Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain expression profiles of two SCN1A antisense RNAs in children and adolescents with epilepsy

Abstract Objective Heterozygous mutations within the voltage-gated sodium channel α subunit (SCN1A) are responsible for the majority of cases of Dravet syndrome (DS), a severe developmental and epileptic encephalopathy. Development of novel therapeutic approaches is mandatory in order to directly target the molecular consequences of the genetic defect. The aim of the present study was to investigate whether cis-acting long non-coding RNAs (lncRNAs) of SCN1A are expressed in brain specimens of children and adolescent with epilepsy as these molecules comprise possible targets for precision-based therapy approaches. Methods We investigated SCN1A mRNA expression and expression of two SCN1A related antisense RNAs in brain tissues in different age groups of pediatric non-Dravet patients who underwent surgery for drug resistant epilepsy. The effect of different antisense oligonucleotides (ASOs) directed against SCN1A specific antisense RNAs on SCN1A expression was tested. Results The SCN1A related antisense RNAs SCN1A-dsAS (downstream antisense, RefSeq identifier: NR_110598) and SCN1A-usAS (upstream AS, SCN1A-AS, RefSeq identifier: NR_110260) were widely expressed in the brain of pediatric patients. Expression patterns revealed a negative correlation of SCN1A-dsAS and a positive correlation of lncRNA SCN1A-usAS with SCN1A mRNA expression. Transfection of SK-N-AS cells with an ASO targeted against SCN1A-dsAS was associated with a significant enhancement of SCN1A mRNA expression and reduction in SCN1A-dsAS transcripts. Conclusion These findings support the role of SCN1A-dsAS in the suppression of SCN1A mRNA generation. Considering the haploinsufficiency in genetic SCN1A related DS, SCN1A-dsAS is an interesting target candidate for the development of ASOs (AntagoNATs) based precision medicine therapeutic approaches aiming to enhance SCN1A expression in DS.
Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice

Abstract Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth–defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux, and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.
Role of street patterns in zone-based traffic safety analysis

Although extensive analyses of road segments and intersections located in urban road networks have examined the role of many factors that contribute to the frequency and severity of crashes, the explicit relationship between street pattern characteristics and traffic safety remains underexplored. Based on a zone-based Hong Kong database, the Space Syntax was used to quantify the topological characteristics of street patterns and investigate the role of street patterns and zone-related factors in zone-based traffic safety analysis. A joint probability model was adopted to analyze crash frequency and severity in an integrated modeling framework and the maximum likelihood estimation method was used to estimate the parameters. In addition to the characteristics of street patterns, speed, road geometry, land-use patterns, and temporal factors were considered. The vehicle hours was also included as an exposure proxy in the model to make crash frequency predictions. The results indicate that the joint probability model can reveal the relationship between zone-based traffic safety and various other factors, and that street pattern characteristics play an important role in crash frequency prediction.
Preferential flow and phosphorus translocation in benchmark soils of West Virginia

Preferential Flow and Phosphorus Translocation in Benchmark Soils of West Virginia Michael B. Harman Preferential flow is a mechanistic description of water movement in a soil profile where much of the soil matrix is bypassed during periods of rapid infiltration. The occurrence of preferential flow could lead to the movement of phosphorus (P) down through the soil profile. The objectives of this research were (i) to verify the presence of preferential flow in benchmark West Virginia soil series and (ii) measure soil test phosphorus (STP) levels within the preferential flow pathways and the surrounding soil matrix to determine the effects of preferential flow on phosphorus distribution within the soil profile. A non-reactive dye (Brilliant Blue FD&C) was applied in a ponding application to identify the preferential flow pathways in selected benchmark soil series in pasture management schemes with long-term historical applications of animal waste. The dye applications were excavated and digital images of the preferential flow pathways were taken. Soil samples from the stained (preferential flow paths) and unstained (surrounding soil matrix) portions of the soil profile were collected within each pedogenic horizon and analyzed for STP. All selected series, exhibited preferential flow. STP levels were statistically higher (p=<0.05) in the stained soil matrix.
Patch-differentiation of vegetation and nutrient cycling in an extensive pasture system.

In extensive grazing systems, ‘patch-grazing’ may lead to the development of a mosaic structure consisting of short, frequently defoliated, and tall, infrequently defoliated patches. If spatial patterns of sward structure are stable over time, this may result in a long-term differentiation of botanical composition and mat-ter fluxes between patch types within a pasture. Patch dynamics, botanical composition and topsoil nutrient concentrations of different patch types were investigated in a long-term grazing experiment in the Solling hills, Germany, where differentiated grazing intensities have been applied for 10 years. Continuously stocked beef cattle grazed to target sward heights of 6 or12 cm in a put-and-take system in replicated 1-ha paddocks. Time series of point-specific sward height measurements showed that patches were relatively stable within-and between-seasons. Botanical composition as well as soil phosphorus and potassium concentrations differed between short and tall patches. While grazing intensity influenced the frequency of short and tall patches within a pasture, differences between patch types were larger than those within the same patch type between different grazing intensities. The results highlight the importance of studying biodiversity as well as nutrient dynamics of extensive pastures in a patch-specific way. Through the development of pasture areas with different functionality, extensive grazing systems have the potential to maintain biodiversity while sustaining agricultural production.
Cognitive Function Is Associated with the Genetically Determined Efficiency of DNA Repair Mechanisms

Several modifiable risk factors for neurodegeneration and dementia have been identified, although individuals vary in their vulnerability despite a similar risk of exposure. This difference in vulnerability could be explained at least in part by the variability in DNA repair mechanisms’ efficiency between individuals. Therefore, the aim of this study was to test associations between documented, prevalent genetic variation (single nucleotide polymorphism, SNP) in DNA repair genes, cognitive function, and brain structure. Community-living participants (n = 488,159; 56.54 years (8.09); 54.2% female) taking part in the UK Biobank study and for whom cognitive and genetic measures were available were included. SNPs in base excision repair (BER) genes of the bifunctional DNA glycosylases OGG1 (rs1052133, rs104893751), NEIL1 (rs7402844, rs5745906), NEIL2 (rs6601606), NEIL3 (rs10013040, rs13112390, rs13112358, rs1395479), MUTYH (rs34612342, rs200165598), NTHL1 (rs150766139, rs2516739) were considered. Cognitive measures included fluid intelligence, the symbol–digit matching task, visual matching, and trail-making. Hierarchical regression and latent class analyses were used to test the associations between SNPs and cognitive measures. Associations between SNPs and brain measures were also tested in a subset of 39,060 participants. Statistically significant associations with cognition were detected for 12 out of the 13 SNPs analyzed. The strongest effects amounted to a 1–6% difference in cognitive function detected for NEIL1 (rs7402844), NEIL2 (rs6601606), and NTHL1 (rs2516739). Associations varied by age and sex, with stronger effects detected in middle-aged women. Weaker associations with brain measures were also detected. Variability in some BER genes is associated with cognitive function and brain structure and may explain variability in the risk for neurodegeneration and dementia.
Learning approach and teaching style preferred by pharmacy students: Implications for educational strategies in Zambia

Introduction: Identifying how students’ approach their learning and ways they prefer to learn can enable educators enhance teaching and learning experiences for quality educational outcomes. Aim: This study explored the learning approaches and teaching style preferences of pharmacy students in Zambia. Methods: The research instrument was the ‘Approaches and Study Skills Inventory for Students’ (ASSIST) questionnaire. Data were collected from 147 undergraduate pharmacy students at University of Zambia and statistically analysed using Stata 13. Results: Strategic learning approach was predominant among a majority (67%) of pharmacy students. Only 25% adopted a deep learning approach and 7% were surface learners. Learning approach was statistically significantly associated with course load ( p =0.028) and programme stage ( p =0.010). The majority (67%) preferred teaching that transmitted information while only 23% preferred teaching styles that encouraged and supported understanding of taught material. There was no statistical association between students’ learning approach and their teaching style preference ( p =0.085). Conclusion: The predominance of strategic learning approach and preference for teaching that transmitted information raises concerns on current educational strategies employed by both the curriculum and educators.
A Small-scale Oscillatory Reconnection and the Associated Formation and Disappearance of a Solar Flux Rope

We present the observations of a small-scale oscillatory reconnection for the first time and its resulting in formation and disappearance of a flux rope with the high-resolution data obtained by the New Vacuum Solar Telescope and the Solar Dynamics Observatory on 2013 July 24 and 25. This oscillatory reconnection consists of four relatively independent magnetic reconnections which last for about 48, 158, 275, and 340 minutes, respectively. The durations of the four magnetic reconnections increase with time. Four current sheets along two nearly perpendicular directions are formed alternately. The oscillatory reconnection experiences two cycles, and the periods of the two oscillations are 206 and 615 minutes, which are much longer than the previous results. The period of the first oscillation is shorter than that of the second oscillation. Furthermore, a flux rope forms during the second magnetic reconnection. Its twist increases with the reconnection and transfers from the reconnection site to one leg, and this leads the flux rope to become more slender. Then, the flux rope disappears in the early stage of the third magnetic reconnection. We conclude that the formation and disappearance of the flux rope are caused by the oscillatory reconnection.
Transformation of Swine Manure and Algal Consortia to Value-added Products

The swine production sector is projected to grow globally. In the past, this growth manifested itself in increased herd sizes and geographically concentrated production. Although economically sound, these trends had negative consequences on surrounding ecosystems. Overapplication of manure resulted in water quality degradation, while long-term storage of manure slurries was found to promote release of potent GHG emissions. There is a need for innovative approaches for swine manure management that are compatible with current scales of production, and increasingly strict environmental regulations. This study aims to investigate the potential for incorporating gasification as part of a novel swine manure management system which utilizes liquid-solid separation and periphytic algal consortia as a phycoremediation vector for the liquid slurry. The gasification of swine manure solids, and algal biomass solids generate both a gaseous fuel product (producer gas) in addition to a biochar co-product. First, the decomposition kinetics for both feedstock, i.e., swine manure solids, and algal solids, were quantified using thermogravimetry at different heating rates (1 ~ 40°C min) under different atmospheres (nitrogen, and air). Pyrolysis kinetics were determined for manure solids from two farms with different manure management systems. Similarly, the pyrolysis kinetics were determined for phycoremediation algae grown on swine manure slurries. Modeling algal solids pyrolysis as first-order independent parallel reactions was sufficient to describe sample devolatilization. Combustion of swine manure solids blended with algal solids, at different ratios, showed no synergistic effects. Gasification of phycoremediation algal biomass was studied using a bench-scale auger gasification system at temperatures between 760 and 960°C. The temperature profile suggested a stratification of reaction zones common to fixed-bed reactors. The producer gas heating value ranged between 2.2 MJ m at 760°C, and 3.6 MJ m at 960°C. Finally, life cycle assessment (LCA) was used to evaluate a proposed swine manure management system that includes a thermochemical conversion sub-system: drying, gasification, and producer-gas combustion (boiler). Liquid manure storage (uncovered tank) was the biggest contributor to GHG emissions. Liquid slurry management stages were credited with the highest fossil fuel use. Improvements to separation and drying technologies can improve this conversion scenario.
Nitrogen Levels Effects on Different Maturity Duration Hybrid Rice at Parwanipur, Bara, Nepal

Two years field experiments were conducted at Directorate of Agricultural Research, Parwanipur, Bara, Nepal from 2016 to 2017 to assess the effect of different hybrid rice varieties and nitrogen levels on yield attributes, yield and economics of rice. The experiment was arranged in two factorial Randomized Complete Block Design with three replications. The experiment comprised 12 treatment combinations of three different maturity duration hybrid rice varieties (Arize 6129 Gold, Arize Tej Gold and Arize 6444 Gold) and four nitrogen levels (0, 60, 120 and 180 kg ha-1). The two years combine analysis revealed that the hybrid varieties Arize 6444 Gold (4313 kg ha-1) and Arize Tej Gold (4274 kg ha-1) recorded significantly higher grain yield over Arize 6129 Gold (3731 kg ha-1). These two hybrid varieties (Arize 6444 Gold and Arize Tej Gold) also recorded significantly higher plant length and grains panicle-1. The nitrogen level of 180 kg ha-1 recorded significantly the highest grain yield at 6357 kg ha-1. Effective tiller m-2 and grains panicle-1 were significantly higher with nitrogen level of 180 kg ha-1. The thousand grains weight was found significantly higher with 180 kg N ha-1, which was statistically similar with 60 and 120 kg ha-1. Moreover, interaction effect between nitrogen levels and varieties revealed that Arize 6444 Gold and Arize Tej Gold equally produced the highest mean grain yield with 180 kg N ha-1. The highest gross return, net return and B:C ratio were observed with 180 kg N ha-1 with Arize 6444 Gold and ArizeTej Gold. Therefore, 180 kg N ha-1 could be optimum dose for Arize 6444 Gold and Arize Tej Gold for Parwanipur, Bara, Nepal.
The effect of montages of transcranial alternating current stimulation on occipital responses—a sham-controlled pilot study

Background Transcranial alternative current stimulation (tACS) refers to a promising non-invasive technique to improve brain functions. However, owing to various stimulation parameters in the literature, optimization of the stimulation is warranted. In this study, the authors aimed to compare the effect of tACS electrode montages on occipital responses. Methods In three montage sessions (i.e., Oz-Cz, Oz-cheek, and sham), 10 healthy young adults participated, receiving 20-min 2-mA alpha-tACS. Pattern-reversal visual evoked potentials (VEPs) were measured before tACS (T0), immediately after (T20), and 20 min (T40) after tACS. Normalized changes in time-domain features (i.e., N75, P100 amplitudes, and P100 latency) and frequency-domain features [i.e., power spectral density in alpha (PSDα) and beta (PSDβ) bands] were evaluated. Results In contrast to our hypothesis, the occipital response decreased immediately (T20) after receiving the 20-min tACS in all montages in terms of P100 amplitude (p = 0.01). This reduction returned to baseline level (T0) in Oz-cheek and sham conditions but sustained in the Oz-Cz condition (T40, p = 0.03) after 20 min of tACS. The effects on N75 amplitude and P100 latency were statistically insignificant. For spectral analysis, both PSDα and PSDβ were significantly increased after tACS at T20, in which the effect sustained until T40. However, there was no differential effect by montages. There was no significant difference in the occurrence of sensations across the montages. The effectiveness of the blinding is supported by the participants’ rate of guessing correctly. Conclusion This study revealed an immediate inhibitory effect of tACS, regardless of the montages. This inhibitory effect sustained in the Oz-Cz montage but faded out in other montages after 20 min.
Holocene sea-ice conditions and circulation at the Chukchi-Alaskan margin, Arctic Ocean, inferred from biomarker proxies

Two sediment cores from the Chukchi Sea margin were investigated for the Arctic sea-ice biomarker IP25, along with marine and terrestrial sterols and glycerol dialkyl glycerol tetraethers (GDGTs). This is the first paleoclimatic application of IP25 in the Chukchi-Alaskan region of the Arctic, which is key for understanding Arctic–Pacific interactions and is experiencing rapid sea-ice retreat under present warming. Sea-ice and related circulation conditions were characterized in this study with a multicentury resolution for the long-term Holocene record to multidecadal for the last several centuries. Sea ice was found to be present during the entire record but with considerable spatial and temporal variability. After very low deglacial IP25 values, possibly related to permanent sea ice and/or an iceberg-dominated environment, cores from the upper slope and shelf show IP25 maxima, interpreted as representing a relative proximity to the sea-ice margin, in the early (ca. 8–9 ka) and middle (ca. 5–6 ka) Holocene, respectively. Along with isoprenoid GDGT distribution, this asynchronicity in sea-ice history probably reflects oceanographic evolution of the Chukchi margin affected by the Beaufort Gyre circulation and Pacific water inflow via Bering Strait. Data for the last several centuries, with elevated values of brassicasterol and terrestrial sterols covarying with dinosterol and IP25, are interpreted in terms of long-distance import by currents combined with diagenetic transformations. We infer that high-amplitude variability in the late ‘Little Ice Age’, starting in the late 18th century, is related to the intensity of the Alaskan Coastal Current. This interval is preceded by three centuries of presumably diminished Alaskan Coastal Current but overall increased Bering Strait Inflow resulting in reduced sea-ice cover according to dinocyst-based data.
Revealing the Antiperspirant Components of Floating Wheat and Their Mechanisms of Action through Metabolomics and Network Pharmacology

Floating wheat is a classical herbal with potential efficacy in the treatment of hyperhidrosis. Aiming at revealing the main components and potential mechanisms of floating wheat, a comprehensive and unique phytopharmacology profile study was carried out. First, common wheat was used as a control to look for chemical markers of floating wheat. In the screening analysis, a total of 180 shared compounds were characterized in common wheat and floating wheat, respectively. The results showed that floating wheat and common wheat contain similar types of compounds. In addition, in non-targeted metabolomic analysis, when taking the contents of the constituents into account, it was found that there indeed existed quite a difference between floating wheat and common wheat and 17 potential biomarkers for floating wheat. Meanwhile, a total of seven components targeted for hyperhidrosis were screened out based on network pharmacology. Seven key differential components were screened, among which kaempferol, asiatic acid, sclareol, enoxolone, and secoisolariciresinol had higher degree values than the others. The analysis of interacting genes revealed three key genes, namely, MAP2K1, ESR1, and ESR2. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that various signaling pathways were involved. Prolactin signaling, thyroid cancer, endocrine resistance, gonadotropin secretion, and estrogen signaling pathways were the main pathways of the intervention of floating wheat in excessive sweating, which was associated with the estrogenic response, hormone receptor binding, androgen metabolism, apoptosis, cancer, and many other biological processes. Molecular docking showed that the screened key components could form good bindings with the target proteins through intermolecular forces. This study reveals the active ingredients and potential molecular mechanism of floating wheat in the treatment of hyperhidrosis and provides a reference for subsequent basic research.
Magnetospheric Cavity Modes Driven by Solar Wind

S. G. Claudepierre and M. K. Hudson, Department of Physics and Astronomy, Dartmouth College,Hanover, NH 03755, USA. (Seth.G.Claudepierre@dartmouth.edu)M. Wiltberger, NCAR, High Altitude Observatory, Boulder, CO 80301, USA.S. R. Elkington, LASP, University of Colorado, Boulder, CO 80303, USA.W. Lotko, Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA.