Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel prognostic gene set for colon adenocarcinoma relative to the tumor microenvironment, chemotherapy, and immune therapy

Background: Colon adenocarcinoma (COAD) is a common aggressive malignant tumor. Heterogeneity in tumorigenesis and therapy response leads to an unsatisfactory overall survival of colon adenocarcinoma patients. Our study aimed to identify tools for a better prediction of colon adenocarcinoma prognosis, bolstering the development of a better personalized treatment and management. Method: We used the least absolute shrinkage and selection operator (LASSO) Cox model to analyze the prognosis-related gene datasets from the Gene Expression Omnibus (GEO) database and verified them using The Cancer Genome Atlas (TCGA) database. The area under the curve (AUC) was calculated using the receiver operating characteristic (ROC) curve to evaluate the predictive ability of the risk score model. Gene Set Enrichment Analysis (GSEA) was used to identify the significantly enriched and depleted biological processes. The tumor immune dysfunction and exclusion (TIDE) algorithm was taken to explore the relationship between the risk score and immunotherapy. The observations collectively helped us construct a nomogram to predict prognosis. Finally, the correlation between drug sensitivity and prognostic gene sets was conducted based on the Cancer Therapeutics Response Portal (CTRP) analyses. Results: We constructed a scoring model to assess the significance of the prognosis risk-related gene signatures, which was relative to common tumor characteristics and tumor mutational burdens. Patients with a high-risk score had higher tumor stage and poor prognosis (p< 0.05). Moreover, the expressions of these genes were in correlation with changes in the tumor microenvironment (TME). The risk score is an independent prognostic factor for COAD (p< 0.05). The accuracy of the novel nomogram model with a risk score and TNM-stage prediction prognosis in the predicting prognosis was higher than that of the TNM stage. Further analysis showed that a high-risk score was associated with tumor immune rejection. Patients with a low-risk score have a better prognosis with chemotherapy than those with a high-risk score. Compared to patients in the high-risk group, patients in the low-risk group had a significant survival advantage after receiving chemotherapy. In addition, the prognostic gene sets aid the assessment of drug sensitivity. Conclusion: This study establishes a new prognostic model to better predict the clinical outcome and TME characteristics of colon adenocarcinoma. We believe, our model also serves as a useful clinical tool to strengthen the functioning of chemotherapy, immunotherapy, and targeted drugs.
Effects of electroacupuncture on bladder dysfunction and the expression of PACAP38 in a diabetic rat model

Objective: To explore the effects and the possible mechanism of electroacupuncture (EA) on diabetic bladder dysfunction (DBD) in streptozotocin-high fat diet (STZ-HFD) induced type 2 diabetes mellitus (T2DM) rats. Methods: The experiment was divided into Control, diabetic bladder dysfunction, electroacupuncture, and Sham electroacupuncture group. After 8 weeks of electroacupuncture intervention, the body mass, 24 h urine volume, intraperitoneal glucose tolerance test (IPGTT), and urodynamics were detected. After the wet weight of the bladder was detected, the hematoxylin-eosin (HE), Masson’s trichrome, and TUNEL were used to analyze histological changes. The PACAP38 expressions in the bladder were detected by Real-time PCR and Western blot. Results: Compared to the Control group, the bladder wet weight, 24 h urine volume, blood glucose, maximum bladder capacity, bladder compliance, bladder wall thickness, the smooth muscle/collagen ratio, and apoptosis rate of the diabetic bladder dysfunction group were significantly increased. Moreover, the body mass and leak point pressure were significantly reduced. Compared with the Sham electroacupuncture group, the bladder wet weight, maximum bladder capacity, bladder compliance, bladder wall thickness, and apoptosis rate of the electroacupuncture group were significantly reduced. In contrast, the leak point pressure was increased. The PACAP38 mRNA and PACAP38 protein expression of the diabetic bladder dysfunction group were significantly lower than the Control group, while electroacupuncture treatment could upregulate PACAP38 mRNA levels and PACAP38 protein expression of diabetic bladder dysfunction model rats. Conclusion: electroacupuncture could ameliorate bladder dysfunction in the diabetic bladder dysfunction model rats by reversing bladder remodeling, which might be mainly mediated by regulating the PACAP38 level.
Effect of different phosphate sources on uranium biomineralization by the Microbacterium sp. Be9 strain: A multidisciplinary approach study

Introduction Industrial activities related with the uranium industry are known to generate hazardous waste which must be managed adequately. Amongst the remediation activities available, eco-friendly strategies based on microbial activity have been investigated in depth in the last decades and biomineralization-based methods, mediated by microbial enzymes (e.g., phosphatase), have been proposed as a promising approach. However, the presence of different forms of phosphates in these environments plays a complicated role which must be thoroughly unraveled to optimize results when applying this remediation process. Methods In this study, we have looked at the effect of different phosphate sources on the uranium (U) biomineralization process mediated by Microbacterium sp. Be9, a bacterial strain previously isolated from U mill tailings. We applied a multidisciplinary approach (cell surface characterization, phosphatase activity, inorganic phosphate release, cell viability, microscopy, etc.). Results and Discussion It was clear that the U removal ability and related U interaction mechanisms by the strain depend on the type of phosphate substrate. In the absence of exogenous phosphate substrate, the cells interact with U through U phosphate biomineralization with a 98% removal of U within the first 48 h. However, the U solubilization process was the main U interaction mechanism of the cells in the presence of inorganic phosphate, demonstrating the phosphate solubilizing potential of the strain. These findings show the biotechnological use of this strain in the bioremediation of U as a function of phosphate substrate: U biomineralization (in a phosphate free system) and indirectly through the solubilization of orthophosphate from phosphate (P) containing waste products needed for U precipitation.
Discovery and significance of tempestites and storm deposits in the Qingshankou Formation of the Gulong Sag, northeastern China

The Qingshankou Formation in the Gulong Sag has attracted significant attention due to its rich shale oil reserves. However, several fundamental geological problems associated with shale from the Qingshankou Formation remain unresolved. The Qingshankou Formation in the Gulong Sag is a set of deep-lake and semi-deep-lake fine-grained deposits primarily composed of mudstone and shale. Recent studies have shown that tempestites and storm deposits commonly occur in the Qingshankou Formation. Fine liquefaction veins often occur at the bottom of the tempestite, indicating that storm-shaking liquefaction is expected in the swale structure. Meanwhile, the mudstone and shales primarily have a sand structure with fine grain size, indicating that the environment is exposed to an undercurrent activity, with a water flow velocity of 20–55 cm s−1. Unlike previous studies, we posit that the ancient water depth was only 20–30 m or shallower. These phenomena have significance for understanding the formation environment and diagenetic process of shale in the first member of the Qingshankou Formation, which provides a reference for oil and gas exploration and development.
The problematic syndrome of right temporal lobe atrophy: Unweaving the phenotypic rainbow

COPYRIGHT © 2023 Belder, Chokesuwattanaskul, Marshall, Hardy, Rohrer and Warren. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. The problematic syndrome of right temporal lobe atrophy: Unweaving the phenotypic rainbow
Identification of rare missense mutations in the glutamate ionotropic receptor AMPA type subunit genes in schizophrenia

Objective The alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors significantly regulate the synaptic transmission and functions of various synaptic receptors. This study aimed to identify single nucleotide mutations in the glutamate receptor, ionotropic, AMPA type (GRIA) gene family, which is associated with schizophrenia. Methods The exon regions of four genes (GRIA1, GRIA2, GRIA3, and GRIA4) encoding glutamate ionotropic receptor AMPA type proteins were resequenced in 516 patients with schizophrenia. We analyzed the protein function of the identified rare mutants via immunoblotting. Results A total of 24 coding variants were detected in the GRIA gene family, including six missense mutations, 17 synonymous mutations, and one frameshift insertion. Notably, three ultra-rare missense mutations (GRIA1p.V182A, GRIA2p.P123Q, and GRIA4p.Y491H) were not documented in the single nucleotide polymorphism database, gnomAD genomes, and 1517 healthy controls available from Taiwan BioBank. Immunoblotting revealed GRIA4p.Y491H mutant with altered protein expressions in cultured cells compared with the wild type. Conclusion Our findings suggest that, in some patients affected by schizophrenia, the GRIA gene family harbors rare functional mutations, which support rare coding variants that could contribute to the genetic architecture of this illness. The in-vitro impacts of these rare pathological mutations on the pathophysiology of schizophrenia are worthy of future investigation.
Investigation of the forkhead box protein P2 gene by the next-generation sequence analysis method in children diagnosed with specific learning disorder

Objective It was aimed to investigate the role of the forkhead box protein P2 (FOXP2) gene in the cause of specific learning disorder (SLD) with the next-generation sequencing method. Material and methods The study included 52 children diagnosed with SLD and 46 children as control between the ages of 6–12 years. Interview Schedule for Affective Disorders and Schizophrenia for School-Age Children, Present and Lifelong Version in Turkish, Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV)-Based Screening and Evaluation Scale for Attention Deficit and Disruptive Behavior Disorders, Specific Learning Disability Test Battery were applied to all participants. The FOXP2 gene was screened by the next-generation sequencing (NGS) method in all participants. Results A total of 17 variations were detected in the FOXP2 gene in participants. The number and diversity of variations were higher in the patient group. In the patient group, c.1914 + 8A>T heterozygous variation and three different types of heterozygous variation (13insT, 13delT and 4dup) in the c.1770 region were detected. It was found that the detected variations showed significant relationships with the reading phenotypes determined by the test battery. Conclusion It was found that FOXP2 variations were seen more frequently in the patient group. Some of the detected variations might be related to the clinical phenotype of SLD and variations found in previous studies from different countries were not seen in Turkish population. Our study is the first to evaluate the role of FOXP2 gene variations in children with SLD in Turkish population, and novel variations in the related gene were detected.
A quantitative measure of structure in the three-dimensional galaxy distribution : sheets and filaments

We introduce a set of structure functions, constructed to quantify the relative prevalence of filamentary, sheetlike and clumplike structures in a three-dimensional particle distribution. The functions are weighted averages of appropriately chosen combinations of the principal moments of inertia of the distribution within randomly placed spherical windows. To illustrate their response, the structure functions are applied to numerous idealized point distributions
Existence and Bifurcation Theorems for the Ginzburg‐Landau Equations

The second‐order transition of a superconducting material from normal to superconducting state according to the Ginzburg‐Landau theory is rigorously discussed. The bifurcation of a superconducting state is proved for both the Abrikosov mixed state and the case of a film in a parallel magnetic field when the flux or external field is slightly less than critical. The existence of a mixed state for all values of flux below the critical value is also proved.
Alfvén QPOs in Magnetars

We investigate torsional Alfven oscillations of relativistic stars with a global dipole magnetic field, via 2D numerical simulations. We find that a) there exist two families of quasi-periodic oscillations (QPOs) with harmonics at integer multiples of the fundamental frequency, b) the lower-frequency QPO is related to the region of closed field lines, near the equator, while the higher-frequency QPO is generated near the magnetic axis, c) the QPOs are long-lived, d) for the chosen form of dipolar magnetic field, the frequency ratio of the lower to upper fundamental QPOs is about 0.6, independent of the equilibrium model or of the strength of the magnetic field, and e) within a representative sample of EOSs and of various magnetar masses, the Alfven QPO frequencies are given by accurate empirical relations that depend only on the compactness of the star and on the magnetic field strength. Compared to the observational frequencies, we also obtain an upper limit on the strength of magnetic field of SGR 1806-20 (if it is dominated by a dipolar component) between ~ 3 and 7×1015 Gauss.
Classification of Four‐Dimensional Riemannian Spaces

A classification of four‐dimensional Riemann spaces with signature +2 is given. The classification depends upon the differential as well as the algebraic properties of the Riemann tensor. The tool employed is the infinitesimal‐holonomy group of the space. An introduction to the concept of the holonomy group is given, and the technique of classification is outlined. A comparison with the classification of empty spaces given by A. Z. Petrov and with the recent work of E. Newman is also given.
Multivariate Extensions of Univariate Life Distributions

A general approach for the development of multivariate survival models, based on a set of given marginal survivals, is presented. Preservation of IFR and IFRA properties and the nature of dependence among the variables are examined, and a recursive relation is suggested to obtain the resultant density function. In particular, an absolutely continuous Weibull distribution is derived and a few of its properties are studied.
X-ray diffraction when the real part of the scattering factor is zero

A formulation of dynamical X-ray diffraction is given for use when studying X-ray diffraction intensities when the real part of the scattering factor is zero. Based on these formulae, the diffraction induced by the imaginary part of the scattering factor alone is studied for both the Bragg and Laue cases.
Calorimetric measurement of absorption loss in orientation-patterned GaP and GaAs

Materials grown by vapor phase techniques such as chemical vapor deposition or hydride vapor phase epitaxy (HVPE) often exhibit very low losses which are difficult to quantify by simple transmission measurements. The measurement of extremely low absorption coefficients can be carried out by laser calorimetric or thermal rise techniques, which determine the absorption coefficients by measuring the temperature increase caused by the absorbed laser radiation. We report here on results of measuring absorption coefficients of bulk HVPE-grown orientation-patterned GaAs (OP-GaAs) and GaP (OP-GaP) crystals using one of the methods of laser calorimetry, called transient calorimetry. In our setup, the sample under test is attached to a high-conductivity copper holder and placed in a vacuum chamber. A 2-micron cw laser beam is transmitted through the sample and the temperature rise in the sample is measured and, through the calorimeter calibration process, related to the power absorbed in the sample. The absorbed power, Pa, is a function of the total attenuation coefficient αtot , the length of the sample, and the laser power Po, defined as Pa = Po exp (-αtot l), where total attenuation αtot is the sum of absorption and scattering: αtot = αabs + αscat. Since scattered light does not cause heating, the calorimetric technique is only applicable to determining αabs. By this technique we have measured 2-micron absorption coefficients in OP-GaAs and OP-GaP as low as 0.007 cm-1.
Thunderstorm Electrification Analysis: The Dependence on the Temperature-LWC Diagram.

Abstract The dependence on liquid water content (LWC) and temperature (T) of the charge transfer, and in particular its sign, during ice crystal–graupel collisions is a matter of controversy. Some of the laboratory measurements do not agree on the general shape of this function, although they agree on the existence of a critical temperature Tr, above which there is one sign and below which the opposite one. In this paper, the authors carry out a numerical study to investigate the behavior of three charging parameterizations in thunderstorm electrification. This study is carried out on one cloud case study, and a limited set of T–LWC values are present. Surprisingly, the general behavior is the same among the three, despite the distinct differences in the charging diagrams.
Extremely Metal-poor Stars. IV. The Carbon-rich Objects

Abundances are presented for some 20 elements in three extremely metal-poor, carbon-rich stars. All have [Fe/H] < -2.5. Based on their high proper motions and spectroscopic gravities two of them have relatively low luminosity: LP 706-7 is on or near the main sequence, while LP 625-44 is a subgiant. The third is the giant CS 22892-052, discovered to be r-processes enriched by Sneden et al. (1994). All three stars have large C and N overabundances, and large enhancements of the heavy neutron-capture elements— ~ 1-2 dex. In contrast to the r-process signature observed in CS 22892-052, however, both LP 625-44 and LP 706-7 are clearly s-process enriched, suggesting that they may be progenitors of the well-known halo CH giants, the peculiarities of which are believed to result from mass transfer across a binary system containing an asymptotic giant branch star. In both LP 625-44 and LP 706-7 the distribution of s-process elements is heavily weighted toward higher atomic number. [hs/ls] ~ 1.5, considerably larger than the values ≲0.5 found in the s-process enhanced near-main-sequence stars of the disk populations. This implies a much higher neutron exposure per seed nucleus in the Population II objects and identifies 13C(α, n)16O as the neutron source. For LP 625-44 radial velocity and Li abundance data are consistent with the binary hypothesis. LP 706-7, however, remains something of an enigma in these respects: it shows no clear evidence for velocity variations, and its Li abundance lies precisely on the Spite Plateau. We estimate that the probability of this occurring in the Ba/CH class of objects is, roughly, ≲1%. In metal-poor stars the incidence of carbon enrichment appears to increase toward the lowest metallicities, and below [Fe/H] = -2.5 supersolar values of [C/Fe] are not uncommon. Comparison of the available observational material with the Galactic chemical enrichment model of Timmes et al. (1995) shows that the model produces too little carbon. While the difference may result in the sensitivity of carbon production to modeling uncertainties such as the treatment of convection, we also discuss the possible role of a class of carbon producing zero heavy element supernovae and of massive “hypernovae” discussed by Woosley & Weaver (1982, 1995) in explaining this result. The carbon problem is also implicit in the suggestion that the r-process signature seen in CS 22892-052 results from normal supernovae enrichment—where then does its large carbon overabundance originate? The models one might invoke to produce carbon overabundances leave black hole remnants in which the layers containing the seed nuclei for the r-process are not available for ejection.
Microdynamics of Plastic Flow at Constant Stress

Arguments are presented which conclude that the mean density of mobile dislocations in a crystalline solid increases linearly with plastic strain for small strains and decays exponentially for large strains, all at constant stress and low temperatures. The resulting analytic expression combined with the strain‐rate equation can be integrated explicitly in terms of tabulated exponential integral functions. This creep equation has a general form that is consistent with many experiments and detailed comparison with a particularly well‐documented experimental curve yields quantitative agreement. The large strain limit of the proposed creep equation is the familiar logarithmic creep law. A simple transformation of the creep equation yields the shape of a slowly propagating plastic front, and it is shown that the predicted shape corresponds to experimental observations for mild steel. The lengths of the incubation periods that precede fast flow, as predicted by the equation, have a stress dependence that agrees.
1986 AECL-UO Critical Heat Flux Lookup Table

This paper describes the derivation of a critical heat flux (CHF) lookup table, which may be used for predicting CHF for water over a very wide range of conditions. The CHF table is based on the Chalk River Nuclear Laboratories' CHF data bank, which contains more than 15.000 CHF data points for water. A comparison of the prediction accuracy of the CHF lookup table and selected CHF correlations is presented. The table method is not designed to replace ad hoc CHF correlations derived for a given geometry over a narrow range of flow conditions; rather it is designed to provide a reasonable estimate of CHF over a very wide range of flow conditions and geometries, especially over the ranges where CHF data are scarce. It may also be used to predict CHF for nonaqueous fluids by fluid-to-fluid modeling techniques