Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA expression profiling of normal and tumor cells following photodynamic therapy with 5-aminolevulinic acid–induced protoporphyrin IX in vitro

Photodynamic therapy using 5-aminolevulinic acid–induced protoporphyrin IX synthesis as a photosensitizing reagent is an encouraging modality for cancer treatment. Understanding the mechanism of tumor phototoxicity is important to provide a basis for combinatory therapy regimens. A normal cell line (UROtsa, urothelial) and two tumor cell lines (RT4, urothelial; HT29, colonic) were treated with cell line–specific LD50 doses of light after exposure to 5-aminolevulinic acid (100 μg/mL), and harvested for RNA extraction 0, 10, and 30 minutes after irradiation. The RNA was hybridized to the metg001A Affymetrix GeneChip containing 2,800 genes, focusing on cancer-related and growth regulatory targets. Comparing the gene expression profiles between the different samples, 40 genes (e.g., SOD2, LUC7A, CASP8, and DUSP1) were identified as significantly altered in comparison with the control samples, and grouped according to their gene ontology. We selected caspase-8 (CASP8) and dual specificity phosphatase 1 (DUSP1) for further validation of the array findings, and compared their expression with the expression of the immediate early gene FOS by quantitative reverse transcription-PCR. RNA expression of CASP8 stayed unchanged whereas DUSP1 RNA was up-regulated in normal and tumor cells starting 30 minutes after irradiation. In contrast, FOS RNA was found continuously up-regulated over time in all three cell lines. Induction of DUSP1 protein expression was clearly shown after 1 hour using Western blot analysis. Interestingly, no changes of caspase-8 protein expression but activation of catalytic activity was detected only in UROtsa cells starting 1 hour after photodynamic therapy, whereas no changes were seen in both tumor cell lines. According to caspase-8, the active caspase 3 fragment was found only in the normal urothelial cell line (UROtsa) 1 hour after photodynamic therapy. Combined data analysis suggests that photodynamic therapy in vitro (LD50) leads to apoptosis in UROtsa and to necrosis in the tumor cell lines, respectively. RNA expression profiling of normal and tumor cell lines following photodynamic therapy with 5-aminolevulinic acid gave insight into the major molecular mechanisms induced by photodynamic therapy.
An immigration–death model to estimate the duration of malaria infection when detectability of the parasite is imperfect

Immigration–death models are proposed to analyse the infection dynamics in longitudinal studies of panels of heavily parasitized human hosts where parasites have been typed at regular intervals by PCR. Immigration refers to the acquisition of a new parasitic genotype, occurring at rate λ, and death refers to the clearance of a parasitic genotype (with rate μ). The models assume that corresponding to each observed process which is the detection or failure to detect a parasitic genotype, is an underlying true process which is hidden as a result of imperfect detection. We consider: (i) a model in which no distinction is made between the different members of the human population, who collectively represent the habitat of the parasites, and (ii) a model that allows for the accrual of infections with age. The models are fitted to a panel data set of malaria genotype of parasites belonging to the msp2 FC27 and 3D7 allelic families from a study of the dynamics of Plasmodium falciparum in Northern Ghana. Maximum likelihood estimates suggest that on average any individual residing in this holo‐endemic area will acquire 16 new infections per year (95 per cent CI, 15–18) (defined by their single locus genotypes) and that infection with any of these genotypes lasts on average 152 days (95 per cent CI, 138–169). We estimate that an average of 47 per cent (95 per cent CI, 42–51) of the parasite types present in the host are detected in a finger‐prick blood sample. This model provides a basis for analyses of how these quantities vary with the age, and hence the immune status of the host. Copyright © 2005 John Wiley & Sons, Ltd.
Understanding the Behavior of Sharing Information of Wechat Users: An Integrated Model

In this paper we propose a holistic view on the behavior of sharing information of Wechat users. We posit not only factors that have been studied before (traditional social factors based on rational action theory) but also social network factors (i.e., trust and habit of users for their sharing information in Wechat) could influence the behavior of sharing information. This study attempts to contribute to the understanding of information sharing behavior in Wechat context.
A study on spiral model of core competitiveness of enterprises based on resource-based view and competence-based view

Based on the resource-based view (RBV) and competence-based view (CBV), this paper concludes the main elements and evolutional process of the core competitiveness of enterprises. Then the paper puts forward the spiral model of core competitiveness of enterprises, splits the evolutional process of the core competitiveness of enterprises up into four stages, including conformity, synergism, linking and internationalization and analyses the model according to different types of enterprises.
A Big Data Fuzzy Grey Relational Analysis Method for social post retrieval - with an application to Facebook's news groups

In social media, after many candidate posts are chosen by satisfying functional criteria of target posts, users require a selection algorithm to further rank the candidate posts with their nonfunctional criteria. Therefore, this study proposes a novel algorithm, named BD-FGRA (Big Data-Fuzzy Grey Relational Analysis), to handle posts on parallel over the Spark platform by selecting the top-N posts that satisfy all the user-specified selection criteria, the ranking criteria and the goals of the nonfunctional attributes most. All the experiments show that BD-FGRA gets convincing performances.
c‐erbB‐2 (HER‐2/neu) gene amplification is a better indicator of poor prognosis than protein over‐expression in operable breast‐cancer patients

Our aim was to compare the prognostic value of c‐erbB‐2 gene amplification analyzed by Southern blot with that of protein (p185) over‐expression measured by immunohistochemistry in 172 patients with operable breast cancer (BC). Amplification and p185 over‐expression were found in 31 (18%) and 51 (30%) BCs, respectively. All but 1 of the tumors showed both amplification and over‐expression, while 21 (12%) tumors displayed over‐expression without amplification. The risk of death associated with c‐erbB‐2 gene amplification and p185 over‐expression was evaluated by multivariate analysis, taking into account tumor size, histoprognostic grade, hormone receptors and axillary node status. During a mean follow‐up of 9.5 (±2) years, node involvement (p < 0.001), c‐erbB‐2 gene amplification (p = 0.02) and negative hormone receptors (p = 0.02) were found to be independent prognostic indicators of the risk of death. Over‐expression of p185 with no amplification was not correlated with this risk. When the risk of death associated with c‐erbB‐2 amplification was studied according to chemo‐ and hormone therapy, no significant difference was observed between subgroups of subjects. Amplification was also associated (p = 0.02) with the risk of multifocal distant metastases (i.e., metastases detected concomitantly in at least 2 sites) and, thus, with BC aggressiveness. These data show the importance of c‐erbB‐2 gene amplification in predicting the long‐term outcome of patients and in selecting eligible patients for c‐erbB‐2–targeted therapies. © 2001 Wiley‐Liss, Inc.
A comparison of energy expenditure estimation of several physical activity monitors.

INTRODUCTION Accurately and precisely estimating free-living energy expenditure (EE) is important for monitoring energy balance and quantifying physical activity. Recently, single and multisensor devices have been developed that can classify physical activities, potentially resulting in improved estimates of EE. PURPOSE This study aimed to determine the validity of EE estimation of a footwear-based physical activity monitor and to compare this validity against a variety of research and consumer physical activity monitors. METHODS Nineteen healthy young adults (10 men, 9 women) completed a 4-h stay in a room calorimeter. Participants wore a footwear-based physical activity monitor as well as Actical, ActiGraph, IDEEA, DirectLife, and Fitbit devices. Each individual performed a series of postures/activities. We developed models to estimate EE from the footwear-based device, and we used the manufacturer's software to estimate EE for all other devices. RESULTS Estimated EE using the shoe-based device was not significantly different than measured EE (mean ± SE; 476 ± 20 vs 478 ± 18 kcal, respectively) and had a root-mean-square error of 29.6 kcal (6.2%). The IDEEA and the DirectLlife estimates of EE were not significantly different than the measured EE, but the ActiGraph and the Fitbit devices significantly underestimated EE. Root-mean-square errors were 93.5 (19%), 62.1 kcal (14%), 88.2 kcal (18%), 136.6 kcal (27%), 130.1 kcal (26%), and 143.2 kcal (28%) for Actical, DirectLife, IDEEA, ActiGraph, and Fitbit, respectively. CONCLUSIONS The shoe-based physical activity monitor provides a valid estimate of EE, whereas the other physical activity monitors tested have a wide range of validity when estimating EE. Our results also demonstrate that estimating EE based on classification of physical activities can be more accurate and precise than estimating EE based on total physical activity.
Dependence of murine obstructive airway disease on CD40 ligand.

BACKGROUND Human lung transplantation carries a poor prognosis because of chronic rejection in the form of obliterative bronchiolitis syndrome (OBS). Using the mouse model of heterotopic tracheal transplantation, we examined the role of costimulation in the allograft rejection that characterizes obstructive airway disease (OAD). METHODS C57BL/6 or BALB/c tracheae were implanted into wild-type control, CD28-/-, muMT (B-cell deficient), or CD40L-/- recipient mice. Grafts were explanted from 7 to 42 days posttransplantation and evaluated. RESULTS Thickening of the basement membrane and a decrease in patent luminal area were first noted at 2 weeks in wild-type allogeneic trachea recipients and to a slightly lesser degree in CD28-/- recipients. In contrast, CD40L-/- recipient mice showed no evidence of cellular infiltrates or fibrosis in transplanted tracheae. To determine whether CD40L interacted with host or donor CD40, CD40-deficient tracheae were transplanted into CD40L+/+, CD40+/+ wild-type mice. Wild-type mice rejected CD40-/- tracheae. Tracheae were transplanted into B-cell-deficient mice to determine the role of B-cell CD40 in chronic pulmonary allograft rejection. The OAD reaction was identical in wild-type and B-cell-deficient mice. CONCLUSIONS Development of OAD in the mouse trachea transplant model is primarily dependent on CD40L and is relatively CD28 independent. The ability of mice to reject CD40-/- tracheae demonstrated that host, not donor, CD40 is required for rejection. Furthermore, the ability of B-cell-deficient mice to reject allogeneic tracheae demonstrated that B-cell CD40-mediated responses are not required for the development of OAD.
Correction to Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion

■ ASSOCIATED CONTENT *S Supporting Information H2O generation curves of all 19 samples, H2O generation curves of ΔV = 50, 60, 70 and 80, potential energy and force curves, H2 loss curve at 2498 K, H2O2 generation curve at 2498 K, species generated in aARRDyn simulations with ΔV = 20 and 40 kcal at 2498 K; the new ReaxFF−OH2014 force field parameters plus some of the validations against QM; results for the Arrhenius analysis, reaction mechanisms and kinetics from the older ReaxFF-CHO2008 force field, the force field file, and the plot script. This material is available free of charge via the Internet at http://pubs.acs. org.
DNA Immunization with the Gene Encoding P4 Nuclease of Leishmania amazonensis Protects Mice against Cutaneous Leishmaniasis

ABSTRACT Infection with the protozoan parasite Leishmania amazonensis can cause diverse clinical forms of leishmaniasis. Immunization with purified P4 nuclease protein has been shown to elicit a protective response in mice challenged with L. amazonensis and L. pifanoi. To explore the potential of a DNA-based vaccine, we tested the L. amazonensis gene encoding P4 nuclease as well as adjuvant constructs encoding murine interleukin-12 (IL-12) and L. amazonensis HSP70. Susceptible BALB/c mice were immunized with the DNA encoding P4 alone, P4/IL-12, or P4/HSP70 prior to challenge with L. amazonensis promastigotes. Mice given P4/IL-12 exhibited no lesion development and had a 3- to 4-log reduction in tissue parasite burdens compared to controls. This protection corresponded to significant increases in gamma interferon and tumor necrosis factor alpha production and a reduction in parasite-specific immunoglobulin G1, suggesting an enhancement in Th1 responses. Moreover, we immunized mice with the L. amazonensis vaccines to determine if this vaccine regimen could provide cross-protection against a genetically diverse species, L. major. While the P4/HSP70 vaccine led to self-healing lesions, the P4/IL-12 vaccine provided negligible protection against L. major infection. This is the first report of successful use of a DNA vaccine to induce protection against L. amazonensis infection. Additionally, our results indicate that different vaccine combinations, including DNA encoding P4, HSP70, or IL-12, can provide significant protection against both Old World and New World cutaneous leishmaniasis.
Green innovation: industrial policy for a low carbon future

This report for the TUC by Prof Paul Ekins and Will McDowall argues that government has a key leadership role in creating a “dynamic and vibrant innovation system” that meets society’s environmental and economic aspirations. The direction the UK’s economic growth now takes depends much on government vision and leadership in driving eco-innovation. Innovation is essential for greening growth. Government role in shaping direction of innovation is inevitable: government cannot simply ‘get out of the way’. Innovation policy is not currently aligned with aspirations for a green economy. A more active, dynamic approach is required.
Testis response to low doses of cadmium in Wistar rats

Although it is well known that cadmium (Cd) causes adverse effects on male rat reproductive organs, few studies have quantified alterations caused by its low doses. Quantification of these alterations, especially in the testis, was measured using morphometry. A single dose of cadmium chloride (1 or 1.2 mg/kg BW) was injected i.p. in adult rats, killed after 7 or 56 days. The lower dose caused slight alterations as measured by morphometrical analysis. The higher dose caused significant reduction in testis and epididymis weight, gonadossomatic index and length of seminiferous tubule (ST) after 7 and 56 days. Cadmium significantly reduced the ST diameter after 56 days. Decreased volume density of ST, after 7 and 56 days, was accompanied by an increase in interstitium volume density. The damage caused by the dose of 1.2 mg/kg can be clearly observed with light microscope. After 7 days, the tubule lumens were filled with degenerated germ cells and multinucleated spermatid aggregates. Vacuolization of the seminiferous epithelium was also observed. After 56 days, increased damage resulted in vacuolated ST, consisting only of Sertoli cells. Scanning electron microscopy examination of the testis showed that, in the group cadmium treated (1.2 mg/kg) and killed after 56 days, the interstitial tissue presents a compact and fibrous appearance with absence of fenestrae. The seminiferous epithelium height diminished and the absence of spermatozoa can be noted. The results show that a very small difference of Cd dose causes a sudden increase in testicular damage, apparently overpowering this tissue’s natural defences.
Cell-based graph cut for segmentation of 2D/3D sonographic breast images

Boundary delineation is the fundamental basis of many sonographic image analyses. In sonographic breast lesion images, it's complicated and time consuming for physicians to delineate the lesion boundaries. When it comes to three dimensional sonographic breast lesions image, delineation of lesion boundary becomes much more complicated. Taking advantage of cell competition algorithm along with its good region structure, generated cells can be served as elegant nodes for graph cut. Further, a similar weight function plays an important role in the estimation of lesion boundary to avoid visible weak edge and isolated node in graph cut. The integration of cell competition and graph cut can be intuitively implemented in three dimensional images, in addition to the reduction of computational time. With efficiency and accuracy of lesion detection, a computer aided system was therefore developed to fulfill clinical applications.
Power-, delay-, and emergency-efficient protocol for ubiquitous wireless sensor networks of silver town

A power- and delay-efficient routing algorithm and emergency-efficient protocol for ubiquitous wireless sensor networks of silver town is presented. For this protocol, the fixed nodes (without any limited resources) are established to one point which can communicate with one-hop to both the sink node and the mobile sensor nodes in the dark region (in which mobile sensor nodes can not communicate to the sink node). The fixed nodes are operated like the fixed cluster header. Our protocol is simulated by using the simulation program for wireless sensor networks. The simulated life time of our routing algorithm is longer than those of LEACH-C and multi-hop and the simulated time delay of our routing algorithm is 1.5 times as fast as one of LEACH-C.
One cell-one immunoglobulin. Origin of limited heterogeneity of myeloma proteins.

Plasma-cell tumour 5563 forms a single molecular species of immunoglobulin IgG(2)a, i.e. one variant of heavy chain and one variant of light chain. The molecules formed are labile and undergo alterations in charge properties, which rapidly lead to heterogeneity of the myeloma protein after synthesis. The single immunoglobulin species originally formed is found only after the shortest time-intervals tested, i.e. 10min incubation. Two types of changes in charge properties take place: (1) The originally formed protein (component o) is converted via an intermediate o' into the most basic form of 5563 myeloma protein found in serum (component a). Charge differences between these components are suppressed at pH8.9, but can be studied by chromatography at pH6.5 or by analysis of isoelectric points by isoelectric focusing in polyacrylamide gel. The conversion of components o and o' into component a apparently commences soon after assembly of the molecules and proceeds to completion extracellularly. (2) The second type of charge difference that distinguishes components a, b, c and d is exhibited over the pH range 6.0-8.9, but not at acid pH, and has been studied by electrophoresis at pH8.9, by chromatography and by isoelectric focusing. Conversion of component a into components b, c, d and e is only partial so that all five components can be found at decreasing concentrations in serum. Both types of charge alteration can be effected in vitro in the presence of serum, with optimum pH8.0. None of the charge differences could be attributed to the secretion process, since a component with the same isoelectric point as component o was found in secreted myeloma protein (1h). We have found no evidence to support the idea that the first type of change from component o to component a is due to ring formation of N-terminal [(14)C]glutamine into pyrrolid-2-one-5-carboxylic acid; however, our findings do not exclude this process happening very rapidly to a precursor of component o, possibly the polypeptide chain during or immediately after synthesis. In studying this point we noted that not only the heavy chains but also the kappa-type light chain of mouse 5563 myeloma protein have a blocked N-terminus.
Toward Mechanism‐based Antioxidant Interventions

It is generally accepted that one of the major and important contributions to skin aging, skin disorders, and skin diseases results from reactive oxygen species. More than other tissues, the skin is exposed to numerous environmental chemical and physical agents, such as ultraviolet light, causing oxidative stress. Accelerated cutaneous UV‐induced aging, photo aging, is only one of the harmful effects of continual oxygen radical production in the skin. Interestingly, our ELISA assays of 8‐oxo‐2′‐deoxyguanosine in skin of young and old Balb/c mice showed that cumene hydroperoxide‐induced accumulation of the biomarker of oxidative DNA damage in skin of 32‐week‐old mice occurred independently of their vitamin E status, while no accumultaion of oxo8‐dG was detectable in the skin of young animals. This suggests that vitamin E is not the major protector of skin against cumene hydroperoxide‐induced oxidative stress. Production and accumulation of apoptotic cells is one of the characteristic features of skin damage by oxidative stress that, in the absence of effective scavenging by macrophages, dramatically enhances oxidative damage and inflammatory response. In our model experiments, we demonstrated that Cu‐OOH induces significant oxidative stress in phospholipids of normal human epidermal keratinocytes (NHEK) whose characteristic feature is an early and profound oxidation of phosphatidylserine (PS), likely related to PS externalization. Since externalized PS is a signal for recognition of apoptotic cells by macrophage scavenger receptors, PS oxidation may be translatable into elimination of thus damaged NHEKs. Experiments are now underway to determine whether inhibition of PS oxidation by antioxidants may interfere with improtant signaling functions of oxidative stress in eliminating apoptotic cells.
Rotational angiography assessment of cerebral aneurysms.

PURPOSE To compare rotational angiography with conventional digital subtraction angiography in the assessment of cerebral aneurysms. METHODS Conventional digital subtraction angiography and rotational angiography were compared in 57 patients investigated for the preoperative diagnosis of subarachnoid hemorrhage and in 13 patients after surgery. Images were compared for location, visibility of the aneurysmal neck, vascular branch anatomy, projection, size, presence of spasm, and shape of the aneurysm. RESULTS Rotational angiography was superior to the digital angiogram in assessing aneurysms and vascular anatomy in the following percentage of cases: 12% for location, 46% for the presence of a neck, 32% in the assessment of branch anatomy, 19% for projection, 12% for size, 3.5% for spasm, and 19% for shape. After surgery, rotational angiography more clearly demonstrated the presence or absence of a neck in 69% of the cases. CONCLUSIONS Rotational angiography often allows better visualization of vascular anatomy and therefore improves the angiographic assessment of aneurysms when compared with conventional digital subtraction angiography, making it an excellent adjunct in the investigation of subarachnoid hemorrhage. The lack of subtraction artifacts from the surgical clips and multiple angles of view also allow better assessment of the presence or absence of a residual neck in postoperative cases.