Miracle-dz/UniFAR-FTUs huggingface dataset:
Cox Models Survival Analysis Based on Breast Cancer Treatments

Background The aim of this study is to evaluate the association between different treatments and survival time of breast cancer patients using either standard Cox model or stratified Cox model. Methods The study was conducted on 15830 women diagnosed with breast cancer in British Columbia, Canada. They were divided into eight groups according to patients’ ages and stage of disease Either Cox’s PH model or stratified Cox model was fitted to each group according to the PH assumption and tested using Schoenfeld residuals. Results The data show that in the group of patients under age 50 years old and over age 50 with stage I cancer, the highest hazard was related to radiotherapy (HR= 3.15, CI: 1.85-5.35) and chemotherapy (HR= 3, CI: 2.29- 3.93) respectively. For both groups of patients with stage II cancer, the highest risk was related to radiotherapy (HR=3.02, CI: 2.26-4.03) (HR=2.16, CI:1.85-2.52). For both groups of patients with stage III cancer, the highest risk was for surgery (HR=0.49, CI: 0.33-0.73), (HR=0.45, CI: 0.36-0.57). For patients of age 50 years or less with stage IV cancer, none of the treatments were statistically significant. In group of patients over age 50 years old with stage IV cancer, the highest hazard was related to surgery (HR=0.64, CI: 0.53-0.78). Conclusion The results of this study show that for patients with stage I and II breast cancer, radiotherapy and chemotherapy had the highest hazard; for patients with stage III and IV breast cancer, the highest hazard was associated with treatment surgery.
Stereovision Based Vehicle Tracking in Urban Traffic Environments

This paper presents an algorithm for tracking the cuboids generated from grouping the 3D points obtained through stereovision. The solution described in the paper takes into consideration the particularities of the scenario and of the sensor, and brings considerable improvement in all the phases of tracking: initialization, prediction, measurement and update. The corner of the cuboid becomes the central working concept, thus improving the handling of partially occluded objects, of objects partially out of the field of view, and of objects whose measurement is fragmented by the sensor inaccuracies. After association at corner level, multiple measurements or validated parts of a measurement form a virtual object, the meta measurement, which is used for track update. The size of a vehicle is tracked using a histogram voting method. The resulted algorithm shows robustness and accuracy in the crowded urban scenario.
Redshifts from Spitzer Spectra for Optically Faint Radio-selected Infrared Sources

Spectra have been obtained with the Infrared Spectrograph on the Spitzer Space Telescope for 18 optically faint sources (R ≳ 23.9 mag) having fν(24 μm) > 1.0 mJy and having radio detections at 20 cm to a limit of 115 μJy. The sources are within the Spitzer First Look Survey. Redshifts are determined for 14 sources from strong silicate absorption features (12 sources) or strong PAH emission features (two sources), with median redshift of 2.1. Results confirm that optically faint sources of ~1 mJy at 24 μm are typically at redshifts z ~ 2, verifying the high efficiency in selecting high-redshift sources based on extreme infrared-to-optical flux ratio, and indicate that 24 μm sources that also have radio counterparts are not systematically different than samples chosen only by their infrared-to-optical flux ratios. Using the parameter q = log[fν(24 μm)/fν(20 cm)], 17 of the 18 sources observed have values of 0 < q < 1, in the range expected for starburst-powered sources, but only a few of these show strong PAH emission as expected from starbursts, with the remainder showing absorbed or power-law spectra consistent with an AGN luminosity source. This confirms previous indications that optically faint Spitzer sources with fν(24 μm) ≳ 1.0 mJy are predominately AGNs and represent the upper end of the luminosity function of dusty sources at z ~ 2. Based on the characteristics of the sources observed so far, we predict that the nature of sources selected at 24 μm will change for fν(24 μm) ≲ 0.5 mJy to sources dominated primarily by starbursts.
Nitrate dynamics in natural plants: insights based on the concentration and natural isotope abundances of tissue nitrate

The dynamics of nitrate (NO−3), a major nitrogen (N) source for natural plants, has been studied mostly through experimental N addition, enzymatic assay, isotope labeling, and genetic expression. However, artificial N supply may not reasonably reflect the N strategies in natural plants because NO−3 uptake and reduction may vary with external N availability. Due to abrupt application and short operation time, field N addition, and isotopic labeling hinder the elucidation of in situ NO−3-use mechanisms. The concentration and natural isotopes of tissue NO−3 can offer insights into the plant NO−3 sources and dynamics in a natural context. Furthermore, they facilitate the exploration of plant NO−3 utilization and its interaction with N pollution and ecosystem N cycles without disturbing the N pools. The present study was conducted to review the application of the denitrifier method for concentration and isotope analyses of NO−3 in plants. Moreover, this study highlights the utility and advantages of these parameters in interpreting NO−3 sources and dynamics in natural plants. We summarize the major sources and reduction processes of NO−3 in plants, and discuss the implications of NO−3 concentration in plant tissues based on existing data. Particular emphasis was laid on the regulation of soil NO−3 and plant ecophysiological functions in interspecific and intra-plant NO−3 variations. We introduce N and O isotope systematics of NO−3 in plants and discuss the principles and feasibilities of using isotopic enrichment and fractionation factors; the correlation between concentration and isotopes (N and O isotopes: δ18O and Δ17O); and isotope mass-balance calculations to constrain sources and reduction of NO−3 in possible scenarios for natural plants are deliberated. Finally, we offer a preliminary framework of intraplant δ18O-NO−3 variation, and summarize the uncertainties in using tissue NO−3 parameters to interpret plant NO−3 utilization.
Attention deficit-hyperactivity disorder and early-onset bipolar disorder: two facets of one entity?

Early-onset bipolar disorder (BD) and attention-deficithyperactivity disorder (ADHD) have recently been the subject of highly controversial debate, due to theories regarding underlying pathophysiological processes and a clinical overlap of symptoms. Epidemiological data, clinical aspect, neuroimaging, neurochemical, and genetic studies suggest that there may be a possible relationship between biological factors and clinical characteristic in the development of symptoms. However, longitudinal data supporting the hypothesis of a diagnostic shift from BD to ADHD symptoms and vice versa are currently not available. These would be essential to enable further investigations into whether these two disorders possibly represent two different aspects of an underlying common psychopathophysioiogical entity.
Performance and plasma metabolites of dairy calves fed starter containing sodium butyrate, calcium propionate or sodium monensin.

This study was conducted to examine the influence of supplementation of sodium butyrate, sodium monensin or calcium propionate in a starter diet on the performance and selected plasma metabolites (plasma glucose, non-esterified fatty acids and β-hydroxybutyrate) of Holstein calves during pre- and post-weaning periods. Twenty-four newborn Holstein calves were housed in individual hutches until 10 weeks of life, receiving water free choice, and fed four liters of milk daily. Calves were blocked according to weight and date of birth, and allocated to one of the following treatments, according to the additive in the starter: (i) sodium butyrate (150 g/kg); (ii) sodium monensin (30 mg/kg); and (iii) calcium propionate (150 g/kg). During 10 weeks, calves received starter ad libitum, while coast cross hay (Cynodon dactylon (L.) pers. ) was offered after weaning, which occurred at the 8th week of age. Weekly, calves were weighted and evaluated for body measurements. Blood samples were taken weekly after the fourth week of age, 2 hours after the morning feeding, for determination of plasma metabolites. No differences were observed among treatments for starter or hay intake, BW and daily gain of the animals. Mean concentrations of selected plasma metabolites were similar in calves fed a starter supplemented with sodium butyrate, sodium monensin and calcium propionate. There was significant reduction in the concentrations of plasma glucose as calves aged. The inclusion of sodium butyrate, calcium propionate or sodium monensin as additives in starter feeds resulted in equal animal performance, before and after weaning, suggesting that sodium monensin may be replaced by organic acid salts.
Design of a Nonlinear Observer for Vehicle Velocity Estimation and Experiments

This brief presents a nonlinear observer for estimating the longitudinal and lateral velocities based on Dugoff's tire model and vehicle dynamics. The observer has a fixed gain structure and can make full use of information about acceleration measurements and nonlinear vehicle model. A sufficient condition is derived to guarantee the stability of the observer, and the robustness of the observer with respect to additive disturbances is analyzed with the help of input-to-state stability theory. The performance of the observer is compared with that of existing approaches and evaluated experimentally under a variety of maneuvers and road conditions.
A Comprehensive Analysis of Connectivity and Aging Over the Adult Life Span

Aging has been associated with decreased intra- and internetwork connectivity during rest and task. Recent work has shown the influential role of the salience network over the default mode network (DMN) and executive control network (ECN). This study comprehensively investigates age-related changes in intra- and internetwork connectivity and effective connectivity between the DMN, ECN, and salience network across the adult life span. Two hundred ten participants completed a working memory task, an inhibition task, and a resting-state functional magnetic resonance imaging scan. Networks were extracted using independent component analysis; then, regression analyses and t-tests between three age groups, 21-40 (younger), 41-60 (middle), and 61-80 (older), were conducted. Older age was associated with decreased intranetwork connectivity. Functional network connectivity analyses revealed older age was associated with increased internetwork connectivity between the salience network and the ECNs and DMNs. In both cases, the effects were more pronounced in the tasks compared to resting state. Granger causality analyses indicated the salience network was influenced by the DMN and ECN in all age groups during both tasks, but not rest. However, middle adults showed increased influence from the salience network to the right ECN compared to younger adults during the flanker task. Taking everything into account, these findings indicate the role of the salience network changes over the life span, which may have implications for the early detection of pathophysiology in older adults.
Logically rectangular mixed methods for Darcy flow on general geometry

The authors consider an expanded mixed finite element formulation (cell centered finite difference) for Darcy flow with a tensor absolute permeability. The reservoir can be geometrically general with internal features, but the computational domain is rectangular. The method is defined on a curvilinear grid that need not be orthogonal, obtained by mapping the rectangular, computational grid. The original flow problem becomes a similar problem with a modified permeability on the computational grid. Quadrature rules turn the mixed method into a cell-centered finite difference method with a 9 point stencil in 2-D and 19 in 3-D. As shown by theory and experiment, if the modified permeability on the computational domain is smooth, then the convergence rate is optimal and both pressure and velocity are superconvergent at certain points. If not, Lagrange multiplier pressures can be introduced on boundaries of elements so that optimal convergence is retained. This modification presents only small changes in the solution process; in fact, the same parallel domain decomposition algorithms can be applied with little or no change to the code if the modified permeability is smooth over the subdomains. This Lagrange multiplier procedure can be used to extend the difference scheme to multi-block domains, and tomore » give a coupling with unstructured grids. In all cases, the mixed formulation is locally conservative. Computational results illustrate the advantage and convergence of this method. « less
Characterization of Human CD8 T Cell Responses in Dengue Virus-Infected Patients from India

ABSTRACT Epidemiological studies suggest that India has the largest number of dengue virus infection cases worldwide. However, there is minimal information about the immunological responses in these patients. CD8 T cells are important in dengue, because they have been implicated in both protection and immunopathology. Here, we provide a detailed analysis of HLA-DR+ CD38+ and HLA-DR− CD38+ effector CD8 T cell subsets in dengue patients from India and Thailand. Both CD8 T cell subsets expanded and expressed markers indicative of antigen-driven proliferation, tissue homing, and cytotoxic effector functions, with the HLA-DR+ CD38+ subset being the most striking in these effector qualities. The breadth of the dengue-specific CD8 T cell response was diverse, with NS3-specific cells being the most dominant. Interestingly, only a small fraction of these activated effector CD8 T cells produced gamma interferon (IFN-γ) when stimulated with dengue virus peptide pools. Transcriptomics revealed downregulation of key molecules involved in T cell receptor (TCR) signaling. Consistent with this, the majority of these CD8 T cells remained IFN-γ unresponsive even after TCR-dependent polyclonal stimulation (anti-CD3 plus anti-CD28) but produced IFN-γ by TCR-independent polyclonal stimulation (phorbol 12-myristate 13-acetate [PMA] plus ionomycin). Thus, the vast majority of these proliferating, highly differentiated effector CD8 T cells probably acquire TCR refractoriness at the time the patient is experiencing febrile illness that leads to IFN-γ unresponsiveness. Our studies open novel avenues for understanding the mechanisms that fine-tune the balance between CD8 T cell-mediated protective versus pathological effects in dengue. IMPORTANCE Dengue is becoming a global public health concern. Although CD8 T cells have been implicated both in protection and in the cytokine-mediated immunopathology of dengue, how the balance is maintained between these opposing functions remains unknown. We comprehensively characterized CD8 T cell subsets in dengue patients from India and Thailand and show that these cells expand massively and express phenotypes indicative of overwhelming antigenic stimulus and tissue homing/cytotoxic-effector functions but that a vast majority of them fail to produce IFN-γ in vitro. Interestingly, the cells were fully capable of producing the cytokine when stimulated in a T cell receptor (TCR)-independent manner but failed to do so in TCR-dependent stimulation. These results, together with transcriptomics, revealed that the vast majority of these CD8 T cells from dengue patients become cytokine unresponsive due to TCR signaling insufficiencies. These observations open novel avenues for understanding the mechanisms that fine-tune the balance between CD8-mediated protective versus pathological effects.
Plant performance was greater in the soils of more distantly related plants for an herbaceous understory species

We performed a glasshouse experiment to test whether degree of phylogenetic relatedness between Aquilegia canadensis and six co-occurring heterospecifics affects A. canadensis biomass through soil legacy effects. We found that A. canadensis performed significantly better in distant relatives' soils than in close relatives' soils, and this effect disappeared with soil sterilization. The greater performance of A. canadensis in soils of more versus less distant relatives is consistent with a hypothesis of phylogenetically-constrained pathogen escape, a phenomenon expected to promote coexistence of phylogenetically distant species.
Retinoblastoma protein complexes with C/EBP proteins and activates C/EBP‐mediated transcription *

The retinoblastoma protein (RB) recruits histone deacetylase (HDAC) to repress E2F‐mediated transactivation that plays a critical role in cell cycle regulation. RB is also involved in activation of expression of a number of tissue specific‐ and differentiation‐related genes. In this study, we examined the mechanism by which RB stimulated the expression of a differentiation‐related gene, the surfactant protein D (SP‐D), which plays important roles in innate host defense and the regulation of surfactant homeostasis. We demonstrated that RB specifically stimulated the activity of human SP‐D gene promoter. The RB family member, p107 but not p130, also increased SP‐D promoter activity. Activation by RB was mediated through a NF‐IL6 (C/EBPβ) binding motif in the human SP‐D promoter, and this sequence specifically bound to C/EBPα, C/EBPβ, and C/EBPδ. RB formed stable complexes with all three C/EBP family members. RB small pocket (amino acid residues 379–792), but not the C‐pocket (amino acid residues 792–928), was necessary and sufficient for its interaction with C/EBP proteins. Furthermore, we demonstrated that the complexes containing RB and C/EBP proteins directly interacted with C‐EBP binding site on DNA. These findings indicate that RB plays a positive, selective, and direct role in the C/EBP‐dependent transcriptional regulation of human SP‐D expression. J. Cell. Biochem. 83: 414–425, 2001. © 2001 Wiley‐Liss, Inc.
Prevention of lens damage associated with cigarette smoke exposure in rats by alpha-tocopherol (vitamin E) treatment.

PURPOSE To evaluate the possible protective effect and mechanism of alpha-tocopherol (vitamin E) treatment on lens degeneration associated with in vivo exposure to cigarette smoke and to further clarify the role of iron in cigarette smoke-generated lens damage. METHODS Twenty-eight male Wistar rats were randomly divided into four equal groups. Rats in groups 3 and 4 were exposed to cigarette smoke for 1 hour each day over 90 consecutive days, and rats in groups 1 and 2 were treated in similar fashion but only exposed to room air. Additionally, vitamin E was given to the rats in groups 2 and 4 via intramuscular route. At the end of the study, both eyes of all the animals were enucleated; one eye was prepared for histopathologic examination, and the fellow eye was used for the measurement of iron and calcium levels. RESULTS Significantly higher iron and calcium levels were observed in the lenses of group 3 rats than in other groups. Similar comparisons performed between groups 1 and 2, groups 1 and 4, and groups 2 and 4 did not show any significant difference. Distinct histopathologic changes in the anterior lens epithelium, such as hyperplasia, hypertrophy, epithelial multilayering, and the presence of epithelial cells over posterior lens capsule, observed in group 3 rats were not present in other groups. CONCLUSIONS Cataractogenesis after cigarette smoke exposure was associated with an accumulation of iron and calcium in the rat lens, and vitamin E supplementation protected such accumulations and cataractogenesis.
Estimates of genetic parameters for chemical traits of meat quality in Japanese black cattle

Abstract Genetic parameters for 54 carcass and chemical traits, such as general composition (moisture, crude fat and crude protein), fatty acid composition and water‐soluble compounds (free amino acids, peptides, nucleotides and sugars) of 587 commercial Japanese Black cattle were assessed. Heritability estimates for carcass traits and general composition ranged between 0.19–0.28, whereas those for fatty acid composition ranged between 0.11–0.85. Most heritability estimates for water‐soluble compounds were lower than 0.30; these traits were affected by aging period. Moderate heritability was observed for glutamine, alanine, taurine, anserine, inosine 5′‐monophosphate (IMP), inosine and myo‐inositol. In particular, heritability estimates were the highest (0.66) for taurine. Traits with moderate heritability were unaffected by aging period, with the exception of IMP, which was affected by aging period but exhibited moderate heritability (0.47). Although phenotypic correlations of water‐soluble compounds with carcass weight (CW), beef marbling standard (BMS) and monounsaturated fatty acid were generally low, genetic correlations between these traits were low to high. At the genetic level, most of the water‐soluble compounds were positively correlated with monounsaturated fatty acid but negatively correlated with CW and BMS. Thus, our results indicate that genetic variance and correlations could exist and be captured for some of the water‐soluble compounds.
The Role of Tradable Planning Permits in Environmental Land Use Planning: A Stocktake of the German Discussion

© 2012 Loehr, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Role of Tradable Planning Permits in Environmental Land Use Planning: A Stocktake of the German Discussion
On the Compound MIMO Broadcast Channel

We consider the Gaussian multi-antenna compound broadcast channel where one transmitter transmits several mes- sages, each intended for a different user whose channel realization is arbitrarily chosen from a finite set. Our investigation focuses on the behavior of this channel at high SNRs and we obtain the multiplexing gain of the sum capacity for a number of cases, and point out some implications of the total achievable multiplexing gain region. 1
Inverse source problem with reactive power constraint

This paper reports a general Lagrangian formulation for constrained electromagnetic inverse source problems. The formulation is applicable to different forms of inverse source problems having different constraints. Two possibilities are emphasized in the paper. One yields the usual minimum energy solution. The other establishes a new minimum energy solution with the additional constraint that the source has a prescribed reactive power (which can be zero). The latter solution incorporates the important reactive energy issues of an antenna which had not been considered before in the context of the inverse source problem. The new solution is shown to obey a homogeneous wave equation in the interior of the source volume, and expressions for the associated interior field and interaction power are also derived. The derived theory is illustrated for a canonical dipolar source and an alternative approach where the reactive power is minimized for a prescribed maximum functional energy is also presented. Advantage is taken of some of the results to briefly discuss some questions about fundamental antenna limits.