Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide High Resolution Expression Map and Functions of Key Cell Fate Determinants Reveal the Dynamics of Crown Root Development in Rice

Shoot borne adventitious/crown roots (AR/CR) shape up the root architecture in grasses. Mechanisms underlying initiation and subsequent outgrowth of CR remain largely unknown. Here, we provide genome-wide modulation in the landscape of transcriptional signatures during distinct developmental stages of CR formation in highly derived grass species, rice. Our studies implicate the role of potential epigenetic modifiers, transcription factors and cell division regulators in priming the initiation of CR primordia followed by progressive activation of conserved transcription regulatory modules to ensure their outgrowth. In depth analysis of spatio-temporal expression patterns of key cell fate determinants and functional analyses of rice WUSCHEL RELATED HOMEOBOX10 (OsWOX10) and PLETHORA (OsPLT1) genes reveal their unprecedented role in controlling root architecture. We further show that OsPLT1 activates local auxin biosynthesis and forms an integral part of ERF3-OsWOX11-OsRR2 regulatory module during CR primordia development. Interestingly, OsPLT genes, when expressed in the transcriptional domain of root-borne lateral root primordia of Arabidopsis plt mutant, rescued their outgrowth demonstrating the conserved role of PLT genes in root primordia outgrowth irrespective of their developmental origin. Together, these findings unveil the molecular framework of cellular reprogramming during trans-differentiation of shoot tissue to root leading to culmination of robust root architecture in grass species which got evolutionary diverged from dicots.
Evidence of shifts towards neural states of stability during the retrieval of real-life episodic memories

How does one retrieve real-life episodic memories? Here, we tested the hypothesis, derived from computational models, that successful retrieval relies on neural dynamics patterns that rapidly shift towards stable states. We implemented cross-temporal correlation analysis of electroencephalographic (EEG) recordings while participants retrieved episodic memories cued by pictures collected with a wearable camera depicting real-life episodes taking place at “home” and at “the office”. We found that the retrieval of real-life episodic memories is supported by rapid shift towards brain states of stable activity, that the degree of neural stability is associated with the participants’ ability to recollect the episodic content cued by the picture, and that each individual elicits stable EEG patterns that were not shared with other participants. These results indicate that the retrieval of autobiographical memory episodes is supported by rapid shifts of neural activity towards stable states.
Disentangling interactions between mercury, immunity, and infection in a Neotropical bat community

Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination can also bring wildlife reservoir hosts into close contact with humans and domestic animals. However, the interactions between contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare. We capitalized on extreme mercury variation in a diverse Neotropical bat community in Belize to test association between contaminants, immunity, and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, we first confirmed bat species with more aquatic prey in their diet had higher fur mercury. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and common bacterial pathogens (hemoplasmas and Bartonella). Lastly, as bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in these mercury–infection relationships. Across the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for both pathogens were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. When considering species-specific relationships between mercury and infection, mercury was associated with especially low odds for Pteronotus mesoamericanus and Dermanura phaeotis for hemoplasmas. Yet for Bartonella, mercury was associated with particularly low odds in the genus Pteronotus but especially high odds within the Stenodermatinae. Synthesis and application: Lower infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e., anemia) or vector mortality as possible causal mechanisms. Strong positive associations between mercury and Bartonella in the Stenodermatinae, however, alongside negative associations between mercury and neutrophils in this clade, suggest these bats could be especially vulnerable to immunosuppression. Greater attention to these potential causal pathways could help disentangle the complex relationships between environmental contaminants, immunity, and infection in natural systems and forecast disease risks.
End-to-End Alignment of Gold Nanorods on Topographically Enhanced, Cylinder Forming Diblock Copolymer Templates and Their Surface Enhanced Raman Scattering Properties

We present a facile methodology for the end-to-end assembly of gold nanorods of various aspect ratios on corrugated, horizontal, cylinder-forming diblock copolymer templates. Although the depth of corrugation is significantly smaller than the diameter of the nanorods, they exhibit excellent selectivity (>98%) and alignment for placement in the polymer grooves due to capillary forces and the substrate’s topography. Enhanced corrugation of the diblock template is achieved by chemical swelling prior to deposition of the metallic nanorods. Graphoepitaxy of the diblock copolymer in nanoconfining channels is employed to achieve essentially perfect long-range orientation of the substrate, while subsequent deposition of nanorod arrays whose alignment maps onto that of the diblock template with high fidelity provides novel organic–inorganic hybrid surfaces whose surface enhanced Raman spectroscopy (SERS) properties are characterized. These arrays of aligned gold nanorods exhibit polarization-dependent spectra for .
Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza

The structure of extracellular domain of MSPL and inhibitor complex helps to understand the TTSP functions, including TMPRSS2, and provides the insights of the infection of influenza and SARS-CoV. Infection of certain influenza viruses is triggered when its HA is cleaved by host cell proteases such as proprotein convertases and type II transmembrane serine proteases (TTSP). HA with a monobasic motif is cleaved by trypsin-like proteases, including TMPRSS2 and HAT, whereas the multibasic motif found in high pathogenicity avian influenza HA is cleaved by furin, PC5/6, or MSPL. MSPL belongs to the TMPRSS family and preferentially cleaves [R/K]-K-K-R↓ sequences. Here, we solved the crystal structure of the extracellular region of human MSPL in complex with an irreversible substrate-analog inhibitor. The structure revealed three domains clustered around the C-terminal α-helix of the SPD. The inhibitor structure and its putative model show that the P1-Arg inserts into the S1 pocket, whereas the P2-Lys and P4-Arg interacts with the Asp/Glu-rich 99-loop that is unique to MSPL. Based on the structure of MSPL, we also constructed a homology model of TMPRSS2, which is essential for the activation of the SARS-CoV-2 spike protein and infection. The model may provide the structural insight for the drug development for COVID-19.
Using High-Frequency Data in Dynamic Portfolio Choice

This article evaluates the economic benefit of methods that have been suggested to optimally sample (in an MSE sense) high-frequency return data for the purpose of realized variance/covariance estimation in the presence of market microstructure noise (Bandi and Russell, 2005a, 2008). We compare certainty equivalents derived from volatility-timing trading strategies relying on optimally-sampled realized variances and covariances, on realized variances and covariances obtained by sampling every 5 minutes, and on realized variances and covariances obtained by sampling every 15 minutes. In our sample, we show that a risk-averse investor who is given the option of choosing variance/covariance forecasts derived from MSE-based optimal sampling methods versus forecasts obtained from 5- and 15-minute intervals (as generally proposed in the literature) would be willing to pay up to about 80 basis points per year to achieve the level of utility that is guaranteed by optimal sampling. We find that the gains yielded by optimal sampling are economically large, statistically significant, and robust to realistic transaction costs.
Inhibiting proBDNF to mature BDNF conversion leads to autism-like phenotypes in vivo

Autism spectrum disorders (ASD) comprise a range of early age-onset neurodevelopment disorders with genetic heterogeneity. Most ASD related genes are involved in synaptic function, which is oppositely regulated by brain-derived neurotrophic factor (BDNF): the precursor proBDNF inhibits while mature BDNF (mBDNF) potentiates synapses. Here we generated a knock-in mouse line (BDNFmet/leu) in which the conversion of proBDNF to mBDNF is inhibited. Biochemical experiments revealed residual mBDNF but excessive proBDNF in the brain. Similar to other ASD mouse models, the BDNFmet/leu mice showed decreased brain volumes, reduced dendritic arborization, altered spines, and impaired synaptic transmission and plasticity. They also exhibited ASD-like phenotypes, including stereotypical behaviors, deficits in social interaction, hyperactivity, and elevated stress response. Interestingly, the plasma level of proBDNF, but not mBDNF, was significantly elevated in ASD patients. These results suggest that proBDNF level, but not Bdnf gene, is associated with autism-spectrum behaviors, and identify a potential blood marker and therapeutic target for ASD.
Forecasting With a Forward-Looking DGE Model - Combining Long-Run Views of Financial Markets With Macro Forecasting

To develop forecasting procedures with a forward-looking dynamic general equilibrium model, we built a small New-Keynesian model and calibrated it to euro area data. It was essential in this context that we allowed for long-run growth in GDP. We brought additional asset price equations based on the expectations hypothesis and the Gordon growth model, into the standard open economy model, in order to extract information on private sector long-run expectations on fundamentals, and to combine that information into the macro economic forecast. We propose a method of transforming the model in forecasting use in such a way, as to match, in an economically meaningful way, the short-term forecast levels, especially of the model's jump-variables, to the parameters affecting the long-run trends of the key macroeconomic variables. More specifically, in the model we have used for illustrative purposes, we pinned down the long-run inflation expectations and domestic and foreign potential growth-rates using the model's steady state solution in combination with, by assumption, forward looking information in up-to-date financial market data. Consequently, our proposed solution preserves consistency with market expectations and results, as a favourable by-product, in forecast paths with no initial, first forecast period jumps. Furthermore, no ad hoc re-calibration is called for in the proposed forecasting procedures, which clearly is an advantage from point of view of transparency in communication.
Gene expression variability in human and chimpanzee populations share common determinants

Inter-individual variation in gene expression has been shown to be heritable and it is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.
Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients

Background: A few studies have been done on the molecular analysis of Iranian influenza A isolates M gene. Methods: In 2014, nasal swabs collected from outpatients with clinical symptoms in the hospital clinics of Tehran, Iran were subjected for influenza detection and subtyping using Real-Time RT-PCR. Sequence and phylogenetic analysis performed on four randomly selected isolates from each subtype (H1N1 and H3N2) using neighbor-joining method. Results: Phylogenetic dendrograms drawn based on M nucleotide sequence of H1N1 isolates showed close relatedness with Omanian isolates while the most isolates of H3N2 have clustered with Kuwait isolates and isolates from outside of geographical location. Amino acid sequence analysis showed S31N substitution in all isolates rendering the virus resistant to adamantanes. Conclusion: This study determined the sequence identity and phylogenetic relatedness of M gene sequence got from Iranian influenza A isolates to elucidate the modality of relationship of this gene in comparison with its counterparts from other regions.
The Impact of EU Regional Support on Growth and Convergence in the European Union

The tendency towards regional convergence that characterised most of the member states of the European Union from the 1950s onwards came to an end around 1980. To the extent that there has been any tendency towards convergence since then, it has been at the country level, related to the catch up by the relatively poor Southern countries that joined the EU during the 1980s. Within countries, however, there has at best been a standstill. A particularly challenging question is to what extent regional support from the EU , designed to help catch-up by relatively poor regions, has had a real impact on this situation. The EU Structural Funds were reformed in 1989. The objective was to make the funds more effective in reducing the gap between advanced and less-advanced regions and strengthening economic and social cohesion in the European Community. Since 1989 the financial resources allocated to these funds have doubled in real terms. The evidence presented in this paper suggests that this reform may have succeeded in improving EU regional policy so that it becomes more effective in its aim, to generate growth in poorer regions and contribute to greater equality in productivity and income in Europe. However it needs to be emphasised that there also are diverging factors at play. For instance, the estimates obtained for the empirical growth model used in this paper suggest that growth in poorer regions is greatly hampered by an unfavourable industrial structure (dominated by agriculture) and lack of R&D. Hence, to get the maximum out of the support, this needs to be accompanied by policies that facilitate structural change and increase R&D capabilities in poorer regions. Such policies must necessarily be of a long-term nature.
Assessing the Effectiveness of Voluntary Solid Waste Reduction Policies: Methodology and a Flemish Case Study

The purpose of this paper is to illustrate the use of statistical techniques to evaluate the effectiveness of voluntary policy instruments for waste management. The voluntary character of these instruments implies that latent characteristics, unobserved by the analyst, might influence the participation decision and might lead to biased estimates of the effectiveness of the policy instrument if standard techniques are used. We propose an extension of the Difference-in-Differences estimator to evaluate the effectiveness of voluntary policy instruments. We illustrate the technique by estimating the effectiveness of voluntary cooperation agreements between the Flemish environmental administration and individual municipalities. We focus on agreements which aim at curbing residential solid waste. Using a dataset covering all 308 Flemish municipalities for the period 2000-2005, our results indicate that municipalities subscribing to the agreement reduced their waste level by less than what could be expected on the basis of their own performance prior to subscription and the performance of the non-subscribers. This result might be explained by rising marginal cost of extra residential solid waste reduction policies. In addition, there are indications that subscribing municipalities refrain from additional reduction efforts once the target waste level of the program is achieved.
Ultraflat, broadband, and highly coherent supercontinuum generation in all-solid microstructured optical fibers with all-normal dispersion

High flatness, wide bandwidth, and high-coherence properties of supercontinuum (SC) generation in fibers are crucial in many applications. It is challenging to achieve SC spectra in a combination of the properties, since special dispersion profiles are required, especially when pump pulses with duration over 100 fs are employed. We propose an all-solid microstructured fiber composed only of hexagonal glass elements. The optimized fiber possesses an ultraflat all-normal dispersion profile, covering a wide wavelength interval of approximately 1.55 μm. An SC spectrum spanning from approximately 1030 to 2030 nm (corresponding to nearly one octave) with flatness <3 dB is numerically generated in the fiber with 200 fs pump pulses at 1.55 μm. The results indicate that the broadband ultraflat SC sources can be all-fiber and miniaturized due to commercially achievable 200-fs fiber lasers. Moreover, the SC pulses feature high coherence and a single pulse in the time domain, which can be compressed to 13.9-fs pulses with high quality even for simple linear chirp compensation. The Fourier-limited pulse duration of the spectrum is 3.19 fs, corresponding to only 0.62 optical cycles.
Historical Evaluation and Future Prediction of Eastern North American and Western Atlantic Extratropical Cyclones in the CMIP5 Models during the Cool Season

AbstractExtratropical cyclone track density, genesis frequency, deepening rate, and maximum intensity distributions over eastern North America and the western North Atlantic were analyzed for 15 models from phase 5 of the Coupled Model Intercomparison Project (CMIP5) for the historical period (1979–2004) and three future periods (2009–38, 2039–68, and 2069–98). The cyclones were identified using an automated tracking algorithm applied to sea level pressure every 6 h. The CMIP5 results for the historical period were evaluated using the Climate Forecast System Reanalysis (CFSR). The CMIP5 models were ranked given their track density, intensity, and overall performance for the historical period. It was found that six of the top seven CMIP5 models with the highest spatial resolution were ranked the best overall. These models had less underprediction of cyclone track density, more realistic distribution of intense cyclones along the U.S. East Coast, and more realistic cyclogenesis and deepening rates. The best.
Symposium : Evolution of Ideas about the Nutritional Value of Dietary Fat Dietary Fatty Acids and the Regulation of Plasma Low Density Lipoprotein Cholesterol Concentrations 1

Epidemiologic studies over the past 25 years have shown that the level of dietary fat intake is positively correlated with the average serum cholesterol value and mortality from coronary heart disease (CHD). A number of different investigators demonstrated that in addition to total fat, the fatty acid composition of diets influenced serum total cholesterol (TC) in humans. In general, saturated fatty acids were found to elevate the serum cholesterol concentration, and unsaturated fatty acids were found to decrease this value. The lipoprotein fraction most affected was the level of cholesterol carried in low density lipoprotein (LDL-C). It has now been demonstrated that the steady-state level of LDL-C is predominantly dictated by metabolic events in the liver. As the amount of dietary cholesterol entering the body is increased, there is expansion of the sterol pool in the liver cell and down regulation of LDL receptors (LDLR) that are primarily responsible for clearing LDL-C from the blood stream. When dietary cholesterol intake is kept constant, however, long-chain saturated fatty acids further suppress hepatic LDLR activity, whereas several unsaturated fatty acids have the opposite effect. These regulatory events depend upon the availability of the various fatty acids to shift intracellular cholesterol between a regulatory and storage pool of cholesterol, and this effect is mediated by the enzyme acyl-CoA:cholesterol acyltransferase (ACAT). J. Nutr. 128: 444S–448S, 1998.
Plasmonic thermal transport in graphene nanodisk waveguides

The thermal radiation properties of guided surface plasmons in one-dimensional co-planar graphene nanodisk arrays are predicted using a semi-analytical electrostatic model. The plasmonic band structure contains nonlocalized dispersion bands that are well-described by the electrostatic model for disk diameters smaller than 200 nm. A nondimensional model is proposed that enables systematic analysis of the waveguiding properties based on scaling laws. The thermal transport is dominated by the lowest-order radial modes and can be controlled by tuning the disk size, the substrate optical properties, and graphene’s doping concentration and electron mobility. The maximum predicted thermal conductivity and thermal diffusivity are 4.5 W m−1 K−1 and 1.3 × 10−3 m2/s, orders of magnitude larger than predictions of thermal transport by guided surface plasmonor phonon-polaritons in other materials. The results suggest that graphene surface plasmons, which can be thermally-activated at room temperature, are a suitable platform for tunable and fast thermal transport, with potential application as photon-based thermotronic interconnects.