Miracle-dz/UniFAR-FTUs huggingface dataset:
Decreased Alertness Reconfigures Cognitive Control Networks

Humans' remarkable capacity to flexibly adapt their behavior based on rapid situational changes is termed cognitive control. Intuitively, cognitive control is thought to be affected by the state of alertness; for example, when drowsy, we feel less capable of adequately implementing effortful cognitive tasks. Although scientific investigations have focused on the effects of sleep deprivation and circadian time, little is known about how natural daily fluctuations in alertness in the regular awake state affect cognitive control. Here we combined a conflict task in the auditory domain with EEG neurodynamics to test how neural and behavioral markers of conflict processing are affected by fluctuations in alertness. Using a novel computational method, we segregated alert and drowsy trials from two testing sessions and observed that, although participants (both sexes) were generally sluggish, the typical conflict effect reflected in slower responses to conflicting information compared with nonconflicting information, as well as the moderating effect of previous conflict (conflict adaptation), were still intact. However, the typical neural markers of cognitive control—local midfrontal theta-band power changes—that participants show during full alertness were no longer noticeable when alertness decreased. Instead, when drowsy, we found an increase in long-range information sharing (connectivity) between brain regions in the same frequency band. These results show the resilience of the human cognitive control system when affected by internal fluctuations of alertness and suggest that there are neural compensatory mechanisms at play in response to physiological pressure during diminished alertness. SIGNIFICANCE STATEMENT The normal variability in alertness we experience in daily tasks is rarely taken into account in cognitive neuroscience. Here we studied neurobehavioral dynamics of cognitive control with decreasing alertness. We used the classic Simon task where participants hear the word “left” or “right” in the right or left ear, eliciting slower responses when the word and the side are incongruent—the conflict effect. Participants performed the task both while fully awake and while getting drowsy, allowing for the characterization of alertness modulating cognitive control. The changes in the neural signatures of conflict from local theta oscillations to a long-distance distributed theta network suggest a reconfiguration of the underlying neural processes subserving cognitive control when affected by alertness fluctuations.
De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

Senna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.
LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer

Until now, existing methods for identifying lncRNA related miRNA sponge modules mainly rely on lncRNA related miRNA sponge interaction networks, which may not provide a full picture of miRNA sponging activities in biological conditions. Hence there is a strong need of new computational methods to identify lncRNA related miRNA sponge modules. In this work, we propose a framework, LMSM, to identify LncRNA related MiRNA Sponge Modules from heterogeneous data. To understand the miRNA sponging activities in biological conditions, LMSM uses gene expression data to evaluate the influence of the shared miRNAs on the clustered sponge lncRNAs and mRNAs. We have applied LMSM to the human breast cancer (BRCA) dataset from The Cancer Genome Atlas (TCGA). As a result, we have found that the majority of LMSM modules are implicated in BRCA and most of them are BRCA subtype-specific. Most of the mediating miRNAs act as crosslinks across different LMSM modules. Moreover, the consistent results suggest that LMSM is robust in identifying lncRNA related miRNA sponge modules. Finally, LMSM can be used to predict miRNA targets. Altogether, our study shows that LMSM is a promising method to investigate modular regulatory mechanism of sponge lncRNAs from heterogeneous data.
Characteristics of Black Glutinous Rice Vinegar as Traditionally Fermented Product of Yeast Tapai and Acetobacter aceti

As the source of nutrition in food, the product of rice vinegar also has advantages as anti-diabetes, anti-oxidation, anti-cholesterol and anti-bacterial which contribute to health. For the current research, the fermentation of black glutinous rice for producing rice vinegar used microbes contained in yeast tape and acetic acid bacteria (BAA). To get high-quality vinegar products, two stages of the optimization process are carried out. The first process is the fermentation process for the production of alcohol using yeast from tapai and the second process is a fermentation process for the production of acetic acid using Acetobacter aceti. The products are analyzed for their physicochemical and functional properties. Vinegar produced in the processes contained 52.04 g/L acetic acid, 21.83% anthocyanin level, 1844.72 (GAE mg / L) total phenolic and 92.71% DPPH inhibition.
Characterization of the complete mitochondrial genome of Silurus soldatovi in Korean river

Abstract The complete mitochondrial genome of Silurus soldatovi firstly collected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 16,525 bp in length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Siluridae. Twenty-eight genes were located on H strand, whereas the remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, S. soldatovi showed highest identity (99.38%) to the Chinese haplotype of S. soldatovi (NC022723) followed by the Chinese haplotype of Silurus asotus (JX087351). Interestingly, intraspecies variations of S. asotus are higher than those of interspecies and further study should be made to elucidate the evolutional relationship between two Silurus species.
A influência da área de poças e seus descritores ambientais sobre a estrutura de comunidades de anfíbios anuros em áreas campestres do Rio Grande do Sul, Brasil

Tamanho e heterogeneidade de habitat estao entre os principais fatores que determinam a riqueza, estrutura e composicao de especies de comunidades de plantas e animais. Entretanto, a distincao entre eles e fundamental para discriminar qual dos descritores tem influencia sobre os padroes locais registrados. Neste estudo, testamos separadamente o efeito da area e da heterogeneidade ambiental de pocas sobre comunidades de anfibios anuros de quatro UAs nos Campos Sulinos do Rio Grande do Sul, Brasil. As amostragens foram realizadas no periodo de setembro a novembro de 2014, primavera, epoca de maior atividade da anurofauna no extremo sul do Brasil. A amostragem constituiu-se de uma parte diurna, na qual larvas de anuros foram coletadas e uma parte noturna, com busca ativa nos sitios de reproducao. Alem disso, foram coletadas caracteristicas ambientais locais, como qualidade fisico-quimica da agua e estrutura da vegetacao emergente e da margem da poca, assim como presenca de peixes. Foram coletadas ainda, caracteristicas ambientais da paisagem, como tipo de matriz de entorno e distância da mata. Identificamos 35 especies de anuros pertencentes a cinco familias: Bufonidae, Hylidae, Leptodactylidae, Microhylidae e Odontophrinidae. Na analise da area das pocas sobre a riqueza de especies observamos ausencia de influencia desse fator, sendo assim, com o aumento da area das pocas a riqueza nao tende a aumentar de maneira significativa. Por outro lado, os fatores ambientais locais, como pH, porcentagem de extrato vegetal emergente e numero de extratos vegetais na agua foram significativamente associados com o aumento da riqueza de especies de anuros. De fato, as caracteristicas da vegetacao nas pocas podem estar relacionadas com a riqueza de especies uma vez que o aumento na porcentagem de vegetacao emergente proporciona maior quantidade de microhabitats, e assim mais recursos para postura de ovos e protecao das larvas. A presenca de peixes mostrou ser um fator nao limitante para a riqueza de especies de anuros, ja a analise onde testamos o efeito dos fatores ambientais locais e da paisagem sobre a composicao de especies de anuros, foi inconclusiva, devido a baixa explicacao dos fatores ambientais locais retidos no modelo, o qual reteve apenas 17% da variância dos dados no eixo 1 e 7% no eixo 2. A ausencia de influencia significativa do tamanho das pocas sobre a riqueza de anuros evidencia o quao importante sao esses corpos d’agua para a conservacao das comunidades de anuros, mesmo que eles sejam pequenos, menores do que os protegidos pelas leis brasileiras.
Cadmium and morphological alterations in the rotifer Philodina cf. roseola (Bdelloidea: Philodinidae) and the worm Aeolosoma hemprichi (Annelida: Aeolosomatidae)

Cadmium is a toxic metal for zooplankton that produces deformations. Therefore, we used two native zooplankton species from Quintana Roo, Mexico, to obtain data regarding cadmium toxicity including the threshold concentration for observable morphological alterations and the percentage of organisms with morphological alterations at the exposure concentrations. We used the rotifer Rotaria sp. and the oligochaeta Aeolosoma hemprichi, both fed with the alga Nannochloropsis oculata. Then, Rotaria sp. and A. hemprichi were exposed to a cadmium concentration range from 0.05 to 10.0 mg L-1. The LC50 for cadmium in Rotaria sp. was 0.7 mg L-1, whereas in A. hemprichi it was 3.38 mg L-1. Cadmium at 0.5 mg L-1 for ≤24 h induced morphological alterations in the lorica of rotifers, foot deformations, and constriction in the middle part of the body. In oligochaetes, damage to the epidermis was noted. The threshold concentration where deformations appeared in rotifer was 0.3 mg L-1 at 24 h and in oligochaeta was 0.5 mg L-1 at 30 min.
CRB2 controls primary ciliogenesis in association with PAR6α, HOOK2 and RAB8A

Ciliogenesis is an essential process in animal development and physiology and when affected, the origin of severe pathologies called ciliopathies. CRB2 has been recently implicated when mutated in several pathologies such as retina degeneration and a ciliopathy-like syndrome. Here, we have investigated the role of CRB2 in primary ciliogenesis and showed that CRB2 depletion blocks the formation of the ciliary vesicle after activation of the mother centriole, indicating a defect in either transport or anchoring of the ciliary vesicle. CRB2 is accumulated in intracellular vesicles in the vicinity of the centrosome and we showed here that CRB2 forms a complex made of HOOK2 and PAR6α, two proteins important for primary ciliogenesis or centrosome integrity. In addition, CRB2 interacts with RAB8A which over-expression rescued CRB2 knockdown. All together, these findings indicate that CRB2 regulates a membrane transport step essential for the formation of the ciliary vesicle.
Reduced functional connectivity between left frontal and right auditory cortices during speech perception in congenital amusia

| Congenital amusia is a condition characterized by disordered perception of and memory for pitch. Investigations of amusia’s neural basis have typically used musical or tonal tasks to demonstrate reduced connectivity between frontal and auditory cortices within the right hemisphere. However, pitch is not only a musical property, but is also an important aspect of spoken language — one which amusics, presumably because of their impairment, tend to rely on less than non-amusic adults. It is an open question whether amusics’ decreased reliance on pitch for speech shares the same right hemispheric neural substrate as their musicrelated deficits. Here we used functional magnetic resonance imaging to scan 15 individuals with amusia and 15 non-amusic controls while they performed a speech categorization task (intonational phrase boundary detection). On each trial, participants matched auditory and visual sentences by relying on pitch cues, duration cues, or both combined. We used a datadriven analysis to identify the strongest functional connectivity differences between the amusics and controls. Group differences in global functional connectivity (Control > Amusia) were strongest in four regions in lateral prefrontal cortex. Connectivity with these ‘seed’ regions was examined with respect to the rest of the brain. Participants with amusia showed prominent decreases in functional connectivity between language-related regions (left inferior and middle frontal gyrus/DLPFC) and pitch-related regions (right auditory and anterior insular cortex). No connectivity differences between the cue conditions were detected and no condition-by-group interactions were found, suggesting that decreased functional connectivity in amusia persisted irrespective of which acoustic cues judgments were based on. There were also no group differences in degree of task-related activation. We conclude that functional connectivity between left—as well as right—frontal cortex and pitch-related right hemisphere regions is decreased in amusia, and suggest this decreased connectivity may reflect amusics’ strategic downweighting of pitch information during processing of spoken language. Our results also suggest that individual differences in auditory abilities relating to specific dimensions (such as pitch) are reflected in differential functional connectivity between regions that process those dimensions. AMUSIA AND LANGUAGE PROCESSING
The derived-band envelope following response and its sensitivity to sensorineural hearing deficits

The envelope following response (EFR) is a sensitive marker of synaptopathy in animal models. However, its amplitude is affected by the spread of basilar-membrane excitation and other coexisting sensorineural hearing deficits. This study aims to (i) improve frequency specificity of the EFR by introducing a derived-band EFR (DBEFR) technique and (ii) investigate the effect of lifetime noise exposure, age and outer-hair-cell (OHC) damage on DBEFR magnitudes. Additionally, we adopt a modelling approach to validate the frequency-specificity of the DBEFR and test how different aspects of sensorineural hearing loss affect peripheral generators. The combined analysis of simulations and experimental data proposes that the DBEFRs extracted from the [2-6]-kHz frequency band is a sensitive and frequency-specific measure of synaptopathy in humans. Individual variability in DBEFR magnitudes among listeners with normal audiograms was explained by their self-reported amount of experienced lifetime noise-exposure and corresponded to amplitude variability predicted by synaptopathy. Older listeners consistently had reduced DBEFR amplitudes in comparison to young normal-hearing listeners, in correspondence to how age-induced synaptopathy affects EFRs and compromises temporal envelope encoding. Lastly, OHC damage was also seen to affect the DBEFR amplitude, hence this marker should be combined with a marker sensitive to OHC-damage to offer a differential diagnosis of synaptopathy in listeners with impaired audiograms.
Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in its environment. However, a detailed understanding of how oscillations in mRNA levels are connected to oscillations in post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach of deep transcriptome sequencing and bioinformatics tools to identify novel circadian regulated genes and splicing events. Using a stringent approach, we identified 109 intron retention, 35 exon skipping, 42 alternative 5’ splice site usage, and 63 alternative 3’ splice site usage events under circadian regulation. We also found 24 and 1765 novel alternative exonic and intronic events. Depletion of the circadian regulated splicing factor SPF30 homolog, resulted in the disruption of a subset of clock controlled splicing events, mainly at CT16. Altogether, our global circadian RNAseq coupled with an in silico, event centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of a large number of circadian regulated splicing events, broadens our current understanding of the level of control that the circadian clock has over this posttranscriptional regulatory layer.
C9orf72-derived arginine-containing dipeptide repeats associate with axonal transport machinery and impede microtubule-based motility

Arginine-rich dipeptide repeats associated with ALS and FTD inhibit machinery for microtubule-based axonal cargo transport. A hexanucleotide repeat expansion in the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). How this mutation leads to these neurodegenerative diseases remains unclear. Here, we show using patient stem cell–derived motor neurons that the repeat expansion impairs microtubule-based transport, a process critical for neuronal survival. Cargo transport defects are recapitulated by treating neurons from healthy individuals with proline-arginine and glycine-arginine dipeptide repeats (DPRs) produced from the repeat expansion. Both arginine-rich DPRs similarly inhibit axonal trafficking in adult Drosophila neurons in vivo. Physical interaction studies demonstrate that arginine-rich DPRs associate with motor complexes and the unstructured tubulin tails of microtubules. Single-molecule imaging reveals that microtubule-bound arginine-rich DPRs directly impede translocation of purified dynein and kinesin-1 motor complexes. Collectively, our study implicates inhibitory interactions of arginine-rich DPRs with axonal transport machinery in C9orf72-associated ALS/FTD and thereby points to potential therapeutic strategies.
Dietary supplementation with combined extracts from garlic (Allium sativum), brown seaweed (Undaria pinnatifida), and pinecone (Pinus koraiensis) improves milk production in Holstein cows under heat stress conditions

Objective This study was conducted to examine the effects of a mixture of pinecone oil, garlic, and brown seaweed extracts (PGBE) on milk production traits as well as physiological and ethological parameters in Holstein cows during the summer season (24 May to 03 July 2015, Korea). Methods Among the extract combinations tested, we found that the level of 2,2′-azino-bis (3-ethylberzothiazoline-6-sulphonic acid) cation radical scavenging activity of the 0.16% PBGE complex at ratio of 1:1:1 (vol/vol) was comparable to that of the control (ascorbic acid; 1 mg/mL). Additionally, the PBGE complex reduced lipopolysaccharide-induced COX-2 expression in bovine mammary epithelial cells. Based on these findings, 40 lactating Holstein cows were used to measure the effects of PBGE complex at ratio of 1:1:1 (vol/vol) on milk production, immune response, metabolites, and behavior patterns by dividing the cows into two groups fed diets containing PGBE complex (n = 20; 0.016%/kg feed dry matter basis) or not containing PGBE complex (control, n = 20) for 40 d. Results Results showed that PGBE complex did not influence milk composition, eating and ear surface temperature patterns, immune response, or metabolic parameters but promoted average milk yield throughout the experimental period. Additionally, a tendency of higher total antioxidant capacity and glutathione in the PGBE group was observed compared to the those in the control. When the temperature-humidity index (THI) exceeded 72 (average THI = 73.8), PGBE complex-fed cows experiencing heat stress showed increased milk yield and a tendency of increased rumination compared to the control. Conclusion We suggest that incorporation of a combined mixture of 0.016% PGBE (1:1:1 ratio, vol/vol) to diet has the potential to improve milk yield and health status of cows under mild to moderate heat stress, denoting that it might be useful as an alternative anti-stressor in the diet of dairy cows under hot conditions.
Microplastic occurrence and effects in commercially harvested North American finfish and shellfish: Current knowledge and future directions

Commercial fisheries yield essential foods, sustain cultural practices, and provide widespread employment around the globe. Commercially harvested species face a myriad of anthropogenic threats including degraded habitats, changing climate, overharvest, and pollution. Microplastics are pollutants of increasing concern, which are pervasive in the environment and can harbor or adsorb pollutants from surrounding waters. Aquatic organisms, including commercial species, encounter and ingest microplastics, but there is a paucity of data about those caught and cultured in North America. Additional research is needed to determine prevalence, physiological effects, and population‐level implications of microplastics in commercial species from Canada, the United States, and Mexico. Investigations into possible human health effects of microplastic exposure from seafood are also greatly needed. This synthesis summarizes current knowledge, identifies data gaps, and provides future research directions for addressing microplastics effects in commercially valuable North American fishery species.
A statistical framework for measuring reproducibility and replicability of high-throughput experiments from multiple sources

Replication is essential to reliable and consistent scientific discovery in high-throughput experiments. Quantifying the replicability of scientific discoveries and identifying sources of irreproducibility have become important tasks for quality control and data integration. In this work we introduce a novel statistical model to measure the reproducibility and replicability of findings from replicate experiments in multi-source studies. Using a nested copula mixture model that characterizes the interdependence between replication experiments both across and within sources, our method quantifies reproducibility and replicability of each candidate simultaneously in a coherent framework. Through simulation studies, an ENCODE ChIP-seq dataset and a SEQC RNA-seq dataset, we demonstrate the effectiveness of our method in diagnosing the source of discordance and improving the reliability of scientific discoveries.