Miracle-dz/UniFAR-FTUs huggingface dataset:
A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor

Genome minimization is an effective way for industrial chassis development. In this study, Zymomonas mobilis ZMNP, a plasmid-free mutant strain of Z. mobilis ZM4 with four native plasmids deleted, was constructed using native type I-F CRISPR-Cas system. Cell growth of ZMNP under different temperatures and industrial effluent of xylose mother liquor were examined to investigate the impact of native plasmid removal. Despite ZMNP grew similarly as ZM4 under different temperatures, ZMNP had better xylose mother liquor utilization than ZM4. In addition, genomic, transcriptomic, and proteomic analyses were applied to unravel the molecular changes between ZM4 and ZMNP. Whole-genome resequencing result indicated that an S267P mutation in the C-terminal of OxyR, a peroxide-sensing transcriptional regulator, probably alters the transcription initiation of antioxidant genes for stress responses. Transcriptomic and proteomic studies illustrated that the reason that ZMNP utilized the toxic xylose mother liquor better than ZM4 was probably due to the upregulation of genes in ZMNP involving in stress responses as well as cysteine biosynthesis to accelerate the intracellular ROS detoxification and nucleic acid damage repair. This was further confirmed by lower ROS levels in ZMNP compared to ZM4 in different media supplemented with furfural or ethanol. The upregulation of stress response genes due to the OxyR mutation to accelerate ROS detoxification and DNA/RNA repair not only illustrates the underlying mechanism of the robustness of ZMNP in the toxic xylose mother liquor, but also provides an idea for the rational design of synthetic inhibitor-tolerant microorganisms for economic lignocellulosic biochemical production.
Myofibroblast stroma differentiation in infiltrative basal cell carcinoma is accompanied by regulatory T‐cells

The implications of infiltrative compared to non‐infiltrative growth of cutaneous basal cell carcinoma (BCC) on the tumor stroma and immune cell landscape are unknown. This is of clinical importance, because infiltrative BCCs, in contrast to other BCC subtypes, are more likely to relapse after surgery and radiotherapy.
Color, Rotation, Age, and Chromospheric Activity Correlations in Late-Type Main-Sequence Stars

A study of the rotation-activity-age relationships in a large sample of single late-type main-sequence stars is carried out, based on rotation period data from the literature, on our measurements of the Mg II k line chromospheric flux in IUE high-resolution spectra, and on Hipparcos parallaxes. The analysis of the rotation period data of open clusters and field stars indicates that the rotational period decreases linearly with increasing mass in stars of the same age and evolves as a power of age as t0.45. This information has enabled us to disentangle the role of age in the chromospheric activity-rotation relationship, as well as to analyze the behavior of the Mg II emission flux in terms of "activity evolutionary paths" and of "activity isochrones. " It is shown that the Mg II emission maintains a saturated level in very young stars until a certain age that depends on stellar mass, while at later stages it decays at a faster rate for more massive stars. We have also determined the convection turnover time from observational data and analyzed the relationship between the Mg II emission flux and the Rossby number. We reach the conclusion that there is no clear advantage in using the Rossby number instead of stellar age in describing the chromospheric Mg II losses, at least with the convective turnover time values currently in use.
Correlations of vorticity and material line elements with strain in decaying turbulence

Correlations of the vorticity and the passive material line element with strains in decaying turbulence are investigated. The mean principal rates of the strain and the growth rates of the vorticity and the material line element due to the nonlinear stretching are all found to be proportional to the square‐root‐mean enstrophy. The ratios of the principal rates are 4:1:−5. It is shown how these ratios help determining the values of free parameters in the phenomenological models of turbulence such as the Burgers vortex model proposed by Ashurst (private communication) and the Lundgren–Townsend vortex model by Pullin and Saffman [Phys. Fluids A 5, 126 (1993); 6, 3010 (1994)]. The mean growth rate of material line elements is slightly larger than the intermediate principal rate, but much less than the most positive one. Numerical results show that the material line element has nearly the same preferences in aligning with the principal directions of the strain corresponding to the mostly positive and the inter.
Deep-water gravity wave instabilities at large steepness

An extension of earlier computations on deep‐water gravity wave instabilities up to a wave steepness of 0.434 is performed to compare the relative strength of class I versus class II instabilities. The three‐dimensional class II, m=1 instabilities are still predominant. However, as the steepness increases, the difference between the growth rates of two‐dimensional and three‐dimensional perturbations decreases rapidly and becomes negligible around a 0.43 wave steepness.
Time-Dependent Density Functional Theory for Open Quantum Systems and Quantum Computation

First-principles electronic structure theory explains properties of atoms, molecules and solids from underlying physical principles without input from empirical parameters. Time-dependent density functional theory (TDDFT) has emerged as arguably the most widely used first-principles method for describing the time-dependent quantum mechanics of many-electron systems. In this thesis, we will show how the fundamental principles of TDDFT can be extended and applied in two novel directions: The theory of open quantum systems (OQS) and quantum computation (QC). In the first part of this thesis, we prove theorems that establish the foundations of TDDFT for open quantum systems (OQS-TDDFT). OQS-TDDFT allows for a firstprinciples description of non-equilibrium systems, in which the electronic degrees of freedom undergo relaxation and decoherence due to coupling with a thermal environment, such as a vibrational or photon bath. We then discuss properties of functionals in OQS-TDDFT and investigate how these differ from functionals in conventional TDDFT using an exactly solvable model system. Next, we formulate OQS-TDDFT in the linear-response regime, which gives access to environmentally broadened excitation spectra. Lastly, we present a hybrid approach in which TDDFT can be used
Single-Cell RNA-Sequencing Reveals Interactions between Endometrial Stromal Cells, Epithelial Cells, and Lymphocytes during Mouse Embryo Implantation

The decidualization of endometrial stromal cells (ESCs) is an essential process facilitating embryo implantation. However, the roles of non-decidualized and decidualized ESCs in regulating the microenvironment of a receptive endometrium remain unclear. We investigated single-cell transcriptomic changes in the uterus of a CD-1 mouse model at the post-implantation stage. The implantation and inter-implantation sites of the uteruses of pregnant mice at 4.5 and 5.5 days post-coitum were dissected for single-cell RNA sequencing. We identified eight cell types: epithelial cells, stromal cells, endothelial cells, mesothelial cells, lymphocytes, myocytes, myeloids, and pericytes. The ESC transcriptome suggests that the four ESC subtypes are involved in the extracellular remodeling during implantation. The trajectory plot of ESC subtypes indicates embryo implantation that involves a differentiation pathway from undifferentiated ESCs (ESC 1) to decidualized ESCs (DEC ESCs), with distinct signaling pathways between the ESC subtypes. Furthermore, the ligand-receptor analysis suggests that ESCs communicate with epithelial cells and immune cells through nectin and ICAM signaling. Collectively, both decidualized and non-decidualized ESCs may regulate the endometrial microenvironment for optimal endometrial receptivity and immune tolerance. This study provides insights on the molecular and cellular characteristics of mouse ESCs in modulating the epithelial and lymphocyte functions during early embryo implantation.
New nanosecond continuum for excited-state spectroscopy

A new nanosecond broad‐band continuum source is described. The continuum is generated by nonlinear optical processes in fiber waveguides pumped with a 20‐kW 10‐ns dye‐laser pulse of broad spectral width (∼150 A). The continuum has a bandwidth of several thousand cm−1 in the visible with a total power ∼1 kW. The new continuum is in many aspects superior to previously known continuum sources for nanosecond time‐resolved excited‐state spectroscopy.
Etiological, clinical, and laboratory evaluation of congenital hypothyroidism and determination of levothyroxine (LT4) dose at treatment interruption in differentiating permanent vs. transient patients

Background/aim Congenital hypothyroidism (CH) is the most common cause of preventable but irreversible mental retardation in children, although the risk has been widely abolished by national neonatal screening programs. The aim of this study was to determine, (a) the cause of CH, (b) the etiological cause of persistent CH and (c) to investigate the role of laboratory and clinical data in predicting persistent and transient CH. Materials and methods Patients diagnosed with CH, who started L-thyroxine treatment and were followed up for at least three years were included. Patient data were reviewed retrospectively. Serum thyroid hormones were measured four weeks after discontinuation of therapy at age three or earlier. Cases with a thyroid-stimulating hormone (TSH) value of >10 mIU/mL were accepted as permanent hypothyroidism, while cases with normal TSH values for six months after cessation were accepted as transient hypothyroidism. Results There were 232 treated cases, of whom 108 (46.6%) were female, and 169 (72.8%) were eventually diagnosed with transient CH. The best cut-off point for predicting permanent status was determined as LT4 cut-off dose ≥1.45 mcg/kg/day. The median (range) duration of L-thyroxine treatment in transient hypothyroid cases was 24 (range: 6–36) months, and treatment was discontinued before the age of three years in 64%. Conclusion It has been shown that the most common etiologic cause of CH is transient hypothyroidism. The thyroxine dose at the time of discontinuation of treatment and free thyroxine and TSH levels at the time of diagnosis are essential determinants in distinguishing permanent/transient CH.
Bearing capacity of two interfering strip footings from lower bound finite elements limit analysis

A rigorous lower bound solution, with the usage of the finite elements limit analysis, has been obtained for finding the ultimate bearing capacity of two interfering strip footings placed on a sandy medium. Smooth as well as rough footing–soil interfaces are considered in the analysis. The failure load for an interfering footing becomes always greater than that for a single isolated footing. The effect of the interference on the failure load (i) for rough footings becomes greater than that for smooth footings, (ii) increases with an increase in ϕ, and (iii) becomes almost negligible beyond S/B > 3. Compared with various theoretical and experimental results reported in literature, the present analysis generally provides the lowest magnitude of the collapse load. Copyright © 2011 John Wiley & Sons, Ltd.
Identification of an Immune-Related Gene Signature Associated with Prognosis and Tumor Microenvironment in Esophageal Cancer

Background Esophageal cancer (EC) is a common malignant tumor of the digestive system with high mortality and morbidity. Current evidence suggests that immune cells and molecules regulate the initiation and progression of EC. Accordingly, it is necessary to identify immune-related genes (IRGs) affecting the biological behaviors and microenvironmental characteristics of EC. Methods Bioinformatics methods, including differential expression analysis, Cox regression, and immune infiltration prediction, were conducted using R software to analyze the Gene Expression Omnibus (GEO) dataset. The Cancer Genome Atlas (TCGA) cohort was used to validate the prognostic signature. Patients were stratified into high- and low-risk groups for further analyses, including functional enrichment, immune infiltration, checkpoint relevance, clinicopathological characteristics, and therapeutic sensitivity analyses. Results A prognostic signature was established based on 21 IRGs (S100A7, S100A7A, LCN1, CR2, STAT4, GAST, ANGPTL5, TRAV39, F2RL2, PGLYRP3, KLRD1, TRIM36, PDGFA, SLPI, PCSK2, APLN, TICAM1, ITPR3, MAPK9, GATA4, and PLAU). Compared with high-risk patients, better overall survival rates and clinicopathological characteristics were found in low-risk patients. The areas under the curve of the two cohorts were 0.885 and 0.718, respectively. Higher proportions of resting CD4+ memory T lymphocytes, M2 macrophages, and resting dendritic cells and lower proportions of follicular helper T lymphocytes, plasma cells, and neutrophils were found in the high-risk tumors. Moreover, the high-risk group showed higher expression of CD44 and TNFSF4, lower expression of PDCD1 and CD40, and higher TIDE scores, suggesting they may respond poorly to immunotherapy. High-risk patients responded better to chemotherapeutic agents such as docetaxel, doxorubicin, and gemcitabine. Furthermore, IRGs associated with tumor progression, including PDGFA, ITPR3, SLPI, TICAM1, and GATA4, were identified. Conclusion Our immune-related signature yielded reliable value in evaluating the prognosis, microenvironmental characteristics, and therapeutic sensitivity of EC and may help with the precise treatment of this patient population.
The effect of interface properties on retaining wall behaviour

A series of finite element analyses have been undertaken to investigate the effects of interface properties on the behaviour of a vertical retaining wall and the deformation of the ground around it. The boundary between a rigid embedded wall and the soil is modelled with zero thickness interface elements. Uniform translation of the wall has been studied. The analyses show the predicted limiting active and passive pressure on the wall are dependent on the maximum wall friction angle and are in reasonable agreement with accepted approximate analytical solutions. The limiting pressure is independent of the stiffness and dilation properties of the interface elements. The dilation properties of the interface have a significant effect on the ground surface deformation around the wall. © 1998 John Wiley & Sons, Ltd.
Is Sanctification Real? Empirical Evidence for and against Christian Moral Transformation

According to a widely held view of the New Testament teaching on sanctification; the Holy Spirit brings about a significant moral transformation in the character of every true believer. This claim about Christian moral transformation (CMT) has empirical implications. Thus, its truth can be evaluated from a scientific perspective. Sociological and psychological data on the relationship of religion and morality suggests that (Christian) religion is negatively correlated with undesirable moral behavior such as alcohol and substance abuse, criminal behavior, domestic abuse, and nonmarital sex, and positively correlated with desirable behavior such as helping. While these correlations are consistent with CMT, they do not necessarily serve as good evidence for it, for they can be more naturally explained by situational factors than by character differences between religious and nonreligious people. Some scientific findings serve as evidence against CMT. Religious believers engage in dishonest behavior and porn viewing at least as much as others. There is also a positive correlation between prejudice and conservative Christian beliefs. These correlations cannot be explained by situational factors as easily as the link between religion and desirable moral behavior. Sociological and psychological research; therefore, provides at least a mild challenge for the truth of CMT.
High Virulence and Multidrug Resistance of Escherichia coli Isolated in Periodontal Disease

Periodontal disease is caused by different gram-negative anaerobic bacteria; however, Escherichia coli has also been isolated from periodontitis and its role in periodontitis is less known. This study aimed to determine the variability in virulence genotype, antibiotic resistance phenotype, biofilm formation, phylogroups, and serotypes in different emerging periodontal strains of Escherichia coli, isolated from patients with periodontal disease and healthy controls. E. coli, virulence genes, and phylogroups, were identified by PCR, antibiotic susceptibility by the Kirby-Bauer method, biofilm formation was quantified using polystyrene microtiter plates, and serotypes were determined by serotyping. Although E. coli was not detected in the controls (n = 70), it was isolated in 14.7% (100/678) of the patients. Most of the strains (n = 81/100) were multidrug-resistance. The most frequent adhesion genes among the strains were fimH and iha, toxin genes were usp and hlyA, iron-acquisition genes were fyuA and irp2, and protectin genes were ompT, and KpsMT. Phylogroup B2 and serotype O25:H4 were the most predominant among the strains. These findings suggest that E. coli may be involved in periodontal disease due to its high virulence, multidrug-resistance, and a wide distribution of phylogroups and serotypes.
Bubble dynamics in a viscoelastic medium with nonlinear elasticity

Abstract In a variety of recently developed medical procedures, bubbles are formed directly in soft tissue and may cause damage. While cavitation in Newtonian liquids has received significant attention, bubble dynamics in tissue, a viscoelastic medium, remains poorly understood. To model tissue, most previous studies have focused on Maxwell-based viscoelastic fluids. However, soft tissue generally possesses an original configuration to which it relaxes after deformation. Thus, a Kelvin–Voigt-based viscoelastic model is expected to be a more appropriate representation. Furthermore, large oscillations may occur, thus violating the infinitesimal strain assumption and requiring a nonlinear/finite-strain elasticity description. In this article, we develop a theoretical framework to simulate spherical bubble dynamics in a viscoelastic medium with nonlinear elasticity. Following modern continuum mechanics formalism, we derive the form of the elastic forces acting on a bubble for common strain-energy functions (e.g. neo-Hookean, Mooney–Rivlin) and incorporate them into Rayleigh–Plesset-like equations. The main effects of nonlinear elasticity are to reduce the violence of the collapse and rebound for large departures from the equilibrium radius, and increase the oscillation frequency. The present approach can readily be extended to other strain-energy functions and used to compute the stress/deformation fields in the surrounding medium.
Calculations of neutron flux spectra induced in the Earth's atmosphere by galactic cosmic rays

Calculations have been carried out to determine the neutron flux induced in the earth's atmosphere by galactic protons and alpha particles at solar minimum for a geomagnetic latitude of 42°N. Neutron flux spectra in the energy range ∼10−8 to ∼105 Mev at various depths in the atmosphere were calculated by using Monte Carlo and discrete ordinates methods, and various comparisons with experimental data are presented. The magnitude and shape of the calculated neutron leakage spectrum at the particular latitude considered support the theory that the cosmic ray albedo neutron decay (Crand) mechanism is the source of the protons trapped in the inner radiation belt.
Virial theory of direct langmuir collapse

A general virial theorem is proved without any assumption of special symmetries and used to calculate the threshold and time for direct collapse of a two-dimensional Langmuir wave packet. The analysis is shown to apply to ''bump-on-tail'' instabilities, when the ''bump'' is broad, low, and at high velocity. The example of the type-III solar radio-burst problem is treated both numerically and analytically.
The Natural Gas Cash-Out Problem: A Bilevel Optimal Control Approach

The aim of this paper is threefold: first, it formulates the natural gas cash-out problem as a bilevel optimal control problem (BOCP); second, it provides interesting theoretical results about Pontryagin-type optimality conditions for a general BOCP where the upper level boasts a Mayer-type cost function and pure state constraints, while the lower level is a finite-dimensional mixed-integer programming problem with exactly one binary variable; and third, it applies these theoretical results in order to find possible local minimizers of the natural gas cash-out problem.
Assumptions of twentieth-century neuroscience: reductionist and computational paradigms

The term neuroscience originated in the early 1960s, but the questions it asks date to antiquity. The nineteenth-century reticular view of the brain as a diffuse net-like synctium was negated by the neuron doctrine, but certain aspects (e.g. glial cells) are better described as a synctium. System views of the brain were popular in the first half of the twentieth century, but a reductionist focus has since dominated with the development of experimental tools that focus on components. This article will begin by considering twentieth-century views of both philosophers and scientists that highlight the tension between integrating in a field while retaining the ability to think critically. This will be illustrated by considering two common assumptions in neuroscience: that reductionist approaches will explain the brain; and the technological metaphor that sees the brain as a computer.
Differentiation in poult plumage color of f1 progeny from crosses between white and black indigenous turkeys

Abstract A study assessed the poult plumage color of F1 progeny from artificially inseminated crossings between white and black indigenous turkeys. 72 hens (32 black, 40 white) and 10 toms were used (5 black and 5 white). The turkeys were grouped into four treatments based on the breeding plans: T1 (White toms × White hens), T2 (Black toms × Black hens), T3 (White toms × black hens), and T4 (Black toms × White hens). Semen was harvested from five white toms, pooled, and inseminated into hens in T1 and T3. Semen harvested from five black toms were also pooled and inseminated into hens in T2 and T4. All inseminations were carried out immediately after collection, and each hen received a dose of 0.02 mL. Insemination was done for 2 consecutive days in week 1 and once weekly; eggs were collected and incubated weekly for 12 weeks. Poult plumage colors were monitored and recorded weekly after the first 28 d. Average fertility in each of the treatments 1 (99.63%), 2 (99.81%), 3 (99.84%), and 4 (99.27%) were not significantly (P > 0.05) different among the treatments. Hatchability was highest in T2 (72.54%) and least in T1 (57.67%). Percentage white plumage poults in treatments 1, 2, 3, and 4 were 88.73%, 31.61%, 58.15%, and 54.63%, respectively. Percentage black plumage poults in T1, T2, T3, and T4 were 6.97%, 33.04%, 15.26%, and 23.76%, respectively, while 4.30%, 35.35%, 26.57%, and 21.61% were percentage checkered plumage poults in T1, T2, T3, and T4, respectively. There was no significant (P > 0.05) difference in the percentage checkered obtained in T2, T3, and T4; percentage of white poult in T3 and T4; percentage of black poult in T3 and T1. The major determinant of poult plumage color concerning quantity was the plumage color of breeder tom semen used for insemination.