Miracle-dz/UniFAR-FTUs huggingface dataset:
Dicarbonyl/l-Xylulose Reductase: A Potential Biomarker Identified by Laser-Capture Microdissection-Micro Serial Analysis of Gene Expression of Human Prostate Adenocarcinoma

To identify genes involved in prostate carcinogenesis, we used laser-capture microdissection-micro serial analysis of gene expression to construct libraries of paired cancer and normal cells from human tissue samples. After computational comparison of the two libraries, we identified dicarbonyl/l-xylulose reductase (DCXR), an enzyme that catalyzes α-dicarbonyl and l-xylulose, as being significantly up-regulated in prostate cancer cells. The specificity of DCXR up-regulation for prostate cancer tissues was confirmed by quantitative real-time reverse transcriptase-PCR, virtual Northern blot, and Western blot analyses. Furthermore, DCXR expression at the protein level was assessed using fresh-frozen tissues and a tissue microarray consisting of 46 cases of organ-confined early-stage prostate cancer and 29 cases of chemohormonally treated prostate cancer. In most normal prostate epithelial cells, DCXR was expressed at low levels and was localized predominantly in the cytoplasmic membrane. In contrast, in virtually all grades of early-stage prostate cancer and in all chemohormonally treated cases, DCXR was strikingly overexpressed and was localized predominantly in the cytoplasm and nucleus. In all samples, the stromal cells were completely devoid of DCXR expression. Based on these findings, we suggest that DCXR overexpression has the potential to be an additional useful biomarker for prostate cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(12):2615–22)
Asset Price Dynamics with Local Interactions under Heterogeneous Beliefs

This paper investigates the effect of network structure on the asset price dynamics. We propose a simple present value discounted asset pricing model with heterogeneous agents. Every period the agents choose a predictor of the future price on the basis of past performance of their own and alternative strategies and form their demands for a risky asset. The information about the performance of an alternative strategy is available only locally from the directly connected agents. Using the rewiring procedure we produce four types of commonly considered networks: a fully connected network, a regular lattice, a small world, and a random network. The results show that the network structure influences asset price dynamics in terms of the region of stability and volatility. This is mostly due to the different speed of information transmission in the different networks.
Changes in myocardial protein expression in pacing‐induced canine heart failure

Canine rapid ventricular pacing produces a low output cardiomyopathic state which is similar to dilated cardiomyopathy. In this study dogs were paced at 245 beats per minute (bpm) for 3—4 weeks until signs of heart failure were apparent. Unpaced dogs were used as controls. A previous study identified myocardial protein changes in the pH region 4—7 following ventricular pacing by using two‐dimensional electrophoresis (2‐DE) (Heinke et al., Electrophoresis 1998 19, 2021—2030). Many of these proteins were associated with mitochondria, energy metabolism within the cardiomyocyte, the cytoskeleton and calcium cycling. The present study aimed to examine the proteins migrating in the more basic region of the 2‐DE pattern using immobilised pH gradient 3—10 strips to separate myocardial proteins. The expression of 31 proteins was altered in the paced myocardium: 21 were decreased and 10 increased. Following the identification of 23 of these spots by either amino acid compositional analysis or peptide mass fingerprinting or a combination of both, we confirm that many of the proteins whose expression is altered following ventricular pacing are associated with the mitochondria and energy production within the cardiomyocyte, including creatine kinase M, triosephosphate isomerase, phosphoglycerate mutase, cytochrome c oxidase, cytochrome b5, hydroxymethyl glutaryl CoA synthase, myoglobin, and 3,2‐trans‐enoyl‐CoA transferase. Additionally, the cytoskeletal protein actin was increased in the paced hearts. These results strongly support the notion that energy production is impaired and mitochondrial dysfunction is involved in the development of heart failure in the paced dog.
LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants

UNLABELLED Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. AVAILABILITY AND IMPLEMENTATION LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci. nih.gov/LDlink/. CONTACT mitchell.machiela@nih.gov.
Sleep monitoring system based on body posture movement using Microsoft Kinect sensor

Sleep activity is one of important factor to determine quality of human life and closely related with sleep quality, which is influenced by several factors such as daily activities, stress, and fatigue. Current sleep monitoring device is called polysomnography, which is commonly used on sleep monitoring systems in hospital by attaching several electrodes to the subject’s head. However, physical contacts between device and subject may leads to disruption of sleep activity because subject feels uncomfortable. Goal of this study is to design a sleep monitoring system using Microsoft Kinect v.2. This device is able to track movements made by the subject. The subject’s sleep quality is determined by the number of movements during bedtime. Joints displacement in time unit is calculated using the Euclidean distance method to calculate activities during sleep. The sleep monitoring system is designed to recognize subject’s dominant sleep posture by using the boundary location method to divide captured body into three parts that separated with three baseline algorithms. Analysis results of sleep monitoring system output are classification of subject’s sleep quality and the dominant sleep posture. Designed system is tested for 105 minutes and subject’s posture changes per minute are called Minutely Posture Movement (MPM). Sleep quality is classified into 3 categories, namely “Good”, “Normal”, and “Bad”. The classification constants of “Good”, “Normal”, and “Bad” are obtained from Q1 and Q3 of 10 subjects MPM. Value Q1 is 0.08 and value Q3 is 0.15. Subject’s sleep quality is categorized as follows: “Good” on MPM <0.08; “Normal” on 0.08≤MPM <0.15; and “Bad” on MPM≥ 0.15. Based on test results of 10 subjects, categorization of subject’s sleep quality are: 20% “Good”, 50% “Normal”, and 30% “Bad”. Based on dominant posture, the results are 70% yearner, 20% soldier, and 10% fetus. The designed system has 87.38% accuracy and 12.62% relative error.Sleep activity is one of important factor to determine quality of human life and closely related with sleep quality, which is influenced by several factors such as daily activities, stress, and fatigue. Current sleep monitoring device is called polysomnography, which is commonly used on sleep monitoring systems in hospital by attaching several electrodes to the subject’s head. However, physical contacts between device and subject may leads to disruption of sleep activity because subject feels uncomfortable. Goal of this study is to design a sleep monitoring system using Microsoft Kinect v.2. This device is able to track movements made by the subject. The subject’s sleep quality is determined by the number of movements during bedtime. Joints displacement in time unit is calculated using the Euclidean distance method to calculate activities during sleep. The sleep monitoring system is designed to recognize subject’s dominant sleep posture by using the boundary location method to divide captured body into th.
Exosomes Derived from Dendritic Cells Treated with Schistosoma japonicum Soluble Egg Antigen Attenuate DSS-Induced Colitis

Exosomes are 30–150 nm small membrane vesicles that are released into the extracellular medium via cells that function as a mode of intercellular communication. Dendritic cell (DC)-derived exosomes modulate immune responses and prevent the development of autoimmune diseases. Moreover, Schistosoma japonicum eggs show modulatory effects in a mouse model of colitis. Therefore, we hypothesized that exosomes derived from DCs treated with S. japonicum soluble eggs antigen (SEA; SEA-treated DC exosomes) would be useful for treating inflammatory bowel disease (IBD). Exosomes were purified from the supernatant of DCs treated or untreated with SEA and identified via transmission electron microscopy, western blotting and NanoSight. Acute colitis was induced via the administration of dextran sulfate sodium (DSS) in drinking water (5.0%, wt/vol). Treatment with exosomes was conducted via intraperitoneal injection (i.p.; 50 μg per mouse) from day 0 to day 6. Clinical scores were calculated based on weight loss, stool type, and bleeding. Colon length was measured as an indirect marker of inflammation, and colon macroscopic characteristics were determined. Body weight loss and the disease activity index of DSS-induced colitis mice decreased significantly following treatment with SEA-treated DC exosomes. Moreover, the colon lengths of SEA-treated DC exosomes treated colitis mice improved, and their mean colon macroscopic scores decreased. In addition, histologic examinations and histological scores showed that SEA-treated DC exosomes prevented colon damage in acute DSS-induced colitis mice. These results indicate that SEA-treated DC exosomes attenuate the severity of acute DSS-induced colitis mice more effectively than DC exosomes. The current work suggests that SEA-treated DC exosomes may be useful as a new approach to treat IBD.
Numerical Analysis of Thermal Dependence of the Spectral Response of Polymer Optical Fiber Bragg Gratings

The thermal dependence of the spectral response (i.e. transmission, reflection and time delay (τr) responses) of uniform polymer optical fiber (POF) Bragg gratings has been investigated. In addition to the temperature dependence, the effects of grating strength (kLg) and fiber index modulation (∆n) have been investigated. Besides high capability of tunable wavelength due to the unique large and negative thermo-optic coefficient of POF, the spectral response for POF Bragg gratings show high stability and larger spectrum bandwidth with temperature variation compare with the silica optical fiber (SOF) Bragg gratings, especially with the increase of the kLg value. It was found that by increasing kLg, the peak reflectance value increases and the bandwidth of the Bragg reflector become narrower. Also it’s shown by increasing the kLg value, τr deceasing significantly and reach its minimum value at the designed wavelength (λB). Furthermore, the τr for POF Bragg gratings is less than that for SOF Bragg gratings at the same value of kLg. Also it’s found that the peak reflectivity value increases to around 60% when the ∆n value increases from 1x10 -4 to 5x10 -4 .
A novel Heart Rate Variability analysis using Lagged Poincaré plot: A study on hedonic visual elicitation

This paper reports on a novel method for the analysis of Heart Rate Variability (HRV) through Lagged Poincaré Plot (LPP) theory. Specifically a hybrid method, LPPsymb, including LPP quantifiers and related symbolic dynamics was proposed. LPP has been applied to investigate the autonomic response to pleasant and unpleasant pictures extracted from the International Affective Picture System (IAPS). IAPS pictures are standardized in terms of level of arousal, i.e. the intensity of the evoked emotion, and valence, i.e. the level of pleasantness/unpleasantness, according to the Circumplex model of Affects (CMA). Twenty-two healthy subjects were enrolled in the experiment, which comprised four sessions with increasing arousal level. Within each session valence increased from positive to negative. An ad-hoc pattern recognition algorithm using a Leave-One-Subject-Out (LOSO) procedure based on a Quadratic Discriminant Classifier (QDC) was implemented. Our pattern recognition system was able to classify pleasant and unpleasant sessions with an accuracy of 71.59%. Therefore, we can suggest the use of the LPPsymb for emotion recognition.
Changes in the Factor Loadings Across Sectors and Economic Dynamics: Evidence for the Japanese Firms

We estimate the equity premium for Japanese firms using the conditional version of Fama and French three-factor model where only the factor loadings are allowed to change unlike Liew and Vassalou (2000) wherein the factor premiums are allowed to change. Then, with considerations to the cyclical components of outputs with the RBC model we investigate the lead and lag relationships between the equity premium of the industry/sector and the measure of business cycles. We try to find the business-cycles related relationship between the cyclical components of the production index and/or GDP and the expected equity premiums for each industry among different sectors of the economy, notably the consumption goods sector and investment goods sector. The RBC model proposed by Boldrin, Christiano, and Fisher (1995, 2000) suggests that these differences exist. We also add a financial sector into this two sector model and then close the model with suitable equilibrium conditions. Within this model it is inferred that the financial sector will have also different business cycles implications. Furthermore, borrowing from the model proposed by Dias-Gomez et al. (1992), we will also be able to incorporate a banking sector, which would also possess different business cycle implications. The empirical relationship we find between the output fluctuations using a simple H-P filter at this first version of the paper and the equity premium changes for the various sectors of the economy shed a new light into the analysis of the business cycles and the equity premium changes, and hence the evolvement of the economy aggregate risk across different sectors of the economy.
Organization of the songbird basal ganglia, including area X

Area X is a songbird basal ganglia nucleus that is required for vocal learning. Both Area X and its immediate surround, the medial striatum (MSt), contain cells displaying either striatal or pallidal characteristics. We used pathway‐tracing techniques to compare directly the targets of Area X and MSt with those of the lateral striatum (LSt) and globus pallidus (GP). We found that the zebra finch LSt projects to the GP, substantia nigra pars reticulata (SNr) and pars compacta (SNc), but not the thalamus. The GP is reciprocally connected with the subthalamic nucleus (STN) and projects to the SNr and motor thalamus analog, the ventral intermediate area (VIA). In contrast to the LSt, Area X and surrounding MSt project to the ventral pallidum (VP) and dorsal thalamus via pallidal‐like neurons. A dorsal strip of the MSt contains spiny neurons that project to the VP. The MSt, but not Area X, projects to the ventral tegmental area (VTA) and SNc, but neither MSt nor Area X projects to the SNr. Largely distinct populations of SNc and VTA dopaminergic neurons innervate Area X and surrounding the MSt. Finally, we provide evidence consistent with an indirect pathway from the cerebellum to the basal ganglia, including Area X. Area X projections thus differ from those of the GP and LSt, but are similar to those of the MSt. These data clarify the relationships among different portions of the oscine basal ganglia as well as among the basal ganglia of birds and mammals. J. Comp. Neurol. 508:840–866, 2008. © 2008 Wiley‐Liss, Inc.
No association between cytochrome P450 2D6 gene polymorphism and risk of acute leukemia: evidence based on a meta‐analysis

Background Many studies indicated the human cytochrome P450 2D6 (CYP2D6) gene polymorphism was associated with acute leukemia (AL) susceptibility, however, the results were inconsistent. So we performed this meta‐analysis to evaluate the relationship between CYP2D6*3 or CYP2D6*4 polymorphism and AL susceptibility. Methods We searched PubMed database up to February 20, 2013, and finally yielded 9 case‐control studies including 1343 cases and 1843 controls which tested the association between CYP2D6*3 or *4 polymorphism and AL. After data extraction, we conducted a meta‐analysis using the Comprehensive Meta Analysis software. Results Overall, no significant association between CYP2D6*3 or *4 polymorphism and AL risk was found in this meta‐analysis (+ vs. ‐: OR=1.13, 95% CI=0.79‐1.63; +/+ vs. ‐/‐: OR=1.73, 95% CI=0.99‐3.02; ‐/+ vs. ‐/‐: OR=1.03, 95% CI=0.68‐1.56; (‐/+ and +/+) vs. ‐/‐: OR=1.08, 95% CI=0.72‐1.63; +/+ vs. (‐/+ and ‐/‐): OR=1.76, 95% CI=0.98‐3.17). Similar results were also been found in stratified subgroup analysis. There was no publication bias. Conclusion CYP2D6*3 or *4 polymorphism might not be associated with AL susceptibility. However, the results need to be further confirmed by well‐designed and high quality randomized controlled trials with larger sample sizes.
Joint Maximum-Likelihood Channel Estimation and Data Detection for V-BLAST Systems

The maximum-likelihood (ML) detection is the optimal detection for vertical Bell Laboratories layered space-time (V-BLAST) systems if the channel is perfectly known at the receiver. Unfortunately, the perfect channel knowledge is always unavailable in practical systems. In this paper, we investigate the joint design of channel estimation and data detection for V- BLAST systems in spatially correlated channels, and develop an optimal joint channel estimation and data detection scheme under the ML criterion. To reduce its complexity, we also propose a simplified scheme based on list sphere decoding (LSD). Moreover, we analyze its relationship with the conventional optimal channel estimation and the conventional optimal detection, and evaluate its performance by computer simulation.
Comparative allozyme and microsatellite population structure in a narrow endemic plant species, Centaurea corymbosa Pourret (Asteraceae)

Centaurea corymbosa Pourret (Asteraceae) is a narrow endemic species known only from six populations located in a 3‐km2 area in the south of France. Earlier field experiments have suggested that pollen and seed dispersal were highly restricted within and among populations. Consistent with the field results, populations were highly differentiated for five allozyme loci and among‐population variation fitted an isolation‐by‐distance model. In the present study, we investigated the genetic structure of C. corymbosa using six microsatellite loci. As with allozymes, microsatellites revealed no within‐population structure and a large differentiation among populations. However, allozyme loci were less powerful than microsatellites in detecting the extent of gene flow assessed by assignment tests. The patterns of structuration greatly varied among loci for both types of marker; we suggest that differences in single‐locus pattern could mainly be an effect of stochastic variation for allozymes and an effect of variation in mutation rate for microsatellites. In contrast to the multilocus results, the two most polymorphic microsatellite loci did not show any isolation‐by‐distance pattern. Our results suggest that highly variable loci might not always be the best suited markers to quantify levels of gene flow among populations.
Extracellular formation and uptake of adenosine during skeletal muscle contraction in the rat: role of adenosine transporters

1 The existence of adenosine transporters in plasma membrane giant vesicles from rat skeletal muscles and in primary skeletal muscle cell cultures was investigated. In addition, the contribution of intracellularly or extracellularly formed adenosine to the overall extracellular adenosine concentration during muscle contraction was determined in primary skeletal muscle cell cultures. 2 In plasma membrane giant vesicles, the carrier‐mediated adenosine transport demonstrated saturation kinetics with Km= 177 ± 36 μm and Vmax= 1.9 ± 0.2 nmol ml−1 s−1 (0.7 nmol (mg protein)−1 s−1). The existence of an adenosine transporter was further evidenced by the inhibition of the carrier‐mediated adenosine transport in the presence of NBMPR (nitrobenzylthioinosine; 72 % inhibition) or dipyridamol (64 % inhibition; P < 0.05). 3 In primary skeletal muscle cells, the rate of extracellular adenosine accumulation was 5‐fold greater (P < 0.05) with electrical stimulation than without electrical stimulation. Addition of the adenosine transporter inhibitor NBMPR led to a 57 % larger (P < 0.05) rate of extracellular adenosine accumulation in the electro‐stimulated muscle cells compared with control cells, demonstrating that adenosine is taken up by the skeletal muscle cells during contractions. 4 Inhibition of ecto‐5′‐nucleotidase with AOPCP in electro‐stimulated cells resulted in a 70 % lower (P < 0.05) rate of extracellular adenosine accumulation compared with control cells, indicating that adenosine to a large extent is formed in the extracellular space during contraction. 5 The present study provides evidence for the existence of an NBMPR‐sensitive adenosine transporter in rat skeletal muscle. Our data furthermore demonstrate that the increase in extracellular adenosine observed during electro‐stimulation of skeletal muscle is due to production of adenosine in the extracellular space of skeletal muscle and that adenosine is taken up rather than released by the skeletal muscle cells during contraction.
The Research Quality Framework and its implications for health and medical research: time to take stock?

As the Australian university sector awaits final decisions about the introduction and stipulations of a research quality framework (RQF), to assess the quality and impact of research, we have studied international commentary on the value of such exercises. This suggests there is little hard evidence to recommend the proposed RQF. The UK government led the field in 1986 with its research assessment exercise (RAE), which is widely believed to have compromised clinical academic medicine by failing to satisfactorily acknowledge the contribution of clinical academics, not only to research but also to teaching and clinical practice. After the 2008 RAE, the UK government will move to a simpler, metrics‐based system for assessing research quality and allocating funding. The New Zealand Performance Based Review Fund (PBRF), introduced in 2003, is based on a combination of peer review and performance indicators. Several concerns have been raised; among them is the real cost–benefit ratio of participation, with reports that many universities have spent more on the exercise than they will gain in funding increases. The scoring system has received the most criticism and, after the partial round assessment scheduled for this year, the controversial unit of assessment will be reviewed. It might be more cost‐effective for Australia to modify existing research assessment processes than to undertake a potentially costly and arduous exercise.