Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.)

A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
Sensory biases in response to novel complex acoustic signals in male and female grey treefrogs, Hyla chrysoscelis

The sensory bias hypothesis proposes that female preferences for male sexual signalling traits evolved in contexts other than mating. Individuals of both sexes may experience similar selection pressures in these contexts; thus males may have similar biases to females for variation in signal traits. We tested this prediction in the grey treefrog, Hyla chrysoscelis, in which males produce simple advertisement calls, but females are more attracted to certain novel complex stimuli. We recorded males' responses to playbacks of both simple advertisement calls and complex calls consisting of the advertisement call with an acoustic appendage (filtered noise, or heterospecific call pulses) either leading or following the call. We tested females’ preferences for the same stimuli in phonotaxis tests. We found evidence for a sensory bias in both sexes: males gave more aggressive calls in response to complex stimuli and females sometimes preferred complex over simple calls. These biases were not universal and depended on both temporal order and appendage characteristics, but how these effects manifested differed between the sexes. Ultimately, our approach of studying biases of both sexes in response to novel mating signals will shed light on the origin of mating preferences, and the mechanisms by which sensory biases operate.
Environmental correlates of temporal variation in the prey species of Australian fur seals inferred from scat analysis

Marine ecosystems in southeastern Australia are responding rapidly to climate change. We monitored the diet of the Australian fur seal (Arctocephalus pusillus doriferus), a key marine predator, over 17 years (1998–2014) to examine temporal changes. Frequency of occurrence (FO) of prey was used as a proxy for ecosystem change. Hard part analysis identified 71 prey taxa, with eight dominant taxa in greater than 70% of samples and predominantly included benthic and small pelagic fish. FO changed over time, e.g. redbait (Emmelichthys nitidus) reduced after 2005 when jack mackerel (Trachurus declivis) increased, and pilchard (Sardinops sajax) increased after 2009. Using generalized additive models, correlations between FO and environmental variables were evident at both the local (e.g. wind, sea surface temperature (SST)) and regional (e.g. El Niño–Southern Oscillation Index (SOI), Southern Annular Mode (SAM)) scales, with redbait and pilchard showing the best model fits (greater than 75% deviance explained). Positive SAM was correlated to FO for both species, and wind and season were important for redbait, while SOI and SST were important for pilchard. Both large-scale and regional processes influenced prey taxa in variable ways. We predict that the diverse and adaptable diet of the Australian fur seal will be advantageous in a rapidly changing ecosystem.
A chemical study of the photodissociation region NGC 7023.

To investigate the effects of the UV radiation on the chemistry of nitrogenated molecules in molecular clouds, we have carried out an observational study of the photodissociation region (PDR) associated with the reflection nebula NGC 7023. We mapped a region of 3' × 3' over the PDR in millimeter transitions of 12 CO, 13 CO, C 18 O, HCO + , HCN, HNC and N 2 H + . Spectra of CS, CN and C 2 H and of the rarer isotopic species H 13 CO + , H 13 CN, and HN 13 C, were also obtained at selected positions. We find evidences of selective photodissociation in the estimated 13 CO/C 18 O ratio
TRACING THE EVOLUTION OF HIGH-REDSHIFT GALAXIES USING STELLAR ABUNDANCES

This paper presents the first results from a model for chemical evolution that can be applied to N-body cosmological simulations and quantitatively compared to measured stellar abundances from large astronomical surveys. This model convolves the chemical yield sets from a range of stellar nucleosynthesis calculations (including asymptotic giant branch stars, Type Ia and II supernovae, and stellar wind models) with a user-specified stellar initial mass function (IMF) and metallicity to calculate the time-dependent chemical evolution model for a “simple stellar population” (SSP) of uniform metallicity and formation time. These SSP models are combined with a semianalytic model for galaxy formation and evolution that uses merger trees from N-body cosmological simulations to track several α- and iron-peak elements for the stellar and multiphase interstellar medium components of several thousand galaxies in the early (z ≥ 6) universe. The simulated galaxy population is then quantitatively compared to two complementary data sets of abundances in the Milky Way stellar halo and is capable of reproducing many of the observed abundance trends. The observed abundance ratio distributions are best reproduced with a Chabrier IMF, a chemically enriched star formation efficiency of 0.2, and a redshift of reionization of 7. Many abundances are qualitatively well matched by our model, but our model consistently overpredicts the carbon-enhanced fraction of stars at low metallicities, likely owing to incomplete coverage of Population III stellar yields and supernova models and the lack of dust as a component of our model.
Experimental study of the shear strength criterion of rock structural plane based on three-dimensional surface description

Abstract The failure of rock mass is mainly due to the failure of the structural plane, which is an important factor to reduce the mechanical properties and stability of rock mass. The shear strength of rock mass is one of the parameters for the stability calculation of large-scale rock mass engineering. The shear strength of a rock structural plane is strongly influenced by surface morphology. Considerable research has been conducted regarding the correlation between two-dimensional structural plane morphology and shear strength. However, quantitative research on three-dimensional (3D) morphology is relatively limited. In this study, 3D printing technology was used to create molds. Using cement and sand as the main materials, additives such as early strength and water-reducing agents were added, and test samples of irregular surface topography were created. The 3D roughness was quantified by formula calculation. Using a ZScanner® 800 hand-held 3D laser scanner to perform scanning on the structural surface, the parameter curve was analysed by generating 3D coordinate information and a 3D image of the fracture surface, and the quantitative parameter M p 3 D {M}_{\text{p}}^{3\text{D}} describing the 3D morphology of the structural surface was constructed. The change rule of R p 3 D {R}_{\text{p}}^{3\text{D}} and joint roughness coefficient (JRC) were analysed under different scanning resolutions, Δ(r), the scanning precision was suggested, and the functional relationship between JRC and M p 3 D {M}_{\text{p}}^{3\text{D}} was established. Finally, a formula for shear strength parameters considering the 3D characteristics of a structural plane surface was established. The model validation results show that the experimental data were within the 95% confidence band of the model curve, the average error of the shear strength was 10.4%, the errors of friction angle and cohesion, C, were 3.4 and 9.4%, and the reliability was fine.
On the Origin of Questions in Process Mining Projects

In line with the growing popularity of process mining, several methodologies have been proposed to guide the conduct of process mining projects. Such methodologies reason that process mining projects start with a concrete question. However, in practice we observe projects with a diﬀerent starting point, often aimed at exploring the data. Existing methodologies provide limited aid in such situations, and as a result, we wonder: how are questions developed within process mining projects? In this paper, we present the results of an interview study that sheds light on question development in process mining. We provide insights from expert interviewees, resulting in six recommendations that enhance existing methodologies. In doing so, we present concrete examples of how process mining analyses can support question formulation and reﬁnement.
Bioinformatic-based identification of 3 immune-related genes for prognostic in breast invasive carcinoma

Breast invasive carcinoma (BRCA) is the leading cause of cancer deaths in female worldwide. Immune cell infiltration is considered to be crucial factor for the success or failure of BRCA therapy. As we all known, early diagnosis of breast cancer can greatly improve the survival rate of patients. Hence, to screen effective biomarkers for breast cancer immunotherapy might be extremely important. In this research, we identified an immune-related, three-gene biomarkers for prognosis of BRCA. We obtained altogether 192 differentially expressed genes (DEGs) from GEO datasets (GSE22820, GSE36295) and GEPIA database, followed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We screened 3 immune-related candidate biomarkers composing by CXCL2, CXCL9 and RBP7 that improves survival prediction outcome in BRCA. Kaplan–Meier analysis was conducted to analyze the patient survival based on 3 genes. In addition, we found that selected biomarkers were closely connected with infiltration levels of different tumor immune cells. Moreover, principal component analysis showed three biomarkers could effectively distinguish tumor samples from normal samples. In summary, these findings suggested that CXCL2, CXCL9 and RBP7 are viable prognostic and diagnostic biomarkers and provide new ideas for immunotherapy solutions of BRCA in the future.
Predicting treatment outcome using kinome activity profiling in HER2+ breast cancer biopsies

In this study, we measured the kinase activity profiles of 32 pre-treatment tumour biopsies of HER2-positive breast cancer patients. The aim of this study was to assess the prognostic potential of kinase activity levels to identify potential mechanisms of resistance and to predict treatment success of HER2-targeted therapy combined with chemotherapy. Indeed, our system-wide kinase activity analysis, based on targeted mass spectrometry measurement of kinase activation loops, allowed us to link kinase activity to treatment response. Overall, high kinase activity in the HER2-pathway was associated with good treatment outcome. Furthermore, we found eleven kinases differentially regulated between treatment outcome groups. Amongst those, well-known players in therapy resistance were found, such as p38a, ERK and FAK, as well as a potential new player in drug resistance, namely MARK. Lastly, we defined an optimal signature of four kinases in a multiple logistic regression diagnostic test for prediction of treatment outcome (AUC=0.926). This kinase signature showed high sensitivity and specificity, indicating its potential as predictive biomarker for treatment success of HER2-targeted therapy.
MRCK controls myosin II activation in the polarized cortex of mouse oocytes and promotes spindle rotation and male pronucleus centration

Asymmetric meiotic divisions in oocytes rely on spindle positioning in close vicinity to the cortex. In mouse oocytes arrested at metaphase II, eccentric spindle positioning is associated with a chromatin-induced remodeling of the overlying cortex, including the build-up of an actin cap surrounded by a ring of activated myosin II. While the role of the actin cap in promoting polar body formation was demonstrated, the role of ring myosin II, and its mechanism of activation, have remained elusive. Here, we show that ring myosin II activation requires Myotonic dystrophy kinase-Related Cdc42-binding Kinase (MRCK), downstream of polarized Cdc42. During anaphase-II, inhibition of MRCK resulted in spindle rotation defects and a decreased rate of polar body emission. Remarkably, some oocytes eventually achieved spindle rotation by disengaging one cluster of chromatids from the anaphase spindle. We show that the MRCK/myosin II pathway also regulates the flattening of the fertilization cone to initiate male pronucleus centration. These findings provide novel insights into mammalian oocyte polarization and the role of cortical myosin II in orchestrating asymmetric division.
Overlapping Neural Representations for Dynamic Visual Imagery and Stationary Storage in Spatial Working Memory

Representations in working memory need to be flexibly transformed to adapt to our dynamic environment and variable task demands. Recent work has demonstrated that activity in the alpha frequency band enables precise decoding of visual information during both perception and sustained storage in working memory. Extant work, however, has focused exclusively on the representation of static visual images. Here we used EEG recordings to examine whether alpha-band activity supports the dynamic transformation of representations in spatial working memory using an imagery task that required the active shifting of a stored position to a new position. In line with recent findings, a common format of alpha-band activity precisely tracked both the initial position stored in working memory as well as the transformed position, with the latter emerging approximately 800-1200 ms following an auditory cue to “rotate” to a new position. Moreover, the time course of this transformation of alpha activity predicted between-subject differences in manual reaction time to indicate the new position (Experiment 1), as well as within-subject variations in saccade latency in a speeded version of the task (Experiment 2). Finally, cross-training analyses revealed robust generalization of alpha-band reconstruction of working memory contents before and after mental transformation. These findings demonstrate that alpha activity tracks dynamic transformations of representations in spatial working memory, and that the format of this activity is preserved across the initial and transformed memory representations. These findings highlight a new approach for measuring voluntary shifts in online memory representations and show common representational formats during dynamic mental imagery and the maintenance of static representations in working memory.
Characterization of sub-tropical maize (Zea Mays L.) inbred lines for the variation in kernel row numbers (KRN)

Genetic dissection of high KRN trait and cob length has been undertaken by several researchers resulting in identification of loci controlling the traits. Further fine mapping of QTLs controlling KRN and cob length and TILLING strategies identified the underlying genes. All these studies are used temperate maize genotypes which are of limited use to researcher in sub-tropical region, and the sub-tropical maize production systems. Present investigation explores the availability of genetic regions responsible for KRN in sub-tropical maize germplasm. A total of 280 subtropical maize germplasm was analyzed for their KRN variation and selected 45 stable lines were subjected to molecular characterization using genes linked to KRN in maize. Diversity analysis was also performed to understand the possible association of character with the KRN gene in deciding its variation in the given population. It was revealed that four genes showed highest probability of influencing KRN traits in these tropical maize inbred lines. The remaining genes not establishing specific pattern of association with high and low KRN genotypes may need further study on its allelic variation.
Interaction between dark energy and dark matter: observational constraints from OHD, BAO, CMB and SNe Ia

In order to test if there is energy transfer between dark energy (DE) and dark matter (DM), we investigate cosmological constraints on two forms of nontrivial interaction between the DM sector and the sector responsible for the acceleration of the universe, in light of the newly revised observations including OHD, CMB, BAO and SNe Ia. More precisely, we find the same tendencies for both phenomenological forms of the interaction term Q = 3γHρ, i.e. the parameter γ to be a small number, |γ| ≈ 10-2. However, concerning the sign of the interaction parameter, we observe that γ > 0 when the interaction between dark sectors is proportional to the energy density of dust matter, whereas the negative coupling (γ < 0) is preferred by observations when the interaction term is proportional to DE density. We further discuss two possible explanations to this incompatibility and apply a quantitative criteria to judge the severity of the coincidence problem. Results suggest that the γmIDE model with a positive coupling may alleviate the coincidence problem, since its coincidence index C is smaller than that for the γdIDE model, the interacting quintessence and phantom models by four orders of magnitude.
Big Crunch-based omnidirectional light concentrators

Omnidirectional light concentration remains an unsolved problem despite such important practical applications as the design of efficient mobile photovoltaic cells. Recently developed optical black hole designs offer partial solutions to this problem. However, even these solutions are not truly omnidirectional since they do not exhibit a horizon, and at large enough incidence angles the light may be trapped into quasi-stationary orbits around such imperfect optical black holes. Here, we propose and realize experimentally another gravity-inspired design of a broadband omnidirectional light concentrator based on the cosmological Big Crunch solutions. By mimicking the Big Crunch spacetime via a corresponding effective optical metric, we make sure that every photon world line terminates in a single point.
Water exchange rates measure active transport and homeostasis in neural tissue

For its size, the brain is the most metabolically active organ in the body. Most of its energy demand is used to maintain stable homeostatic physiological conditions. Altered homeostasis and active states are hallmarks of many diseases and disorders. Yet there is currently no reliable method to assess homeostasis and absolute basal activity or activity-dependent changes non-invasively. We propose a novel, high temporal resolution low-field, high-gradient diffusion exchange NMR method capable of directly measuring cellular metabolic activity via the rate constant for water exchange across cell membranes. Using viable ex vivo neonatal mouse spinal cords, we measure a component of the water exchange rate which is active, i.e., coupled to metabolic activity. We show that this water exchange rate is sensitive primarily to tissue homeostasis and viability and provides distinct functional information in contrast to the Apparent Diffusion Coefficient (ADC), which is sensitive primarily to tissue microstructure but not activity. SIGNIFICANCE STATEMENT Despite what physiology text-books may report, water transport across membranes is not only a passive process. However, current understanding is limited because standard techniques can only measure net flux (the difference between water moving in and water moving out). Even so, water is constantly exchanging between the inside and outside of cells and organelles without net flux during homeostasis. We developed a Magnetic Resonance method able to “see” water molecules exchanging on shorter timescales than could be observed before. In neural tissue we find most water exchange is active, that is, linked to ATP-driven processes. This method may one day be translated to clinical MRI applications for measuring cellular function and activity in the human brain and body.
Dysregulation of Acid Ceramidase-mediated Sphingolipid Metabolism Contributes to Tumor Progression in Tuberous Sclerosis Complex

Tuberous Sclerosis Complex (TSC) is disorder of multi-system benign neoplasia in the brain, heart, kidneys and lungs. Lymphangioleiomyomatosis (LAM) is a progressive pulmonary disease affecting exclusively women. Both are caused by mutations in TSC1 and TSC2, resulting in mTORC1 hyperactivation. Single cell RNA sequencing of LAM lungs identified activation of genes in the sphingolipid pathway. Independent validation studies showed that acid ceramidase (ASAH1) and dihydroceramide desaturase (DEGS1), key enzyme for regulating sphingolipid and ceramide metabolism, were significantly increased in TSC2-null cells, and their expression and activity were rapamycin-insensitive. TSC2 negatively regulated the biosynthesis of tumorigenic sphingolipids. Suppression of ASAH1 by shRNA or the inhibitor ARN14976 (17a) markedly decreased the viability of TSC2-null cells. In vivo, 17a significantly decreased the growth of Tsc2-null cell derived mouse xenografts. When combined with rapamycin, 17a more strongly inhibited the progression of renal cystadenomas in Tsc2+/- mice than either agent alone, evaluated by pathology and MRI. Collectively, our studies identify a rapamycin-insensitive disorder of sphingolipid metabolism in TSC2-null cells and tumors and validate the novel hypothesis that TSC2 regulates sphingolipid production and action via ASAH1. Targeting aberrant sphingolipid metabolism pathways may have therapeutic value in TSC and LAM, and possibly in mTORC1-hyperactive neoplasms.