Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of human papillomavirus DNA in urinary bladder carcinoma by in situ hybridisation.

AIMS: To investigate the sensitivity of an in situ hybridisation system to detect human papillomavirus (HPV) infection in transitional cell bladder cancer and to evaluate the advantages of analysing multiple biopsies; to examine the correlation between HPV tumour infection detected by in situ hybridisation and the presence of serum anti-HPV antibodies detected by enzyme linked immunosorbent assay (ELISA); and to relate the presence of viral infection to grade, stage, and follow up in cases of bladder cancer. METHODS: The in situ hybridisation technique was used with broad spectrum and type specific (6/11, 16/18, 31/33/35) probes against HPV DNA in formalin fixed, paraffin embedded tissues from 43 cases of bladder cancer. The results were analysed for the presence and type of papillomavirus and correlated with clinicopathological variables. RESULTS: The presence of HPV DNA was identified by the in situ hybridisation technique in 17 of 43 cases of bladder cancer; 12 of these were serum antibody positive and 10 had had multiple biopsies. Fifteen of the cases that were negative for HPV DNA by in situ hybridisation had positive serum serology when tested by ELISA. In 14 cases, the HPV was either types 16/18 or types 31/33/35, both of which carry high oncogenic risk. The stage (p < 0.05) and grade (NS) of the tumour and the outcome on follow up (p < 0.05) were correlated with the presence of HPV infection. CONCLUSIONS: ELISA is not useful in identifying patients with HPV positive bladder cancer, but the use of several probes and multiple biopsies increases the detection rate of HPV in neoplastic tissues. The association between tumour virus infection and high grade/high stage tumours and worse outcome suggests that HPV infection of neoplastic tissue has a negative effect on the behaviour and evolution of transitional cell bladder carcinoma.
Precoder design for space shift keying in MIMO systems with limited feedback

In multiple-input multiple-output (MIMO) systems adopting space shift keying (SSK), the use of adaptive precoder on transmitter offers the opportunity to improve its performance significantly. One major challenge in precoder operation is the difficulty in obtaining the full channel state information on transmitter (CSIT). In this work, we investigate the precoder design for SSK-MIMO systems with limited feedback through using the codebook for the precoding. We formulate a distortion metric to evaluate the quality of a codebook based on the maximum minimum Euclidean distance criterion and propose a codebook design criterion accordingly. Two effective codebook design algorithms are proposed based on thorough analysis of the criterion. Simulation results show the performance improvement of the proposed codebook-based precoding, and also support our analyses on the codebook design.
Rapid cold-hardening of Drosophila melanogaster (Diptera: Drosophiladae) during ecologically based thermoperiodic cycles.

In contrast to most studies of rapid cold-hardening, in which abrupt transfers to low temperatures are used to induce an acclimatory response, the primary objectives of this study were to determine (i) whether rapid cold-hardening was induced during the cooling phase of an ecologically based thermoperiod, (ii) whether the protection afforded was lost during warming or contributed to increased cold-tolerance during subsequent cycles and (iii) whether the major thermally inducible stress protein (Hsp70) or carbohydrate cryoprotectants contributed to the protection afforded by rapid cold-hardening. During the cooling phase of a single ecologically based thermoperiod, the tolerance of Drosophila melanogaster to 1 h at -7 degrees C increased from 5 +/- 5% survival to 62.5 +/- 7.3% (means +/- S.E.M., N=40-60), while their critical thermal minima (CTmin) decreased by 1.9 degrees C. Cold hardiness increased with the number of thermoperiods to which flies were exposed; i.e. flies exposed to six thermoperiods were more cold-tolerant than those exposed to two. Endogenous levels of Hsp70 and carbohydrate cryoprotectants were unchanged in rapidly cold-hardened adults compared with controls held at a constant 23 degrees C. In nature, rapid cold-hardening probably affords subtle benefits during short-term cooling, such as allowing D. melanogaster to remain active at lower temperatures than they otherwise could.
The Properties of Automatic Gets Modelling

We describe some recent developments in PcGets, and consider their impact on its performance across different (unknown) states of nature. We discuss the consistency of its selection procedures, and examine the extent to which model selection is non-distortionary at relevant sample sizes. The problems posed in judging performance on collinear data are noted. We also describe how PcGets has been extended to assist non-experts in model formulation, handle more variables than observations, and tackle non-linear models.
MicroRNAs modulate the chemosensitivity of tumor cells

MicroRNAs are strongly implicated in such processes as development, carcinogenesis, cell survival, and apoptosis. It is likely, therefore, that they can also modulate sensitivity and resistance to anticancer drugs in substantial ways. To test this hypothesis, we studied the pharmacologic roles of three microRNAs previously implicated in cancer biology (let-7i, mir-16, and mir-21) and also used in silico methods to test pharmacologic microRNA effects more broadly. In the experimental system, we increased the expression of individual microRNAs by transfecting their precursors (which are active) or suppressed the expression by transfection of antisense oligomers. In three NCI-60 human cancer cell lines, a panel of 60 lines used for anticancer drug discovery, we assessed the growth-inhibitory potencies of 14 structurally diverse compounds with known anticancer activities. Changing the cellular levels of let-7i, mir-16, and mir-21 affected the potencies of a number of the anticancer agents by up to 4-fold. The effect was most prominent with mir-21, with 10 of 28 cell-compound pairs showing significant shifts in growth-inhibitory activity. Varying mir-21 levels changed potencies in opposite directions depending on compound class; indicating that different mechanisms determine toxic and protective effects. In silico comparison of drug potencies with microRNA expression profiles across the entire NCI-60 panel revealed that ∼30 microRNAs, including mir-21, show highly significant correlations with numerous anticancer agents. Ten of those microRNAs have already been implicated in cancer biology. Our results support a substantial role for microRNAs in anticancer drug response, suggesting novel potential approaches to the improvement of chemotherapy. [Mol Cancer Ther 2008;7(1):1–9]
Geldanamycin, a Potent and Specific Inhibitor of Hsp90, Inhibits Gene Expression and Replication of Human Cytomegalovirus

The effect of geldanamycin (GA), a specific inhibitor of heat shock protein 90 (Hsp90), on gene expression and replication of human cytomegalovirus (HCMV) was studied in human embryonic lung (HEL) fibroblasts. Kinetic analysis indicated that GA delayed synthesis of major immediate early (MIE), early and late viral proteins, and blocked a second tier of the synthesis of these proteins that occurred in untreated cells after 48 h post-infection (pi). Moreover, when HCMV-infected HEL cells were maintained with medium containing 40 nM GA for 6 days, with medium changes at 2-day intervals, the virus yield was reduced to an undetectable level. On a molecular level, the cellular kinase Akt and the transcription factor NFκB were activated in HCMV-infected cells within 30 min pi. NFκB was shown to be essential for MIE gene expression. However, in GA-treated cells, activation of both Akt and NFκB was greatly inhibited. Because LY294002, an inhibitor of cellular phosphatidylinositol 3-kinase (PI3-K), also prohibited HCMV-mediated activation of Akt and NFκB and synthesis of the MIE proteins, PI3-K signalling was necessary for expressing the MIE genes. These results suggest that the inhibitory effect of GA on HCMV replication is primarily caused by the disruption of the PI3-K signalling pathway, leading to the activation of NFκB, which plays a crucial role in expression of the critical MIE genes.
Diurnal and spatial variation of xylem dielectric constant in Norway Spruce (Picea abies [L.] Karst.) as related to microclimate, xylem sap flow, and xylem chemistry

Spatial and temporal variations in vegetation dielectric properties strongly influence the microwave backscatter characteristics of forested landscapes. This paper examines the relationship between xylem tissue dielectric constant, xylem sap flux density, and xylem sap chemical composition as measured in the stems of two Norway Spruce (Picea abies [L.] Karst.) trees in the Fichtelgebirge region of Northern Bavaria, Germany. Dielectric constant and xylem sap flux were monitored continuously from June through October 1995, at several heights along the tree trunks. At the end of the measurement series, each tree was harvested, and its xylem sap extracted and analyzed to determine the concentrations of amino acids and cations. Results show that the sap flux density was correlated with vapor pressure deficit (VPD) at all heights in the stem. In contrast, the xylem tissue dielectric constant is influenced by VPD but can exhibit a significant temporal lag relative to changes in VPD. This lag varies with position along the tree trunk. The temporal variability of the dielectric constant is compared with both trees at several positions along the tree trunks. Results of xylem sap chemical analysis are presented. We show that spatial and temporal variability in the xylem tissue dielectric constant is influenced not only by water content, but by variations in xylem sap chemistry as well. This has important implications for microwave remote sensing of forested landscapes, as useful information may be acquired regarding stand physiology and water relations and where variations in dielectric properties within individual trees and across geographic areas can be significant error sources for forest inventory mapping.
Sea turtles in the Mediterranean : Distribution, threats and conservation priorities

The Mediterranean Sea is a virtually enclosed basin that is frequented by three sea turtle species. In the last three decades the interest in sea turtles in the Mediterranean has continuously increased, motivated by a growing concern for these threatened animals. There has also been a great interest and need to develop adequate knowledge about their threats and about the biological and ecological parameters that are relevant for their conservation. However, the number of countries, the variety of languages and the number of people involved in the region represent intrinsic difficulties for the diffusion of information and for coordinating large-scale actions. This report approaches these challenges head-on, by providing information about turtle occurrence, threats, conservation status and perspectives for each country. It can also help to diffuse information about successful models and lessons that have been learned throughout the region, and ultimately promote and improve cooperation for conservation.
Spontaneous Action Potentials of Cells in the Canine Sinus Node

Right atria were excised from the hearts of 20 young dogs (15 ± 5 weeks old) and maintained in vitro in order to perform microelectrode impalements. The atria contracted spontaneously for at least 6 hours at a stable rate of 127/min when they were perfused with Krebs-Ringer bicarbonate solution through the sinus node artery. Cells within a small area near the sinus node artery and between tbe superior vena cara and right atrium consistently yielded transmembrane potentials typical of pacemaker cells. This area was verified bistologically to be the midportion of the sinus node. Electrical characteristics of these sinus node pacemaker cells were: maximum diastolic potential, -56 ± 7 mV (mean ± 1 sd); action potential amplitude, 56 ± 8 nrV; overshoot, 0 ± 2 mV. Smooth transitions from phase 4 to phase 0 were always present. From these experiments we conclude that the excised perfused canine right atrium provides a useful new experimental cardiac preparation be cause it maintains stable spontaneous activity for many hours in vitro and the sinus node within it is readily accessible for study by intracellular microelectrodes.
The Relationship Between Plasma Cytokine Levels and Response to Selective Serotonin Reuptake Inhibitor Treatment in Children and Adolescents with Depression and/or Anxiety Disorders.

OBJECTIVE In adults there is growing evidence that antidepressant (AD) treatment results in a decline in inflammatory cytokines. This is the first report, to our knowledge, of the relationship between response to selective serotonin reuptake inhibitor (SSRI) treatment for anxiety and/or depression and cytokine levels in children and adolescents. METHODS Forty-one patients who met Diagnostic and Statistical Manual for Mental Disorders, 4th ed. (DSM-IV) criteria for major depressive disorder (MDD) or anxiety disorders participated in study. Their ages ranged from 9 to 18 (14.12 ± 2.30) years. The patients were treated with fluoxetine for 8 weeks. Plasma concentrations of tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-1β were measured by enzyme linked immunosorbent assays (ELISA) before and after fluoxetine treatment. Clinical response was measured with several scales, including the Children's Depression Rating Scale-Revised (CDRS-R), the Beck Depression Inventory (BDI), and the Screen for Child Anxiety Related Emotional Disorders (SCARED) Results: The overall response rate was 56%. Antidepressant treatment significantly reduced TNF-α levels (p = 0.037), with no significant changes in the levels of IL-6 and IL-1β. All three proinflammatory cytokines were significantly (p < 0.05) higher in SSRI-refractory than in SSRI-responsive patients. CONCLUSIONS Higher levels of TNF-α, IL-6, and IL-1β might predict nonresponse to fluoxetine treatment in children.
Warts (non-genital).

INTRODUCTION Warts are caused by the human papillomavirus (HPV), of which there are over 100 types, which probably infects the skin via areas of minimal trauma. Risk factors include use of communal showers, occupational handling of meat, and immunosuppression. In immunocompetent people, warts are harmless and resolve as a result of natural immunity within months or years. METHODS AND OUTCOMES We conducted a systematic review and aimed to answer the following clinical question: What are the effects of treatments for warts (non-genital)? We searched: Medline, Embase, The Cochrane Library, and other important databases up to June 2008 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). RESULTS We found 12 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. CONCLUSIONS In this systematic, review we present information relating to the effectiveness and safety of the following interventions: intralesional bleomycin; cimetidine; contact immunotherapy; cryotherapy; duct tape occlusion; formaldehyde, glutaraldehyde; homeopathy; photodynamic treatment; pulsed dye laser; surgical procedures; topical salicylic acid; and zinc sulphate.
Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis*

Background: Class I and II diterpene synthases, although poorly understood, generate diverse products. Results: Reported here is the structure of the bifunctional abietadiene synthase and supporting experimental/computational work. Conclusion: Visualization of the class I and II active sites confirms known and implicates new determinants of product formation. Significance: Residues, previously unrecognized, are assigned specific roles in substrate binding and catalysis. Abietadiene synthase from Abies grandis (AgAS) is a model system for diterpene synthase activity, catalyzing class I (ionization-initiated) and class II (protonation-initiated) cyclization reactions. Reported here is the crystal structure of AgAS at 2.3 Å resolution and molecular dynamics simulations of that structure with and without active site ligands. AgAS has three domains (α, β, and γ). The class I active site is within the C-terminal α domain, and the class II active site is between the N-terminal γ and β domains. The domain organization resembles that of monofunctional diterpene synthases and is consistent with proposed evolutionary origins of terpene synthases. Molecular dynamics simulations were carried out to determine the effect of substrate binding on enzymatic structure. Although such studies of the class I active site do lead to an enclosed substrate-Mg2+ complex similar to that observed in crystal structures of related plant enzymes, it does not enforce a single substrate conformation consistent with the known product stereochemistry. Simulations of the class II active site were more informative, with observation of a well ordered external loop migration. This “loop-in” conformation not only limits solvent access but also greatly increases the number of conformational states accessible to the substrate while destabilizing the nonproductive substrate conformation present in the “loop-out” conformation. Moreover, these conformational changes at the class II active site drive the substrate toward the proposed transition state. Docked substrate complexes were further assessed with regard to the effects of site-directed mutations on class I and II activities.
Comparison of four methods of assessing airflow resistance before and after induced airway narrowing in normal subjects.

Four methods for assessing airflow resistance were compared in seven normal adults at baseline and after inducing airway narrowing with inhaled methacholine. Airway resistance (Raw) was measured during panting at 1-2 Hz within a body plethysmograph; total lung resistance was measured by using an esophageal balloon during quiet breathing (RLq) and with doubling of frequency while maintaining the original tidal volume; total respiratory resistance (Rrs) was measured at 6 Hz during forced oscillation applied at the airway opening, and interruption resistance (Rint) was measured at midtidal expiratory flow. Three methods of obtaining Rint after airflow interruption were compared [smooth curve fit of mouth pressure (Pm) back extrapolated to valve closure; two-point linear fit of Pm back extrapolated to 15 ms after closure; and Pm at 100 ms after valve closure]. We found similar basal median values (cmH2O.l-1.s) of Raw (1.3), RLq (1.4), RL of double resting frequency (1.9), Rrs (1.7), and smooth curve fit of Pm back extrapolated to valve closure (1.5); basal values of two-point linear fit of Pm back extrapolated to 15 ms after closure (2.4) and Pm at 100 ms after valve closure (4.4) were considerably larger. After induced airway narrowing, all methods of measuring resistance showed significant increases; these were largest with RLq (median %change of 265) and smallest with the three Rint methods (median %change of 62-72). Rint and Rrs methods had poorer sensitivity for detecting bronchoconstriction than lung resistance of Raw. Of the Rint methods, end interruption pressure was the most sensitive. (ABSTRACT TRUNCATED AT 250 WORDS)
The abundance of nitrogen in starburst nucleus galaxies

We show that the excess of nitrogen emission ob- served in a large sample of Starburst Nucleus Galaxies (SBNGs) can only be explained at a given metallicity by an overabundance of nitrogen with respect to normal Hii regions in the disks of late-type spirals. The N/O ratios in the SBNGs are comparable to the values found in the bulges of normal early-type spirals, which suggests that what we observe could be the main produc- tion of nitrogen in the bulges of these galaxies. The variation of the N/O ratio as a function of metallicity in SBNGs follows a primary + secondary relation, but the increase of nitrogen does not appear as a continuous process. In SBNGs, nitrogen is probably produced by different popula- tions of intermediate-mass stars, which were formed during past sequences of bursts of star formation. This assumption pushes the origin of the main bursts 2-3 Gyrs back in the past. On a cosmological scale, this time interval corresponds to redshifts z 0:2-0:3, where a significant increase of star formation ac- tivity occurred. The origin of the SBNG phenomenon would thus have cosmological implications, it would be related to a more active phase of star formation in the Universe sometime in its recent past.
3-DOF Cartesian Force Limiting Device Based on the Delta architecture for safe physical human-robot interaction

This paper presents a device that significantly improves the safety of ceiling-mounted robots whose end effector orientation remains constant with respect to the vertical direction (e.g. Scara-type robots). The device consists of a three-degree-of-freedom (DOF) parallel mechanism with the Delta architecture on which the revolute actuators have been replaced with torque limiters. The resulting Cartesian force limiting device (CFLD) is implemented as a mechanical connection between the robot and the effector. It is rigid unless excessive forces are applied on the end effector, for example during a collision. The magnitude of force that activates the mechanism is set by properly adjusting the threshold of the torque limiters. Furthermore, a collision can be rapidly detected with a limit switch placed on one of the links of the mechanism and a signal can be sent directly to brakes that will stop the robot, without passing through a controller and thus improving the reliability and reaction-time of the safety system. By mechanically disconnecting the robot from its end effector, the device ensures that the person involved in the collision is only subjected to the inertia of the end effector and thus potential injuries are greatly reduced. This work is the extension of a previous 2-DOF CFLD that was sensitive only to horizontal forces. The new architecture reacts to collisions occuring in any direction and is geometrically optimized for the proposed application.
The Influence of Herding on Departure Choice in Case of an Evacuation : Design and Analysis of a Serious Gaming Experimental Set-up

Extensive research is available on travel choice behaviour which occurs during evacuations in case of natural disasters. Due to the disadvantages of existing data collection techniques, more research is needed to better understand evacuation choice behaviour. The main objective of this thesis is twofold: (1) to develop, apply and assess a new experimental set-up to study evacuation choice behaviour and (2) to quantify the effect of herding on evacuation choice behaviour. The developed experimental set-up consists of the serious game Everscape and a questionnaire. In Everscape, participants are confronted with an earthquake and have to evacuate from a tsunami. The Everscape data consist per second of the exact location and viewing direction of each participant. The questionnaire collects information on characteristics of the participants (e.g. age, gender) and focusses on what participants did during the Everscape part of the experiment and why they did this. In total 14 experiments were conducted in which around 400 people participated. The data collected with these experiments were analysed and two main conclusions were drawn. On the one hand, the results support results from literature, meaning realistic evacuation behaviour is found with the experimental set-up. On the other hand, a first step is made towards validly quantifying the effect of herding behaviour on evacuation decisions with empirical data.