Miracle-dz/UniFAR-FTUs huggingface dataset:
A genome‐wide association study identifies a new variant associated with word reading fluency in Chinese children

Reading disability exhibited defects in different cognitive domains, including word reading fluency, word reading accuracy, phonological awareness, rapid automatized naming, and morphological awareness. To identify the genetic basis of Chinese reading disability, we conducted a genome wide association study (GWAS) of the cognitive traits related to Chinese reading disability in 2284 unrelated Chinese children. Among the traits analyzed in the present GWAS, we detected one genome wide significant association (p<5×10-8) on reading fluency for one SNP on 4p16.2, within EVC genes (rs6446395, p=7.55×10−10). Rs6446395 also showed significant association with word reading accuracy (p=3.39×10−4), phonological awareness (p=7.12×10−3), and rapid automatized naming (p=4.71×10−3), implying multiple effects of this variant. Gene-based analyses identified a gene to be associated with reading fluency at the genome-wide level. The eQTL data showed that rs6446395 affected EVC expression in the cerebellum. Our study discovered a new candidate susceptibility variant for reading ability and provide new insights into the genetics of development dyslexia in Chinese Children.
Sex- and GABAergic-modulated neuronal subnetwork assemblies in the developing somatosensory cortex

Neuronal subnetworks are common features of adult cortical circuits and serve as functional units for information processing and encoding. To determine when neuronal subnetworks are established, we employed in vivo calcium imaging to monitor neuronal activity in the primary somatosensory cortex (S1) of awake mice during early postnatal development. We found several striking developmental trajectories: (1) neuronal activity frequencies and network synchrony were sex-dependent; (2) neuronal subnetworks merged as early as P11; (3) the number of neurons in a subnetwork decreases with increasing age; (4) subnetwork neurons are initially spatially segregated, but become intermingled with other subnetworks neurons with increasing age; (5) neurons within the same subnetwork acquire a more cohesive activity pattern as age increases, and (6) enhancing GABAergic activity at P15 acutely increased female but not male subnetwork coherence. Together, our findings demonstrate that P11-P21 is the critical time for subnetwork assembly and GABAergic inputs strengthen subnetwork coherence.
Hierarchical differences in the encoding of sound and choice in the subcortical auditory system

Detection of sounds is a fundamental function of the auditory system. While studies of auditory cortex have gained substantial insight into detection performance using behaving animals, previous subcortical studies have mostly taken place under anesthesia, in passively listening animals, or have not measured performance at threshold. These limitations preclude direct comparisons between neuronal responses and behavior. To address this, we simultaneously measured auditory detection performance and single-unit activity in the inferior colliculus (IC) and cochlear nucleus (CN) in macaques. The spontaneous activity and response variability of CN neurons were higher than those observed for IC neurons. Signal detection theoretic methods revealed that the magnitude of responses of IC neurons provided more reliable estimates of psychometric threshold and slope compared to the responses of single CN neurons. However, pooling small populations of CN neurons provided reliable estimates of psychometric threshold and slope, suggesting sufficient information in CN population activity. Trial-by-trial correlations between spike count and behavioral response emerged 50-75 ms after sound onset for most IC neurons, but for few neurons in the CN. These results highlight hierarchical differences between neurometric-psychometric correlations in CN and IC, and have important implications for how subcortical information could be decoded. New & Noteworthy The cerebral cortex is widely recognized to play a role in sensory processing and decision-making. Accounts of the neural basis of auditory perception and its dysfunction are based on this idea. However, significantly less attention has been paid to midbrain and brainstem structures in this regard. Here we find that subcortical auditory neurons represent stimulus information sufficient for detection, and predict behavioral choice on a trial-by-trial basis.
Tackling the challenges of group network inference from intracranial EEG data

Intracranial EEG (iEEG) data is a powerful way to map brain function, characterized by high temporal and spatial resolution, allowing the study of interactions among neuronal populations that orchestrate cognitive processing. However, the statistical inference and analysis of brain networks using iEEG data faces many challenges related to its sparse brain coverage, and its inhomogeneity across patients. We review these challenges and develop a methodological pipeline for estimation of network structure not obtainable from any single patient, illustrated on the inference of the interaction among visual streams using a dataset of 27 human iEEG recordings from a visual experiment employing visual scene stimuli. 100 ms sliding window and multiple band-pass filtered signals are used to provide temporal and spectral resolution. For the connectivity analysis we showcase two connectivity measures reflecting different types of interaction between regions of interest (ROI): Phase Locking Value as a symmetric measure of synchrony, and Directed Transfer Function - asymmetric measure describing causal interaction. For each two channels, initial uncorrected significance testing at p<0.05 for every time-frequency point is carried out by comparison of the data-derived connectivity to a baseline surrogate-based null distribution, providing a binary time-frequency connectivity map. For each ROI pair, a connectivity density map is obtained by averaging across all pairs of channels spanning them, effectively agglomerating data across relevant channels and subjects. Finally, the difference of the mean map value after and before the stimulation is compared to the same statistic in surrogate data to assess link significance. The analysis confirmed the function of the parieto-medial temporal pathway, mediating visuospatial information between dorsal and ventral visual streams during visual scene analysis. Moreover, we observed the anterior hippocampal connectivity with more posterior areas in the medial temporal lobe, and found the reciprocal information flow between early processing areas and medial place area. To summarize, we developed an approach for estimating network connectivity, dealing with the challenge of sparse individual coverage of intracranial EEG electrodes. Its application provided new insights into the interaction between the dorsal and ventral visual streams, one of the iconic dualities in human cognition.
Graphicacy across age, education, and culture: a new tool to assess intuitive graphics skills

Data plots are widely used in science, journalism and politics, since they efficiently allow to depict a large amount of information. Graphicacy, the ability to understand graphs, thus became a fundamental cultural skill. Here, we introduce a new measure of graphicacy that assesses the ability to detect a trend in noisy scatterplots (“does this graph go up or down? ”). In 3943 educated participants, responses vary as a sigmoid function of the t-value that a statistician would compute to detect a significant trend. We find a minimum level of core graphicacy even in unschooled participants living in remote Namibian villages (N=87) and 6-year-old 1st-graders who never read a graph (N=27). However, the sigmoid slope (the “graphicacy index”) varies across participants, increases with education, and tightly correlates with statistical knowledge, showing that experience contributes to refining graphical intuitions. Our tool is publicly available online and allows to quickly evaluate intuitive graphics skills. STATEMENT OF RELEVANCE The rising cost of gas, the number of Covid deaths, the evolution of temperatures during the summer months: we often face graphs depicting these phenomena. The scientific literature has shown that human adults can intuit, within milliseconds, the statistical trend of these graphs. However, we do not know if these intuitions generalized to unschooled people and, most importantly, how to measure their variations in the population. In this study we show that intuitive graphics skills are present even in 6-year-old children who never saw a graph and in the Himba of Namibia, an indigenous people with no access to formal schooling. Furthermore, we developed a quantitative assessment of such intuitive graphics skills (which we called the “graphicacy index”), that everyone can easily obtain for free, through a short (10 minutes) online test: https://neurospin-data.cea. fr/exp/lorenzo-ciccione/graphicacy-index/. In summary, our study provides the first attempt to formally quantify human intuitions of statistical graphs.
DRAM1 promotes antibacterial autophagy and lysosomal delivery of Mycobacterium marinum in macrophages

Damage-Regulated Autophagy Modulator 1 (DRAM1) is an infection-inducible membrane protein, whose function in the immune response is incompletely understood. Based on previous results in a zebrafish infection model, we have proposed that DRAM1 is a host resistance factor against intracellular mycobacterial infection. To gain insight into the cellular processes underlying DRAM1-mediated host defence, here we studied the interaction of DRAM1 with Mycobacterium marinum in murine RAW264.7 macrophages. We found that shortly after phagocytosis, DRAM1 localised in a punctate pattern to mycobacteria, which gradually progressed to full DRAM1 envelopment of the bacteria. Within the same time frame, DRAM1-positive mycobacteria colocalised with the LC3 marker for autophagosomes and LysoTracker and LAMP1 markers for (endo)lysosomes. Knockdown analysis revealed that DRAM1 is required for recruitment of LC3 and for acidification of mycobacteria-containing vesicles. A reduction in the presence of LAMP1 further suggested reduced fusion of lysosomes with mycobacteria-containing vesicles. Finally, we show that DRAM1 knockdown impairs the ability of macrophages to control mycobacterial infection. Together, these results support that DRAM1 promotes the trafficking of mycobacteria through the degradative (auto)phagolysosomal pathway. Considering its prominent effect on host resistance to intracellular infection, DRAM1 is a promising target for therapeutic modulation of the microbicidal capacity of macrophages.
Acute phase response elicited by experimental bovine diarrhea virus (BVDV) infection is associated with decreased vitamin D and E status of vitamin-replete preruminant calves 1

Studies in young animals have shown an association between vitamin deficiencies and increased risk of infectious disease; however, there is a paucity of information regarding the effect of acute infection on the vitamin status of the vitamin-replete neonate. To characterize the effects of acute infection on vitamin D and E status of the neonate, 6 vitamin-replete preruminant Holstein bull calves were experimentally infected with bovine viral diarrhea virus (BVDV; strain BVDV2-1373). Six mock-inoculated calves served as controls. Sustained pyrexia, leukopenia, and asynchronous increases in serum haptoglobin and serum amyloid A characterized the response of calves to infection with BVDV. Infection was also associated with increased serum IFN-γ, IL-2, and IL-6 concentrations. During the last 8 d of the 14-d postinoculation period, serum 25-hydroxyvitamin D and α-tocopherol concentrations in infected calves decreased by 51 and 82%, respectively. The observed inverse association between vitamin D and E status and serum amyloid A in infected calves suggests that the infection-induced acute phase response contributed to the reduced vitamin status of these animals. Additional studies are necessary to determine if the negative effect of infection on status are unique to this specific infection model or is representative of preruminant calf’s response to acute infection. Studies are also needed to characterize mechanisms underlying infection-related changes in vitamin D and E status and to determine whether additional vitamin D or E supplementation during an acute infection diminishes disease severity and duration in the young animal.
Ai, Skill, and Productivity: The Case of Taxi Drivers

Preliminary and Incomplete. Comments are more than welcome. Abstract Artiﬁcial Intelligence (AI) is documented to have diﬀerential impacts across occupations. However, micro-level evidence is scant on how AI aﬀects the productivity of workers with diﬀerent skill levels within occupation. We study the impact of a demand-forecasting AI on productivity in the context of taxi drivers. We ﬁnd that the AI improves drivers’ productivity by shortening the time to search for customers by 5% on average. Importantly, the productivity gain is concentrated on low-skilled drivers (10%) whereas the corresponding gain on high-skilled drivers is nearly zero. This result suggests that AI, unlike past technologies, may not accompany skill-biased technological change.
Separated borders: Exponential-gap fanin-hierarchy theorem for approximative depth-3 circuits

Mulmuley and Sohoni (2001) proposed an ambitious program, the Geometric Complexity Theory (GCT), to prove $P\neq NP$ and related conjectures using algebraic geometry and representation theory. Gradually, GCT has introduced new structures and questions in complexity. GCT tries to capture the algebraic/geometric notion of ’approximation’ by defining border classes. Surprisingly, (Kumar ToCT’20) proved the universal power of the border of top-fanin- 2 depth-3 circuits $(\overline{\Sigma^{[2]}\Pi\Sigma})$; which is in complete contrast to its classical model. Recently, (Dutta,Dwivedi,Saxena, FOCS’21) put an upper bound, by showing that bounded-top-fanin border depth-3 circuits $(\overline{\Sigma^{[k]}\Pi\Sigma}$ for constant $k)$ can be computed by a polynomial-size algebraic branching program (ABP). It was left open to show an exponential separation between the class of ABPs and $\overline{\Sigma^{[k]}\Pi\Sigma}$. In this article, we show a strongly-exponential separation between any two consecutive border classes, $\overline{\Sigma^{[k]}\Pi\Sigma}$ and $\Sigma^{[k+1]}\Pi\Sigma$, establishing an optimal hierarchy of constant topfanin border depth- 3 circuits. Put in GCT language: we prove an exponential-hierarchy for padded- k-th-secant-varieties of the Chow variety of $\mathbb{F}^{n+1} $. This positively answers [Open question 2 of Dutta,Dwivedi,Saxena FOCS’21] and [Problem 8.10 with constant r, of Landsberg, Annal.Ferrara’15]. Full version: https://www.cse. iitk.ac. in/users/nitin/papers/exphierarchy.pdf
Decadal variability in extratropical Rossby wave packet amplitude, phase, and phase speed

The ongoing global, yet spatially inhomogeneous warming prompts the inspection of decadal variability in the extratropical upper-tropospheric circulation properties. This study provides observational evidence in this regard by utilizing reanalysis data to unveil past trends in the probability distribution of Rossby wave packet (RWP) amplitude ( E ), phase ( Φ ), and phase speed ( c p ) that may creep behind interannual variability. First, a comparison between the NE Paciﬁc and N Atlantic regions indicates that the 300 hPa E probability distribution exhibits a seasonally- and regionally-varying decadal variability. 5 No apparent discrepancy arises between different reanalysis datasets, except from the JJA season where the historical ones systematically underestimate E . Further exploiting the local in space and time character of the employed diagnostics in ERA5 reveals that, while many areas experience pronounced RWP property variations at interannual and/or decadal time scales, patterns of robust trends in the 1979–2019 period do emerge. Notably, the Northern Hemisphere E ﬁeld exhibits positive trends in N Paciﬁc, NE Atlantic, and S Asia in DJF, whereas negative trends are found in a substantial portion of the extratropics in 10 JJA. In terms of c p , distinct patterns characterize MAM, with positive trends in parts of N Atlantic and most of Europe and negative trends to the north of these regions and parts of N Paciﬁc. The Southern Hemisphere features a poleward shift in the band of climatologically-maximum E values in DJF, widespread positive E trends in MAM, and positive c p trends in large parts of the extratropics in DJF and MAM. Assessing the decadal variability of RWP phase reveals zonally-extended patterns of alternating trends in the trough-ridge occurrence ratio for MAM in the Northern Hemisphere and JJA in both hemispheres. Furthermore, no covariance is observed between area-averaged daily-mean E and c p at decadal time scales, as revealed by the E – c p bivariate distribution trends for the different regions and seasons. Finally, it is shown that many parts of N Paciﬁc and N America experience a shift to increasing occurrence of large-amplitude and/or quasi-stationary RWPs in DJF during 1999– 2019, thus reﬂecting the temporal variation in trends that characterizes areas and seasons that feature pronounced variability at interannual-to-decadal time scales.
Use of machine learning to retrieve nitrogen dioxide with hyperspectral imagers in the ultraviolet and blue spectral range

Nitrogen dioxide ( NO 2 ) is an important trace-gas pollutant and climate agent whose presence also leads to spectral interference in ocean color retrievals. NO 2 column densities have been retrieved with satellite UV-Vis spectrometers such as the Ozone Monitoring Instrument (OMI) and Tropospheric Monitoring Instrument (TROPOMI) that typically have spectral resolutions of the order of 0.5 nm or better and spatial footprints as small as 3.5 km × 5 km. These NO 2 observations are used to estimate emissions, monitor pollution trends, and study effects on human health. Here, we investigate whether it is possible 5 to retrieve NO 2 amounts with lower spectral resolution hyper-spectral imagers such as the Ocean Color Instrument (OCI) that will ﬂy on the Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) satellite set for launch in early 2024. OCI will have a spectral resolution of 5 nm and a spatial resolution of ∼ 1 km with global coverage in 1-2 days. At this spectral resolution, small scale spectral structure from NO 2 absorption is still present. We use real spectra from the OMI to simulate OCI spectra that are in turn used to estimate NO 2 slant column densities (SCDs) with an artiﬁcial neural network trained on target OMI retrievals. 10 While we obtain good results with no noise added to the OCI simulated spectra, we ﬁnd that the expected instrumental noise substantially degrades the OCI NO 2 retrievals. Nevertheless, the NO 2 information from OCI may be of value for ocean color retrievals, as our simulations suggest that it will be of similar or slightly better quality as compared with TROPOMI NO 2 data at TROPOMI spatial resolution on a daily basis and will be available simultaneously. OCI retrievals can also be temporally averaged over time-scales of the order months to reduce noise and provide higher spatial resolution maps that may be useful 15 for downscaling information provided by lower spatial resolution instruments such as OMI and TROPOMI, for high resolution emissions estimates, and other applications. In addition, we explore the possibility of using an extended ﬁtting window for NO 2 retrievals as compared with traditional approaches. We demonstrate that the use of an extended spectral ﬁtting window can reduce random errors in a current state-of-the-art OMI NO 2 SCD product. Machine learning approaches with extended ﬁtting windows, once trained, can also substantially speed up NO 2 spectral ﬁtting algorithms as applied to OMI, TROPOMI, 20 and similar instruments that are ﬂying or will soon ﬂy in geostationary orbit.
Quality of light from fluorescent lamps in cucumber growth and severity of Oidium sp.

The quality of light affects the development of plants, due to the specific effects on photosynthesis, photomorphogenesis and other physiological and biochemical processes. It also has an important role in plant-pathogen interactions and controls various metabolic activities of fungi that determine their pathogenicity and severity. Three experiments were carried out under completely randomized designs to know the influence of fluorescent lamps of cool, neutral and warm white light, on the morphology and growth of cucumber plants ( Cucumis sativus L.) and the severity of powdery mildew ( Oidium sp.). In the growth chambers used, the photosynthetic photon flux density (PPFD) averaged 305 μmol m -2 s -1 , but the spectral parameters related to red light (R:WWL> NWL> CWL) and blue light (B:CWL> NWL> WWL) were contrasting. The highest absolute amount of light R (122.04 μmol m -2 s -1 ), relative amount of R:PPFD (40.09%) and proportional amount of R:B (2.67) and R:FR (3.25) of WWL promoted greater height, leaf area, fresh and dry weight of leaves, stem and root of plants, while the greater absolute amount of light B (84.19 μmol m -2 s -1 ), relative amount of B:PPFD (27.48%) and proportional amount of B:R (1.04) and B:FR (2.65) of CWL induced lower plant height and greater stem thickness and leaf greenness index. The spectral parameters of CWL also disturbed the development of Oidium sp. , which was reflected in less severity of powdery mildew compared to NWL or WWL.