Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis

Background Colorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying hub genes associated with the progression of CRC. Method The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data sets GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened. Results After validation using the TCGA-COAD dataset, a total of 10 hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in CRC tissues were higher than normal tissues (p-value < 0.05). The expressions of MT1X, MT2A, IL10RA and KIT in CRC tissues were lower than normal tissues (p-value < 0.05). Conclusions By combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC.
Variability and trend analysis of rainfall data of Jhalawar district of Rajasthan, India

An attempt has been made to study the variability and trends of annual and seasonal rainfall for the period of 38 years (1973-2010) for all seven tehsils of Jhalawar district of Rajasthan. The mean annual rainfall of the district was found to 910 mm with standard deviation 218 mm and coefficient of variation 24 per cent. Annual rainfall varied from about 831 mm in Khanpur to more than 1022 mm in the Pirawa tehsil of the district. The annual rainfall showed declined trend (-0.23 to -17.41 mm/year) in all seven tehsils of the district. The negative trends at Pirawa (17.407 mm/year), Manoharthana (11.595 mm/year) and Aklera (5.789 mm/year) are statistically significant at less than 0.001, 0.05 and 0.05 levels, respectively. During the study period maximum dry period was recorded during postmonsoon and winter. Also, for the entire 38 years period maximum dry months were recorded during December till April. August was normal month for about 87 per cent followed by July and June for about 84 per cent and 66 per cent respectively. It was evident that the onset of south-west (SW) monsoon took place in the month of June and chancesof drought occurrence during kharif season were very low. Hence, SW monsoon rainfall is found ideal for raising kharif crops like soybeans, urd, moong, jowar, maize, tomato, brinjal, chilli, okra, kharif onion, amaranth, rainfed green gram, red gram, castor, etc in the district.
The complete chloroplast genome sequence of traditional medical herb, Plantago depressa Willd. (Plantaginaceae)

Abstract Plantago depressa Willd. (Plantaginaceae) belonging to the section Mesembrynia and subgenus Plantago has been used as a traditional medicine. Here, we presented the complete chloroplast genome of P. depressa which is 164,617 bp long and has four subregions: 82,933 bp of large single copy (LSC) and 4,908 bp of small single copy (SSC) regions are separated by 38,388 bp of inverted repeat (IR) regions including 139 genes (93 protein-coding genes, eight rRNAs, and 38 tRNAs). The overall GC contents of the chloroplast genome were 38.0% and in the LSC, SSC, and IR regions were 36.6%, 30.6%, and 39.9%, respectively. Phylogenetic tree constructed with concatenated 79 protein-coding genes sequences of the chloroplast genomes in Plantaginaceae from APG group presents the phylogenetic position of P. depressa.
Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility

Plant root-associated microbes promote plant growth and induce systemic resistance (ISR) to foliar pathogens. In an attempt to find novel growth-promoting and ISR-inducing strains, we previously identified strains of root-associated Pseudomonas spp. that promote plant growth but unexpectedly induced systemic susceptibility (ISS) rather than ISR to foliar pathogens. Here we demonstrate that the ISS-inducing phenotype is common among root-associated Pseudomonas spp. Using comparative genomics, we identified a single P. fluorescens locus that is unique to ISS strains. We generated a clean deletion of the 11-gene ISS locus and found that it is necessary for the ISS phenotype. Although the functions of the predicted genes in the locus are not apparent based on similarity to genes of known function, the ISS locus is present in diverse bacteria and a subset of the genes have previously been implicated in pathogenesis in animals. Collectively these data show that a single bacterial locus contributes to modulation of systemic plant immunity. Importance Microbiome-associated bacteria can have diverse effects on health of their hosts, yet the genetic and molecular basis of these effects have largely remained elusive. This work demonstrates that a novel bacterial locus can modulate systemic plant immunity. Additionally, this work demonstrates that growth promoting strains may have unanticipated consequences on plant immunity and this is critical to consider when engineering the plant microbiome for agronomic improvement.
Identification of Ovarian Cancer Gene Expression Patterns Associated with Disease Progression and Mortality

Ovarian cancer (OC) is a common cause of death from cancer among women worldwide, so there is a pressing need to identify factors influencing mortality. Much OC patient clinical data is now publically accessible (including patient age, cancer site stage and subtype), as are large datasets of OC gene transcription profiles. These have enabled studies correlating OC patient survival with clinical variables and with gene expression but it is not well understood how these two aspects interact to influence mortality. To study this we integrated clinical and tissue transcriptome data from the same patients available from the Broad Institute Cancer Genome Atlas (TCGA) portal. We investigated OC mRNA expression levels (relative to normal patient tissue) of 26 genes already strongly implicated in OC, assessed how their expression in OC tissue predicts patient survival then employed Cox Proportional Hazard regression models to analyse both clinical factors and transcriptomic information to determine relative risk of death associated with each factor. Multivariate analysis of combined data (clinical and gene mRNA expression) found age, ovary tumour site and cancer stage IB significantly correlated with patient survival. Univariate analysis also confirmed significant differences in patient survival time when altered transcription levels of KLK6, CD36, MEF2C and SCGB2A1 were evident, while multivariate analysis that considered the 26 genes simultaneously revealed a significant relationship of mortality with KLK6, CD36 and E2F1 genes. However, analysis that considered all 26 genes with clinical variables together identified WFDC2, E2F1, BRCA1, KLK6, SCGB2A1 and SLPI genes as independently related to mortality in OC. This indicated that the latter genes affect OC patient survival, i.e., provided mechanistic and predictive information in addition to that of the clinical traits and provide strong evidence that these genes are critical markers of processes that underlie OC progression and mortality.
Evolutionarily stable strategy analysis of Quantitative investment strategy

Based on Chinese Stock Index Future, this study focuses on two types of market price changes, trends and shake. How investors’ strategies evolve to influence the market from trend to shake or from shake to trend to obtain the “evolutionary stable strategy” (ESS) of the market is conducted. The results show that trend strategies are more favourable in most market environments, and find a single strategy cannot survive in the market, and trading frequency should be appropriately reduced to reduce transaction costs, so as to survive in the market for a long time.
Do prairie voles (Microtus ochrogaster) change their activity and space use in response to domestic cat (Felis catus) excreta?

Abstract Behavioral changes that reduce the risk of predation in response to predator-derived odor cues are widespread among mammalian taxa and have received a great deal of attention. Although voles of the genus Microtus are staples in the diet of many mammalian predators, including domestic cats (Felis catus), there are no previous studies on vole space utilization and activity levels in response to odor cues from domestic cats. Therefore, the objective of our study was to investigate responses of adult prairie voles (Microtus ochrogaster) living in semi-natural habitats to odor cues from domestic cat excreta. Contrary to expectations, neither adult males or females showed significant changes in space use or willingness to enter traps in response to cat odors. One hypothesis to explain our results are that prairie voles have not co-evolved with domestic cats long enough to respond to their odors. Other possible explanations include whether levels of odors in the environment were sufficient to trigger a response or that the perceived risk of predation from odor cues alone did not outweigh relative costs of changing space use and activity levels. Future studies should consider multiple factors when determining what cues are sufficient to elicit antipredatory behavior.
Obtainment, selection and characterization of a mutant strain of Kluyveromyces marxianus that displays improved production of 2‐phenylethanol and enhanced DAHP synthase activity

Yeasts produce 2‐phenylethanol (2‐PE) from sugars via de novo synthesis; however, its synthesis is limited due to feedback inhibition on the isofunctional 3‐deoxy‐d‐arabino‐heptulosonate‐7‐phosphate (DAHP) synthases (Aro3p and Aro4p). This work aimed to select Kluyveromyces marxianus mutant strains with improved capacity to produce 2‐PE from sugars.
Elevated CO2 and Water Stress in Combination in Plants: Vanguards for Adaptation to Changing Climate

The changing dynamics in climate is the primary and important determinant of agriculture productivity. The effects of this changing climate on overall productivity in agriculture can be understood when we study the effects of individual components contributing to the changing climate on plants and crops. Elevated CO2 and drought due to low variability in rainfall is one of the important manifestations of the changing climate. There is considerable amount literature that addresses these aspects in terms of effects on plants systems from molecules to ecosystems. Of particular interest is the effect of increased CO2 on plants in relation to drought and water stress. As it is known that one of the consistent effects of increased CO2 in the atmosphere is increased photosynthesis, especially in C3 plants, it will be interesting to know the effect of drought in relation to elevated CO2. The possible mechanisms by which this occurs will be discussed in this minireview. Interpreting the effects of short term and long term exposure of plants to elevated CO2 in context of ameliorating the negative impacts of drought will show us the possible ways by which there can be effective adaption to crops in the changing climate scenario.
The Predictive Skills of Elastic Coulomb Rate-and-State Aftershock Forecasts during the 2019 Ridgecrest, California, Earthquake Sequence

Operational earthquake forecasting protocols commonly use statistical models for their recognized ease of implementation and robustness in describing the short-term spatiotemporal patterns of triggered seismicity. However, recent advances on physics-based aftershock forecasting reveal comparable performance to the standard statistical counterparts with significantly improved predictive skills when fault and stress-field heterogeneities are considered. Here, we perform a pseudoprospective forecasting experiment during the first month of the 2019 Ridgecrest (California) earthquake sequence. We develop seven Coulomb rate-and-state models that couple static stress-change estimates with continuum mechanics expressed by the rate-and-state friction laws. Our model parameterization supports a gradually increasing complexity; we start from a preliminary model implementation with simplified slip distributions and spatially homogeneous receiver faults to reach an enhanced one featuring optimized fault constitutive parameters, finite-fault slip models, secondary triggering effects, and spatially heterogenous planes informed by pre-existing ruptures. The data-rich environment of southern California allows us to test whether incorporating data collected in near-real time during an unfolding earthquake sequence boosts our predictive power. We assess the absolute and relative performance of the forecasts by means of statistical tests used within the Collaboratory for the Study of Earthquake Predictability and compare their skills against a standard benchmark epidemic-type aftershock sequence (ETAS) model for the short (24 hr after the two Ridgecrest mainshocks) and intermediate terms (one month). Stress-based forecasts expect heightened rates along the whole near-fault region and increased expected seismicity rates in central Garlock fault. Our comparative model evaluation not only supports that faulting heterogeneities coupled with secondary triggering effects are the most critical success components behind physics-based forecasts, but also underlines the importance of model updates incorporating near-real-time available aftershock data reaching better performance than standard ETAS. We explore the physical basis behind our results by investigating the localized shut down of pre-existing normal faults in the Ridgecrest near-source area.
Solving High-Resolution Forward Problems for Extra- and Intracranial Neurophysiological Recordings Using Boundary Element Fast Multipole Method

We present a general numerical approach for solving the forward problem in high-resolution. This approach can be employed in the analysis of noninvasive electroencephalography (EEG) and magnetoencephalography (MEG) as well as invasive electrocorticography (ECoG), stereoencephalography (sEEG), and local field potential (LFP) recordings. The underlying algorithm is our recently developed boundary element fast multipole method (BEM-FMM) that simulates anatomically realistic head models with unprecedented numerical accuracy and speed. This is achieved by utilizing the adjoint double layer formulation and zeroth-order basis functions in conjunction with the FMM acceleration. We present the mathematical formalism in detail and validate the method by applying it to the canonical multilayer sphere problem. The numerical error of BEM-FMM is 2-10 times lower while the computational speed is 1.5–20 times faster than those of the standard first-order FEM. We present four practical case studies: (i) evaluation of the effect of a detailed head model on the accuracy of EEG/MEG forward solution; (ii) demonstration of the ability to accurately calculate the electric potential and the magnetic field in the immediate vicinity of the sources and conductivity boundaries; (iii) computation of the field of a spatially extended cortical equivalent dipole layer; and (iv) taking into account the effect a fontanel for infant EEG source modeling and comparison of the results with a commercially available FEM. In all cases, BEM-FMM provided versatile, fast, and accurate high-resolution modeling of the electromagnetic field and has the potential of becoming a standard tool for modeling both extracranial and intracranial electrophysiological signals.
Neogene Tree Trunk Fossils from the Meshgin Shahr Area, Northwest Iran

In 2016, an extensive fossil forest was discovered near Meshgin Shahr, northwest Iran. Silicified tree trunks occur in Miocene fluvial sediments and at multiple stratigraphic levels within a 27-m thick sequence of Pleistocene volcaniclastics. The Miocene trunks likely represent stream transport. Pleistocene examples originated during repeated eruptive events when volcaniclastic sediments buried a standing forest. The site, informally named Meshgin Shahr Fossil Forest, was registered in 2017 as a national natural monument by the Iranian Cultural, Handicraft and Tourism Organization. To date, 16 fossilized trunks have been found, all but one of them representing gymnosperms. The ancient coniferous forest was very different from modern forests in Iran and adjacent Azerbaijan, a result of climatic changes that were principally caused by the demise of the Paratethys Sea and by rain shadow effects caused by the uplift of the Alborz and Zagros mountain ranges. X-ray diffraction patterns reveal that woods from the fossil forest contain three types of silica: opal-CT, pure quartz, and a mixture of opal-CT and quartz. In addition, optical photomicrographs show the abundant presence of amorphous opal-A. Mineralogic variations occur among different fossil trees and within a single trunk. These silica polymorphs resulted from a combination of processes: silica minerals precipitated in multiple episodes under differing geochemical conditions and the diagenetic transformation of an opaline parent material.
Ultraviolet Photodetection Application in Magnesium Indium Oxide Thin Film Transistors via Co-Sputtering Deposition

A magnesium-doped indium oxide (In2O3:Mg) ultraviolet (UV) thin film phototransistor was fabricated via cosputtering of MgO and In2O3. Three samples with different sputtering power values of In2O3 ranging from 40 to 60 W, namely, sample A with 40 W, sample B with 50 W, and sample C with 60 W, were used in this study. Results confirmed that oxygen vacancy concentration evidently indicates indium content. The experimental results showed that responsivities of samples, defined as the ratio of photocurrent under illumination per input power, increase from 0.0086 to 2.6 A/W. Rejection ratios were 1.2 × 104, 4.3 × 105, and 4.8 × 105 for samples A, B, and C, respectively. Based on our results, sample C is the best among the three MgInO UV phototransistors investigated in this study.
Seismic Performance Assessment of an Existing RC Wall Building with Irregular Geometry: A Case-Study of a Hospital in Croatia

Buildings of strategic importance should be able to resist seismic forces in accordance with potential earthquakes that may occur at the location and remain fully operational afterwards. However, many of them were constructed before the modern principles of seismic design were known (especially regarding detailing and ductility), and therefore may be considered substandard. The first step in mitigating the seismic risk of such structures is to assess their seismic performance and, in particular, to identify their structural deficiencies. This study presents a comprehensive methodology for the seismic performance assessment of individual buildings, applied to an existing reinforced concrete (RC) hospital. This building is of an irregular layout, constructed as a structural wall system, and it is located in the seismically active region of Croatia. It includes the assessment of seismic hazards on the location, ambient noise measurements, experimental determination of structural modal parameters, creation of a detailed numerical model calibrated with experimental data, and a seismic performance assessment using various analysis methods. As a result, the building collapse mechanisms were determined and critical structural elements identified, which is the basis for future actions directed to the reduction of its risk (e.g., applications of specific measures for a target retrofit, proposal of evacuation routes and safe places inside the building, etc.).
‘I didn’t want to be a statistic’: Black males, urban schooling, and educational urgency

ABSTRACT Drawing upon resilience and educational urgency, this longitudinal study explores the narratives of 20 college-aged Black males as they make sense of their secondary school experiences at Marcus Garvey Academy (pseudonym), an all-boys public school in a large urban city in the U.S. In paying particular attention to some of the challenges they faced, findings indicate that a complex set of personal, family, peer, and school factors affect these students’ lives during their secondary school years. In their efforts to overcome these difficulties, students scripted resistance into their self-concept, identified ways that they benefitted from a supportive schooling environment, and translated some of their self-learning into educational urgency. These students’ experiences and meaning making serve as a critical counternarrative to how they are stereotyped and limited by deficit framing and lowered expectations and speak powerfully to ways to better theorize, understand, and appreciate Black males’ schooling experiences, resistance efforts, and aspirations.
Day length as a key factor moderating the response of coccolithophore growth to elevated pCO2

The fate of coccolithophores in the future oceans remains uncertain, in part due to key factors having not been standardized across experiments. A potentially moderating role for differences in day length (photoperiod) remains largely unexplored. We therefore cultured four different geographical isolates of the species Emiliania huxleyi, as well as two additional species, Gephyrocapsa oceanica (tropical) and Coccolithus braarudii (temperate), to test for interactive effects of pCO2 with the light : dark (L : D) cycle. We confirmed a general regulatory effect of photoperiod on the pCO2 response, whereby growth and particulate inorganic carbon and particulate organic carbon (PIC : POC) ratios were reduced with elevated pCO2 under 14 : 10 h L : D, but these reductions were dampened under continuous (24 h) light. The dynamics underpinning this pattern generally differed for the temperate vs. tropical isolates. Reductions in PIC : POC with elevated pCO2 for tropical taxa were largely through reduced calcification and enhanced photosynthesis under 14 : 10 h L : D, with differences dampened under continuous light. In contrast, reduced PIC : POC for temperate strains reflected increases of photosynthesis that outpaced increases in calcification rates under 14 : 10 h L : D, with both responses again dampened under continuous light. A multivariate analysis of 35 past studies of E. huxleyi further demonstrated that differences in photoperiod account for as much as 40% (strain B11/92) to 55% (strain NZEH) of the variance in reported pCO2‐induced reductions to growth but not PIC : POC. Our study thus highlights a critical role for day length in moderating the effect of ocean acidification on coccolithophore growth and consequently how this response may play out across latitudes and seasons in future oceans.