0.001), the other four traits were positively associated, with the highest association for neuroticism (rho = 0.116, ≤ 0.001), whereas neuroticism showed a positive correlation (rho = 0.142, ≤ 0.001) with DSB, extraversion (rho = −0.042, ≤ 0.001), agreeableness (rho = −0.028, ≤ 0.001), and conscientiousness (rho = −0.025, ≤ 0.001) correlated negatively with it. Regression analyses showed a small extent of the effect of personality traits. Moreover, neuroticism mediated the association between COVID-19-fear and DSB (positive-directed). Conclusions: Even though our results on correlations between personality, pandemic fear, and related behavior are in line with the existing literature studies, the analyses clearly show that the impact of personality traits, including neuroticism, on pandemic behavior is very small. Rather, pandemic fear has a much larger influence on the safety behavior mediated through neuroticism. Further studies should bear in mind that personality traits can not only have influencing effects but also mediating effects.
Significance of AtMTM1 and AtMTM2 for Mitochondrial MnSOD Activation in Arabidopsis

The manganese (Mn) tracking factor for mitochondrial Mn superoxide dismutase (MnSOD) has been annotated as yMTM1 in yeast, which belongs to the mitochondrial carrier family. We confirmed that Arabidopsis AtMTM1 and AtMTM2 are functional homologs of yMYM1 as they can revive yeast MnSOD activity in yMTM1-mutant cells. Transient expression of AtMnSOD-3xFLAG in the AtMTM1 and AtMTM2-double mutant protoplasts confirmed that AtMTM1 and AtMTM2 are required for AtMnSOD activation. Our study revealed that AtMnSOD interacts with AtMTM1 and AtMTM2 in the mitochondria. The expression levels of AtMTM1, AtMTM2, and AtMnSOD respond positively to methyl viologen (MV) and metal stress. AtMTM1 and AtMTM2 are involved in Mn and Fe homeostasis, root length, and flowering time. Transient expression of chloroplast-destined AtMnSOD revealed that an evolutionarily conserved activation mechanism, like the chloroplastic-localized MnSOD in some algae, still exists in Arabidopsis chloroplasts. This study strengthens the proposition that AtMTM1 and AtMTM2 participate in the AtMnSOD activation and ion homeostasis.