Miracle-dz/UniFAR-FTUs huggingface dataset:
Anisotropic ductile damage fully coupled with anisotropic plastic flow: Modeling, experimental validation, and application to metal forming simulation

The main goal of this paper is the modeling, numerical simulation, and experimental validation of the anisotropic ductile damage effects on initially anisotropic plastic flow with mixed (isotropic and kinematic) nonlinear hardening under large plastic strains for metal forming processes simulation. A symmetric second-rank damage tensor together with a symmetrized fourth-rank damage-effect tensor is used to describe the anisotropic ductile damage evolution and its effect on the large plastic flow with hardening. Following the concept of effective state variables in the framework of the total energy equivalence assumption, the “Murakami” fourth-rank damage-effect tensor is chosen to describe the anisotropic damage effect on the elastic-plastic behavior including the mixed hardening. The “Lemaitre” ductile anisotropic damage evolution relationships, where the principal directions of the damage rate tensor are governed by those of the plastic strain rate tensor, are used. As difference with the works cited above, the nonlinear mixed isotropic and kinematic hardening is taken into account considering the full and strong damage effects through the effective state variables deduced from the total energy equivalence assumption initially proposed by Saanouni et al. The non-associative plasticity theory is considered, and the “Hill 1948” quadratic (equivalent) stress norm is used to describe the large plastic anisotropic flow accounting for mixed isotropic and kinematic hardening with anisotropic damage effects. The formulation is performed assuming finite plastic strains and small elastic strains through the so-called rotated frame formulation. The obtained model was implemented into ABAQUS/Explicit® FE software thanks to the user’s developed subroutine VUMAT. The numerical aspects related to the time discretization of the fully coupled anisotropic constitutive equations are carefully described. Finally and for the validation purpose, the model is identified using an appropriate experimental data base concerning the grade 316L stainless steel to simulate numerically some metal forming processes.
Relative Entropy in Biological Systems

In this paper we review various information-theoretic characterizations of the approach to equilibrium in biological systems. The replicator equation, evolutionary game theory, Markov processes and chemical reaction networks all describe the dynamics of a population or probability distribution. Under suitable assumptions, the distribution will approach an equilibrium with the passage of time. Relative entropy - that is, the Kullback--Leibler divergence, or various generalizations of this - provides a quantitative measure of how far from equilibrium the system is. We explain various theorems that give conditions under which relative entropy is nonincreasing. In biochemical applications these results can be seen as versions of the Second Law of Thermodynamics, stating that free energy can never increase with the passage of time. In ecological applications, they make precise the notion that a population gains information from its environment as it approaches equilibrium.
Non-static Dimensional Reduction of QED_3 at Finite Temperature

We study an extreme non-static limit of 2+1-dimensional QED obtained by making a dimensional reduction so that all fields are spatially uniform but time dependent. This dimensional reduction leads to a 0+1-dimensional field theory that inherits many of the features of the 2+1-dimensional model, such as Chern-Simons terms, time-reversal violation, an analogue of parity violation, and global U(2) flavor symmetry. At one-loop level, interactions induce a Chern-Simons term at finite T with coefficient tanh(beta m_F/2), where m_F is the fermion mass. The finite temperature two loop self-energies are also computed, and are non-zero for all temperatures.
How to measure path length

Path length measuring is a relevant engineering problem. Leonardo Da Vinci designed for the military appropriate equipment, the podometer, to do so. Modern equipment such as step meters and map meters are quite similar to Da Vinci? s design, despite geometrical statistical - stereological - methods based on theorems of Cauchy and Buffon that were potentially available for a long period of time for doing a better job. The theorems have moreover been applied earlier for the engineering purposes indicated in this paper. Even Saltikov? s reintroduction for quantitative image analysis purposes in 1945 was ignored. Gradually, the last half of a century, stereological methods became more popular in concrete technology. Nevertheless, the stereology-based global averaging operation required to make the step from materials technology to engineering properties is inherent to making errors, as the literature demonstrates. The methodological framework has been described in earlier papers by this author as to path length measurements in sections of cracked concrete and on X-ray images of steel fibre reinforced concrete (SFRC). By laying side by side in this paper the direct engineering approach (from Da Vinci to map meter) and the science (stereology)-based approaches, the profit in economy and reliability can nevertheless be stressed. Particularly the element of geometric averaging based on simple mathematical-statistical notions is highlighted, because the literature reflects still major violations to these scientific principles. Three-dimensional information in the indicated fields of materials engineering is also readily obtained, provided proper sampling is guaranteed.
Mutations Enabling Displacement of Tryptophan by 4-Fluorotryptophan as a Canonical Amino Acid of the Genetic Code

The 20 canonical amino acids of the genetic code have been invariant over 3 billion years of biological evolution. Although various aminoacyl-tRNA synthetases can charge their cognate tRNAs with amino acid analogs, there has been no known displacement of any canonical amino acid from the code. Experimental departure from this universal protein alphabet comprising the canonical amino acids was first achieved in the mutants of the Bacillus subtilis QB928 strain, which after serial selection and mutagenesis led to the HR23 strain that could use 4-fluorotryptophan (4FTrp) but not canonical tryptophan (Trp) for propagation. To gain insight into this displacement of Trp from the genetic code by 4FTrp, genome sequencing was performed on LC33 (a precursor strain of HR23), HR23, and TR7 (a revertant of HR23 that regained the capacity to propagate on Trp). Compared with QB928, the negative regulator mtrB of Trp transport was found to be knocked out in LC33, HR23, and TR7, and sigma factor sigB was mutated in HR23 and TR7. Moreover, rpoBC encoding RNA polymerase subunits were mutated in three independent isolates of TR7 relative to HR23. Increased expression of sigB was also observed in HR23 and in TR7 growing under 4FTrp. These findings indicated that stabilization of the genetic code can be provided by just a small number of analog-sensitive proteins, forming an oligogenic barrier that safeguards the canonical amino acids throughout biological evolution.
Staging of Neurofibrillary Pathology in Alzheimer's Disease: A Study of the BrainNet Europe Consortium

It has been recognized that molecular classifications will form the basis for neuropathological diagnostic work in the future. Consequently, in order to reach a diagnosis of Alzheimer's disease (AD), the presence of hyperphosphorylated tau (HP‐tau) and β‐amyloid protein in brain tissue must be unequivocal. In addition, the stepwise progression of pathology needs to be assessed. This paper deals exclusively with the regional assessment of AD‐related HP‐tau pathology. The objective was to provide straightforward instructions to aid in the assessment of AD‐related immunohistochemically (IHC) detected HP‐tau pathology and to test the concordance of assessments made by 25 independent evaluators. The assessment of progression in 7‐µm‐thick sections was based on assessment of IHC labeled HP‐tau immunoreactive neuropil threads (NTs). Our results indicate that good agreement can be reached when the lesions are substantial, i.e., the lesions have reached isocortical structures (stage V–VI absolute agreement 91%), whereas when only mild subtle lesions were present the agreement was poorer (I–II absolute agreement 50%). Thus, in a research setting when the extent of lesions is mild, it is strongly recommended that the assessment of lesions should be carried out by at least two independent observers.
Glycosphingolipids: deuterium NMR study of the influence of carbohydrate headgroup structure on ceramide acyl chain behavior in glycolipid-phospholipid bilayers

Galactosyl- and glucosylceramide, globoside, and dihydrolactosylceramide, bearing (2,2-{sup 2}H{sub 2})stearic acid, have been studied at a concentration of 10 mol % in bilayers of dimyristoylphosphatidylcholine by {sup 2}H NMR. The quadrupolar splittings {Delta}v{sub Q} of the C2 deuterons were measured at several temperatures in the range of 30-60{degree}C. Spin-lattice relaxation times T{sub 1} of C2 deuterons were determined in the same temperature range for all lipids but globoside. T{sub 1} values for the GlcCer and GalCer systems increased with temperature, indicating that the motions responsible for relaxation were in the short correlation time regime. T{sub 1} for deuterons at the acyl chain C2-position of LaCer was observed to decrease with increasing temperature, indicating that the motion(s) dominating relaxation are in the long correlation time regime. Thus the mobility of the acyl chain at the 2-position is reduced in the LacCer with respect to GlcCer and GalCer.
The potential use of polymer flocculants for pharmaceuticals removal in wastewater treatment

The appearance of pharmaceuticals in wastewater has become a significant concern to both the water treatment industry as well as consumers. The availability of advanced treatment methods has optimized the removal of these compounds present in wastewater sources. The latest development in polymers as flocculants and combining it with other treatment helps to reduce the quantities of these pharmaceuticals in the final wastewater effluent. This paper gives an insight on the potential usage of polymer flocculants and its combination with particles, organic substances and conventional adsorbents towards removing pharmaceutical compounds from wastewater. Polymer flocculants alone will have a limited ability in pharmaceuticals removal. The flocculation process combination with adsorption on natural components and particles is always necessary. Interaction of polymers with adsorbents in the wastewater could also play an important role in their removal by polymer flocculants due to its proven implementation. An understanding of the changes in processes and mechanisms involving the polymers is essential for achieving effective removal rate. Combination of polymer flocculants with conventional adsorbents such as carbon and clays during the treatment process could lead to a new effective and economic approach in removal of the pharmaceutical compound.
Effects of sulfur forms on heavy metals bioleaching from contaminated sediments

The use of recyclable forms of sulfur will exclude the risk of sediment reacidification and reduce the cost of bioleaching process. Three different forms of sulfur (namely sulfur powder, prills and pieces) were used to examine the utilization and recycle of sulfur, used as energy substrate for sulfur-oxidizing bacteria (SOB) in the bioleaching of heavy metal-contaminated sediments. The results showed that despite their relatively smaller surface areas, the efficiency of metal bioleaching with sulfur prills and pieces were comparable to that with sulfur powder. After 13 days of bioleaching, 71–74% of Zn, 58–62% of Cu, and 22–31% of Cr could be leached from the sediments, respectively. During bioleaching, most of the oxidizable and reducible forms of metals were transformed to acid soluble, posing a favorable condition for final metals removal. Sulfur recycling experiments showed that the recovered sulfur prills and pieces were as the same effective in pH reduction as fresh sulfur, revealing the feasibility of eventual reuse of the recycled sulfur in the bioleaching process. Further studies are required to testify the performance of these recyclable forms of sulfur in future large-scale bioleaching reactor.
Spatiotemporal motion estimation for respiratory-correlated imaging of the lungs.

PURPOSE Four-dimensional computed tomography (4D CT) can provide patient-specific motion information for radiotherapy planning and delivery. Motion estimation in 4D CT is challenging due to the reduced image quality and the presence of artifacts. We aim to improve the robustness of deformable registration applied to respiratory-correlated imaging of the lungs, by using a global problem formulation and pursuing a restrictive parametrization for the spatiotemporal deformation model. METHODS A spatial transformation based on free-form deformations was extended to the temporal domain, by explicitly modeling the trajectory using a cyclic temporal model based on B-splines. A global registration criterion allowed to consider the entire image sequence simultaneously and enforce the temporal coherence of the deformation throughout the respiratory cycle. To ensure a parametrization capable of capturing the dynamics of respiratory motion, a prestudy was performed on the temporal dimension separately. The temporal parameters were tuned by fitting them to diaphragm motion data acquired for a large patient group. Suitable properties were retained and applied to spatiotemporal registration of 4D CT data. Registration results were validated using large sets of landmarks and compared to consecutive spatial registrations. To illustrate the benefit of the spatiotemporal approach, we also assessed the performance in the presence of motion-induced artifacts. RESULTS Cubic B-splines gave better or similar fitting results as lower orders and were selected because of their inherently stronger regularization. The fitting and registration errors increased gradually with the temporal control point spacing, representing a trade-off between achievable accuracy and sensitivity to noise and artifacts. A piecewise smooth trajectory model, allowing for a discontinuous change of speed at end-inhale, was found most suitable to account for the sudden changes of motion at this breathing phase. The spatiotemporal modeling allowed a reduction of the number of parameters of 45%, while maintaining registration accuracy within 0.1 mm. The approach reduced the sensitivity to artifacts. CONCLUSIONS Spatiotemporal registration can provide accurate motion estimation for 4D CT and improves the robustness to artifacts.
Intelligence and neuroticism in relation to depression and psychological distress: evidence of interaction using data from Generation Scotland: Scottish Family Health Study and UK Biobank

Background Neuroticism is a risk factor for selected mental and physical illnesses and is inversely associated with intelligence. Intelligence appears to interact with neuroticism and mitigate its detrimental effects on physical health and mortality. However, the inter-ralationships of neuroticism and intelligence for major depressive disorder (MDD) and psychological distress has not been well examined. Methods Associations and interactions between neuroticism and general intelligence (g) on MDD and psychological distress were examined in two population-based cohorts: Generation Scotland: Scottish Family Health Study (GS:SFHS, N=19,200) and UK Biobank (N=90,529). The Eysenck Personality Scale Short Form-Revised measured neuroticism and g was extracted from multiple cognitive ability tests in each cohort. Family structure was adjusted for in GS:SFHS. Results Neuroticism was associated with MDD and psychological distress in both samples. A significant interaction between neuroticism and g in predicting MDD status was found in UK Biobank (OR = 0.96, p < .01), suggesting that higher g ameliorated the adverse effects of neuroticism on the likelihood of having MDD. This interaction was not found in GS:SFHS. In both samples, higher neuroticism and lower intelligence were associated with increased psychological distress. A significant interaction was also found in both cohorts (GS:SFHS: ß = -0.05, p < .01; UK Biobank: ß = -0.02, p < .01), such that intelligence protected against the deleterious effect of neuroticism on psychological distress. Conclusions From two large cohort studies, our findings suggest intelligence acts a protective factor in mitigating the effects of neuroticism on risk for depressive illness and psychological distress.
Estimating the depth of myometrial involvement by endometrial carcinoma: efficacy of transvaginal sonography vs MR imaging.

OBJECTIVE In this study we compare transvaginal sonography with MR imaging for use in detecting the depth of myometrial involvement by endometrial carcinoma. SUBJECTS AND METHODS Forty-two consecutive patients with stage I endometrial carcinoma had transvaginal sonography and MR imaging at 0.5 T. All the patients had a hysterectomy within 1-10 days after the imaging studies. The results of histologic examination of the surgical specimen were considered the gold standard of the study. We compared transvaginal sonography and MR imaging for use in assessing myometrial invasion by endometrial carcinoma by means of the staging classification of the International Federation of Gynecology and Obstetrics: stage Ia (tumor limited to endometrium), stage Ib (invasion of less than half the myometrium), stage Ic (invasion of more than half the myometrium). The overdiagnoses and the underdiagnoses for both techniques were calculated. We also evaluated the sensitivity and specificity of the two techniques for assessing the presence of myometrial invasion (stage Ib + stage Ic) and the presence of deep myometrial invasion (stage Ic). The diagnostic indexes evaluated and the differences between them were analyzed by using McNemar's test and 95% confidence intervals. The staging diagnoses based on MR imaging and sonographic findings were compared with staging diagnoses based on histologic examination, and a score was assigned to each diagnosis: these scores were then evaluated with Wilcoxon's signed rank test for paired data. RESULTS Histologic examination showed that six of the 42 patients had tumor confined to the endometrium (stage Ia), 14 had involvement of the inner half of the myometrium (stage Ib), and 22 had involvement of the outer half of the myometrium (stage Ic). The staging was concordant between the two imaging techniques in 32 cases (concordance, 76%). Among the 10 discordant cases, diagnosis was correct in six cases for MR and four cases for sonography. Overall staging based on sonography was correct with respect to histologic staging in 29 cases (69%; 95% confidence interval, 52-81%). Five tumors (12%) were underdiagnosed and eight (19%) were overdiagnosed. Staging based on MR findings was correct with respect to histologic staging in 31 cases (74%; 95% confidence interval, 58-85%). Five tumors (12%) were underdiagnosed, and six (14%) were overdiagnosed. CONCLUSION In our experience, there is no difference in the staging diagnoses of transvaginal sonography and MR imaging. Also, concordance with histologic staging diagnoses and sensitivity and specificity indexes did not show statistical differences between the two techniques, although these last results have to be considered with caution because of the low power of the statistical tests.
Oxysterol profiles of normal human arteries, fatty streaks and advanced lesions

Objective: Human atherosclerotic lesions of different stages have quantitative differences in cholesterol and oxysterol content, but information on the oxysterol profile in fatty streaks is limited. This study aims to provide more detailed oxysterol quantification in human fatty streaks, as well as normal aorta and advanced lesions. Methods: A newly adapted method was used, including oxysterol purification by means of a silica cartridge; and it was ensured that artifactual oxysterol formation was kept to a minimum. Cholesterol and oxysterols were estimated by GC and identification confirmed by GC-MS in samples of normal human arterial intima, intima with near-confluent fatty streaks and advanced lesions, in necropsy samples. Results: The oxysterols 7α-hydroxycholesterol, cholesterol-5β, 6β-epoxide, cholesterol-5α, 6α-epoxide, 7β-hydroxycholesterol, 7-ketocholesterol and 27-hydroxycholesterol (formerly known as 26-hydroxy-cholesterol) were found in all the lesions, but were at most very low in the normal aorta, both when related to wet weight and when related to cholesterol. Most components of the normal artery showed some cross-correlation on linear regression analysis, but cross-correlations were weaker in the fatty streaks and advanced lesions. However, in fatty streak there was a marked positive correlation between 27-hydroxycholesterol and cholesterol. Conclusion: The findings confirm that oxysterols are present in fatty streaks and advanced lesions and may arise from different cholesterol oxidation mechanisms, including free radical-mediated oxidation and enzymatic oxidation.
Alkaline Phosphatase Content and the Effects of Prednisolone on Mammalian Cells in Culture

The alkaline phosphatase content of different tissue culture cell lines has been shown to vary from no detectable activity to high enzyme concentration. Within the epithelial lines studied alkaline phosphatase is either constitutive or inducible. Two epithelial cell strains in which alkaline phosphatase was "absent" could be induced to develop significant amounts of the enzyme when grown in the presence of Δ1-hydrocortisone. Phosphate did not repress enzyme induction by prednisolone. Under conditions of deadaptation the induced enzyme was diluted by cell multiplication. The mouse fibroblastic L line and several human fibroblastic lines did not contain alkaline phosphatase when grown under the conditions described nor could they be induced to produce the enzyme when cultivated in medium with prednisolone. Δ1-Hydrocortisone has other characteristic effects on established mammalian cell cultures which vary among cell lines. Human epithelial lines show reduction in cell multiplication with increase in mitotic index. The cytoplasm is increased and cell volume is nearly doubled. Mouse fibroblasts show a similar reduction in cell multiplication with a decrease in mitotic index. There is no increase in cell cytoplasm. Human fibroblast strains show no inhibition of multiplication or alteration in total cell protein when grown in medium containing prednisolone. Antisera prepared against "negative" prednisolone-inducible human cell lines and against a positive human line inhibited alkaline phosphatase activity to an equal degree.