Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Hyperspectral Unmixing Based on Geometric Characteristics of Bilinear Mixture Models

Recently, many nonlinear spectral unmixing algorithms that use various bilinear mixture models (BMMs) have been proposed. However, the high computational complexity and intrinsic collinearity between true endmembers and virtual endmembers considerably decrease these algorithms’ unmixing performances. In this paper, we come up with a novel abundance estimation algorithm based on the BMMs. Motivated by BMMs’ geometric characteristics that are related to collinearity, we conduct a unique nonlinear vertex ${p}$ to replace all the virtual endmembers. Unlike the virtual endmembers, this vertex ${p}$ actually works as an additional true endmember that gives affine representations of pixels with other true endmembers. When the pixels’ normalized barycentric coordinates with respect to true endmembers are obtained, they will be directly projected to be their approximate linear mixture components, which removes the collinearity effectively and enables further linear spectral unmixing. After that, based on the analysis of projection bias, two strategies using the projected gradient algorithm and a traditional linear spectral unmixing algorithm, respectively, are provided to correct the bias and estimate more accurate abundances. The experimental results on simulated and real hyperspectral data show that the proposed algorithm performs better compared with both traditional and state-of-the-art spectral unmixing algorithms. Both the unmixing accuracy and speed have been improved.
Differential and cooperative actions of Olig1 and Olig2 transcription factors on immature proliferating cells after contusive spinal cord injury

Spontaneous remyelination after spinal cord injury (SCI) is limited probably due to inadequate signaling to generate sufficient OLs from progenitor cells. The present study tested a hypothesis that introduction of olig genes, critical regulators of OL development, into immature proliferating cells could increase oligodendrogenesis after contusive SCI in adult rats. Recombinant retroviruses encoding Olig1 and Olig2 transcription factors, separately or in combination, with green fluorescent protein (GFP) were injected into the injured spinal cord. Unexpectedly, introduction of Olig2‐GFP retroviruses led to a marked hyperplasia of GFP+ cells at 1 week, and soft agar colony forming assay of isolated GFP+ cells confirmed Olig2‐induced tumorous transformation. In contrast, Olig1 did not alter the number of GFP+ cells. Simultaneous expression of Olig1 and Olig2 (Olig1/2) led to a marked increase in the number of GFP+ cells without tumor formation. The proportion of GFP+ cells with OL progenitor markers was increased by Olig1/2. Moreover, Olig1/2 robustly increased the proportion of mature OLs and expression of myelin related proteins, while Olig1 alone exhibited only modest effects. Olig1/2 upregulated Sox10, which drives terminal OL differentiation, implicating Sox 10 as a mediator of Olig1/2 effects on the maturation. Finally, injection of Olig1/2 retroviruses significantly improved a quality of hindpaws locomotion and increased the total number of OLs after SCI. Activation of both Olig1 and Olig2 may be beneficial by both increasing the progenitor cell proliferation and enhancing OL differentiation in the injured spinal cord. © 2011 Wiley‐Liss, Inc.
Variability of Physical Activity Patterns by Type of Day and Season in 8-10-Year-Old Boys

Accurate measures of physical activity are needed to elucidate the relationship between physical activity and health. In children, objective measures are preferred, as children lack the cognitive ability to recall details of their physical activity patterns accurately (Welk, Corbin & Dale, 2000). Several researchers have shown that to obtain a reliable measure of physical activity using accelerometry or pedometry, 4–5 days of monitoring are needed (Gretebeck & Montoye, 1992; Janz, Witt & Mahoney, 1995; Trost, Pate, Freedson, Sallis & Taylor, 2000), and weekend days as well as week days should be included (Gretebeck & Montoye, 1992; Trost et al., 2000). Therefore, when using an objective measure, physical activity is typically assessed continuously over 3–7 sequential days (e.g., Loucaides, Chedzoy & Bennett, 2003; Rowlands, Eston, & Ingledew, 1999; Rowlands et al., 2002; Trost et al., 2000; Trost et al., 2002). Time spent outdoors has been identified as a correlate of physical activity (Baranowski, Thompson, Durant, Baranowski, & Puhl, 1993; Burdette, Whitaker, & Daniels, 2004). Due to weather patterns in Britain, more time is spent outdoors in the summer than in winter. Consequently, seasonal variation in activity level exists, with physical activity measures in summer being greater than physical activity measured in winter time (RifasShiman et al., 2001). Amount of physical activity has also varied according to whether it is assessed during school or free time (Gavarry, Giacomoni, Bernard, Seymat & Falgairette 2003; Mota, Santos, Guerra, Ribeirio, & Duarte, 2003) or during weekdays or weekends (Rowlands et al., 1999; Trost et al., 2000). Therefore, activity would be expected to differ depending on whether it is assessed during school or vacation, and the extent of this difference would be expected to differ by season. British children spend approximately 38 weeks a year in school and 14 weeks out of school; therefore, both periods contribute substantially to the overall activity pattern. Assessing physical activity over one isolated period may not provide an overall picture of physical activity. When assessing relationships with health, or comparing physical activity to predetermined thresholds (e.g., Tudor-Locke et al., 2004), it may be important to provide a picture of overall activity accounting for differences due to season and school/vacation time. For example, if thresholds were determined from measurements taken in the summer, comparing children’s winter activity levels to the thresholds would be misleading. Thus, the aims of this study were to: (a) compare physical activity across two seasons and, within those seasons, across school and vacation time, and (b) compare the proportion of children meeting the activity thresholds recommended by Tudor-Locke et al. (2004) at each time point.
Evidence supporting a role for the calcium‐sensing receptor in Alzheimer disease

The calcium‐sensing receptor (CASR) is a G‐protein coupled, transmembrane receptor that responds to changes in Ca2+ levels. We hypothesized that the CASR could have a role in Alzheimer disease (AD) given expression of the CASR in brain, knowledge that calcium dysregulation promotes susceptibility to neuronal cell damage, the important role that the CASR plays in calcium regulation, and the fact that systemic calcium homeostasis and G‐protein signal transduction are altered in AD patients. To investigate the association of CASR variation in AD susceptibility, we genotyped a polymorphic dinucleotide repeat marker within intron 4, one SNP within the promoter region and three non‐synonymous SNPs within exon 7 of the CASR gene and tested for association analysis, using a well‐characterized cohort of AD cases (n = 692) and controls (n = 435). The dinucleotide repeat polymorphism was significantly associated with AD status (OR = 1.62; 95% CI: 1.27–2.07, P = 0.00037, Bonferroni corrected P = 0.0011) and the three non‐synonymous SNP haplotype was boarderline associated with AD status (P = 0.032, Bonferroni corrected P = 0.096). Stratifying by APOE4 allele carrier status revealed that the significant association was only in non‐APOE4 carriers (OR of 1.90; 95% CI: 1.37–2.62, P = 0.0001). We also investigated whether apoE or β amyloid could activate the calcium‐sensing receptor. The receptor activation assays revealed that apoE as well as β amyloid activated the CASR and that the level of activation appeared to be isoform dependent for apoE. These data support our hypothesis that the CASR has a role in AD susceptibility, particularly in individuals without an APOE4 allele. © 2008 Wiley‐Liss, Inc.
Charge transition levels of boron and silicon impurities in GaAs

Full ab-initio Car-Parrinello (CP) calculations have been performed to study effects of defects, vacancies and antisites, as well as various boron sites in silicon doped GaAs. The calculations, which include full relaxation of all ionic coordinates, show that the triple negative gallium vacancy has the minimal formation energy in n-type conducting As-rich GaAs. In p-type semi-insulating As-rich GaAs arsenic antisites are more likely. Furthermore, in boron doped GaAs the acceptor B<sup>−</sup><inf>Ga</inf> is predicted to be the dominat defect, while silicon impurities stabalize the B<sup>−</sup><inf>As</inf> acceptor by forming (B<inf>As</inf>Si<inf>Ga</inf>) complex defects.
MxA RNA Quantification in Febrile Patients Who Underwent Hematopoietic Cell Transplantation for Primary Immunodeficiency

The presence of myxovirus resistance protein A (MxA) RNA was studied in 55 febrile children with primary immunodeficiency, 27 of whom underwent hematopoietic cell transplantation, and in 28 age-matched controls. The level of MxA RNA was above the cutoff, established as the 95th percentile found in controls, with primary immunodeficiency either undergoing transplantation or not in febrile patients, and with a documented diagnosis of infection by adenovirus, cytomegalovirus, Epstein-Barr virus, respiratory syncytial virus, and rotavirus. The presence of rare viral infections, unrecognized among those that more frequently occur in patients with primary immunodeficiency and in patients undergoing transplantation, may explain the high MxA RNA levels observed in some patients with fever but undetectable genomes or antibodies for the more common viruses. The level of MxA in febrile patients with acute graft versus host disease was below the cutoff, with a median level comparable with that observed in patients with primary immunodeficiency, who did not undergo transplantation and were without fever and infections, but significantly lower compared with controls. The level of MxA was well correlated with viral infections in follow-up samples. These data indicate that the measurement of MxA RNA is simple and useful to detect viral infections and in distinguishing them from acute graft versus host disease after allogeneic cell transplantation.
Clustering of discrete cell properties essential for tumorigenicity and metastasis. II. Studies of syrian hamster embryo fibroblasts transformed by rous sarcoma virus

Tumorigenic and metastasizing activities (TGA; MA) and susceptibility, or resistance to H202 and PGE‐releasing activity (H2OR2 + PGEs+ phenotype) have been examined in 6 Syrian hamster embryo cell strains transformed in vitro with Rous sarcoma viruses (Schmidt‐Ruppin and Prague strains). Early observations of extremely high level of TGA and even MA of RSV‐SR‐transformants never selected in vivo have been confirmed. The correspondence of these properties with a high level of expression of H2OR2 + PGEs+ phenotype and its clustering character were demonstrated in 4 RSV‐SR trans‐formants, while significantly lower expression of all these characteristics, including TGA, was observed in 2 RSV‐Prague transformants. High level of spontaneous MA was noticed in some RSV‐SR transformants. A tumor cell line induced in vivo by RSV‐SR did not differ from the cell strain transformed in vitro by RSV‐SR. inhibition of H2OR2 + PGEs+ phenotype in one of RSV‐SR transformants was obtained with non‐toxic doses of BCNU and indomethacin, leading to a marked decrease of TGA.
Empirical Derivation to Improve the Definition of the Metabolic Syndrome in the Evaluation of Cardiovascular Disease Risk

OBJECTIVE To examine whether a quantitatively derived metabolic syndrome definition predicts incident cardiovascular disease (CVD) events better than do existing definitions. RESEARCH DESIGN AND METHODS Data were pooled from the Atherosclerosis Risk in Communities, Cardiovascular Health, and Framingham Offspring studies (n = 20,581). Incident coronary heart disease and stroke events were ascertained over 9 years. RESULTS The sensitivity for incident CVD events was higher and the specificity lower for the empirically derived versus the Adult Treatment Panel (ATP) III, International Diabetes Federation (IDF), or Harmonized metabolic syndrome definitions (sensitivity/specificity 0.65/0.53 vs. 0.53/0.63, 0.51/0.66, and 0.64/0.56, respectively), resulting in no overall improvement in discrimination. Multivariable-adjusted hazard ratios for incident CVD events were similar across definitions and were 1.7 (95% CI 1.6–1.9) for ATP III, 1.8 (1.6–2.0) for IDF, 1.9 (1.7–2.0) for Harmonized, and 1.7 (1.6–1.9) for the empirically derived definition. CONCLUSIONS Empirical derivation of the metabolic syndrome definition did not improve CVD discrimination or risk prediction.
A Recursive Algorithm for Reducing the Order of Controller while Guaranteeing Performance

In this paper, a procedure for the recursive reduction of the order of the stabilizing controller is introduced for SISO systems. Since all achievable closed loop maps are affine in the Q (Youla) parameter, we devise a sufficient condition for order reduction: Suppose there exists a Q parameter to induce a pole zero cancellation in the closed loop map to decrease the order of the closed loop system by m, then the corresponding controller is reduced in order by m. By appropriately choosing Q, we formulate a procedure for the recursive reduction of the order of the stabilizing controller and guarantee a performance describable through a complex stabilization technique.
The Price of Silence: Scientists' Trade-offs Between Publishing and Pay

A growing body of research draws on the notion that scientists face trade-offs between publishing research results and larger financial returns associated with limited disclosure. Yet little is known how scientists resolve such trade-offs. Using survey data from 1,400 junior life scientists, we find considerable heterogeneity in the ? price? scientists assign to publishing when they consider research positions in industry that allow versus restrict publishing, including scientists who are willing to give up publishing ? for free? Analyzing sources of heterogeneity, we find that the required wage premium increases with a scientist? s preference for publishing but decreases with the preference for money. Scientists who value publishing primarily as a currency in the labor market require a smaller wage premium, ceteris paribus, than scientists who value publishing as a mechanism to advance scientific knowledge, presumably reflecting different degrees of substitutability between publishing and pay. Finally, ability and the quality of training have a positive relationship with the required wage premium. We discuss implications for research on the economics of science, for managers seeking to attract and retain academically trained scientists, and for firms considering their participation in ? open science?
Genotoxicity of drinking water from Chao Lake.

Genotoxic activity appears to originate primarily from reactions of chlorine with humic substances in the source waters. Comparisons of extracts of settled versus chlorinated water have confirmed that chlorinating during water treatment produces mutagenic activity in the mutagenicity tests. Present work on XAD-2 extracts of raw, chlorinated (treated), and settled water from the Chao Lake region of China has involved a battery of mutagenicity assays for various genetic endpoints: the Salmonella test, the sister-chromatid exchange (SCE) induction in Chinese hamster lung (CHL) cells, and the micronucleus (MN) induction in the peripheral blood erythrocytes of silver carp. Extracts of raw and treated water but not the settled water are mutagenic in the Salmonella assay. On the other hand, extracts of three water samples show activity in the SCE and MN assays, especially the raw and treated water. These data show that contamination and chlorinating contribute mutagens to drinking water and suggest that the mammalian assays may be more sensitive for detecting mutagenicity in aquatic environment than the Salmonella test.
Dose-dependent survival of K562 cells subjected to irradiation, time course of endogenous enzyme activity and protective effect of applied superoxide dismutase.

PURPOSE Irradiation-generated reactive species are proven to affect the cell survival and antioxidant enzyme levels. Radioresistance is a phenomenon which includes many cell mechanisms and signaling pathways. Superoxide dismutase (SOD) acts in and outside of cells after irradiation. The aim of this study was to determine LD50 (lethal dose for 50% of K562 cells), to monitor the effect of a chosen dose and exogenously applied superoxide dismutase (ExSOD) on the cell number and the activity of SOD, glutathione peroxidase (GSH-Px) and catalase (CAT). METHODS The survival of irradiated (20-32.5 Gy) K562 cells was determined using the trypan-blue exclusion. Besides irradiated and non-irradiated cells (controls), another two groups of cells were treated with SOD (10-6 M) which then served as SOD-treated controls or were irradiated (30 Gy) one hour later. The number of cells and the activity of SOD, GSH-Px and CAT (using kinetic methods) were monitored after 1, 24, 48, 72 and 96 hrs in unirradiated, irradiated, SOD-treated and SOD-treated/irradiated experimental groups. RESULTS K562 cells showed dose-dependent survival in the chosen range of doses. A dose of 30 Gy induced 50% cell mortality and increased the activity of all three investigated enzymes after 24 hrs. Pretreatment with SOD preserved the survival of irradiated cells and increased SOD, GSH-Px and CAT activity. ExSOD induced an increase of the activity of all examined enzymes. CONCLUSION A balanced enhancement in endogenous antioxidative activity may be the cause of the increased radioresistance of K562 SOD-pretreated cells.
The major autolysin of Staphylococcus lugdunensis, AtlL, is involved in cell separation, stress-induced autolysis and contributes to bacterial pathogenesis.

Staphylococcus lugdunensis is a human skin commensal organism, but it is considered as a virulent Staphylococcus species. In a previous study, we described the first S. lugdunensis autolysin, AtlL. This enzyme displays two enzymatic domains and generates two peptidoglycan hydrolases, an N-acetylmuramoyl-l-alanine amidase and an N-acetylglucosaminidase. In this study, to further investigate the functions of this autolysin, a ΔatlL mutant was constructed. The microscopic examination of the mutant showed cell aggregates and revealed a rough outer cell surface demonstrating, respectively, the roles of AtlL in cell separation and peptidoglycan turnover. This ΔatlL mutant exhibited a lower susceptibility to Triton X-100-induced autolysis assays and appears to be more resistant to cell wall antibiotic-induced lysis and death compared with its parental strain. The atlL mutation affected the biofilm formation capacity of S. lugdunensis. Furthermore, the ΔatlL mutant showed trends toward reduced virulence using the Caenorhabditis elegans model. Overall, AtlL appears as a major cell wall autolysin of S. lugdunensis implicated in cell separation, in stress-induced autolysis and in bacterial pathogenesis.
Symptom Prevalence and Related Distress in Cancer Patients Undergoing Chemotherapy.

BACKGROUND Much has been done to examine the psychological impact of cancer treatment, but it remains unclear to what extent anxiety and depression is related to symptom prevalence. The present study concerned the characteristics and frequency of distress as related to symptom prevalence in cancer patients undergoing chemotherapy in Malaysia. MATERIALS AND METHODS Participants were 303 consecutive adult cancer patients undergoing chemotherapy in an academic medical center. The short form Memorial Symptom Assessment Scale (MSAS-SF), which covers three domains of symptoms (global distress, physical- and psychological symptoms) was used to cross-sectionally measure symptom frequency and associated distress via self-reporting. One-way ANOVA and t-tests were used to test mean differences among MSAS-SF subscale scores. RESULTS Complete data were available for 303 patients. The mean number of symptoms was 14.5. The five most prevalent were fatigue, dry mouth, hair loss, drowsiness and lack of appetite. Overall, symptom burden and frequency were higher than in other published MSAS-SF studies. Higher symptom frequency was also found to be significantly related to greater distress in cancer patients undergoing chemotherapy. CONCLUSIONS Patients undergoing chemotherapy suffer from multiple physical and psychological symptoms. Better symptom control or palliative care is needed. Greater frequency of reported symptoms may also indicate a subconscious bid by patients for care and reassurance - thus tailored intervention to manage distress should be offered.
A Potential Psychological Mechanism Linking Disaster-Related Prenatal Maternal Stress With Child Cognitive and Motor Development at 16 Months: The QF2011 Queensland Flood Study

Fetal exposure to prenatal maternal stress can have lifelong consequences, with different types of maternal stress associated with different areas of child development. Fewer studies have focused on motor skills, even though they are strongly predictive of later development across a range of domains. Research on mechanisms of transmission has identified biological cascades of stress reactions, yet links between psychological stress reactions are rarely studied. This study investigates the relationship between different aspects of disaster-related prenatal maternal stress and child cognitive and motor development, and proposes a cascade of stress reactions as a potential mechanism of transmission. Mothers in the Queensland Flood Study (QF2011) exposed to a major flood during pregnancy completed questionnaires assessing flood exposure, symptoms of peritraumatic distress, dissociation, and posttraumatic stress (PTSD), and cognitive appraisal of the overall flood consequences. At 16 months post-partum, children’s (N = 145) cognitive and motor development was assessed using the Bayley-III. Flood exposure predicted child cognitive development and maternal PTSD symptoms and negative cognitive appraisal were significantly negatively related to child motor development, with all relationships moderated by timing of exposure. Together, a cascade of stress reactions linked maternal flood exposure to poorer fine motor development. These findings suggest that the way stress reactions operate together is as important as the way they operate in isolation, and identifies a potential psychological mechanism of transmission for the effects of prenatal stress. Results have implications for conceptualizing prenatal stress research and optimizing child development in the wake of natural disasters.