Miracle-dz/UniFAR-FTUs huggingface dataset:
2 , 3 , 7 , 8-Tetrachlorodibenzo-p-dioxin Upregulates FoxQ 1 b in Zebrafish Jaw

Vertebrate jaw development can be disrupted by exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)—a potent activator of the aryl hydrocarbon receptor (AHR) transcription factor required for transducing the toxic effects of TCDD. We used zebrafish (Danio rerio) embryos to investigate transcriptional responses to TCDD with the goal of discovering novel, jaw-specific genes affected by TCDD exposure. Our results uncovered a novel target of TCDD-activated Ahr belonging to the evolutionarily conserved family of forkhead box transcription factors. Quantitative real-time polymerase chain reaction analysis demonstrated that FoxQ1b was upregulated by TCDD 7and 10fold at 24 and 48 h postfertilization (hpf), respectively. The rate of TCDD-induced FoxQ1b expression was more rapid than that of Cyp1a, a known direct target of TCDD-activated Ahr. TCDDmediated induction of FoxQ1b was suppressed in the presence of an Ahr antagonist, αnaphthoflavone, as well as following knockdown of Ahr2 expression using an Ahr2-specific morpholino antisense oligonucleotide. In situ hybridization analysis of FoxQ1b expression at 48 hpf demonstrated that FoxQ1b is specifically expressed in the jaw primordium where it discretely outlines a developing jaw structure known as Meckel’s cartilage—a conserved structure in all jawed vertebrates that develops abnormally in the presence of TCDD. These results identify a novel target of TCDD-activated Ahr and suggest that FoxQ1b may play a role in craniofacial abnormalities induced by developmental exposure to TCDD.
A Sociotechnical View of Information Diffusion and Social Changes: From Reprint to Retweet

This research in progress study explores the role of Twitter during the 2011 Egypt revolution. Drawing on a research method of historians who investigated the role of print technology during the Protestant Reformation in Western Europe during the early 16th century, we explicate the socio-technical implications of information diffusion through retweeting during radical social changes. Through retweet analysis, we identify inseparable dynamics of (1) existence of a few opinion leaders, (2) a large number of supporting individuals, and (3) the emergence of attendant collective sensemaking process as a critical antecedent of radical social changes.
Paradigms for Non-classical Substitutions

We will present three paradigms for non-classical substitution. Firstly, we have the classical substitution of variables with terms. This is written in a strict categorical form supporting presentation of the other two paradigms. The second paradigm is substitutions of variables with many-valued sets of terms. These two paradigms are based on functors and monads over the category of sets. The third paradigm is the substitution of many-valued sets of variables with terms over many-valued sets of variables. The latter is based on functors and monads over the category of many-valued sets. This provides a transparency of the underlying categories and also makes a clear distinction between set-theoretic operation in the meta language and operations on sets and many-valued sets as found within respective underlying categories.
Extreme Learning Machine for Real Time Recognition of Brazilian Sign Language

The quantity of computing application that interacts with users through gesture or body motion has been growing. Among these applications is the sign language recognizer used to help hearing impaired people. This work proposes an architecture able to recognize Brazilian sign language (LIBRAS) in an embedded platform. The system focuses on a simple feature from 'finger spelling expressions' represented by a series of hands gestural images, and uses the Extreme Learning Machine network to classify them. The proposed structure uses camera images only and does not need any gloves or sensors. The obtained results are 5 times faster and 16 times better than classical approaches.
Focus Spot Reduction by Brush Scrubber Cleaning

of preventive backside cleaning steps. These cleaning steps can be introduced after processes that generated high backside defect counts or right before a lithographic wafer exposure. In this study that was performed at imec’s 300mm cleanroom facility, the study objective was to evaluate the focus spot reduction performance of a stand-alone scrubber in a case study featuring known focus spot generating equipment sets. In the first part of the study, monitoring of various production tools in terms of backside cross-contamination was done. A set of equipment’s that generated high backside defect counts was selected for generating adequate backside contaminated test material for the cleaning evaluation. This backside contaminated test material was used in our cleaning experiments and evaluation of focus spot reduction by performing leveling tests on an immersion scanner that was able to measure out of plane deviations.
A Method of Estimating the Degree of Active Participation During Stepping in a Driven Gait Orthosis Based on Actuator Force Profile Matching

Visual biofeedback with information about the patients' degree of activity is a valuable adjunct to robot-assisted gait training as means of increasing the motivation and participation of the patients during highly repetitive training sessions. In the driven gait orthosis (DGO) Lokomat, an estimation of the patient's activity level was based on man-machine interaction forces as measured at the hip and knee actuators of the exoskeletal device. In an early approach, theoretical assumptions about the expected man-machine interaction forces, due to the varying behavior of the patients, were formulated for the calculation of quantitative biofeedback. In contrast to this theory-based approach, we have developed a novel method where the biofeedback calculations were based on measured reference man-machine interaction force profiles of healthy subjects when walking with different degrees of activity. To account for intrasubject and intersubject variability, reference force profiles were processed in a model to generate multiple force profiles describing each activity state. To estimate the activity of a subject walking in the DGO, the man-machine interaction force profile was measured, matched to each of the generated force profiles, and the best fitting profile of the different activity states was identified by the smallest Euclidian distance, respectively. By calculating the difference between these Euclidian distances, a quantitative estimate of the patient's degree of activity was obtained. The novel method was evaluated and compared to the conventional approach in a study with 18 healthy subjects. This comparison showed that the novel method was more reliable in detecting different activity states and is, therefore, a promising approach for future biofeedback systems.
Electricity Generation with Looped Transmission Networks: Bidding to an ISO

This paper uses a bi-level game to model markets for delivery of electrical power on looped transmission networks. It analyzes the effectiveness of an independent system operator (ISO) when generators (and, in some cases, retailers) with market power bid a single parameter of their linear supply (demand) functions to the ISO. The ISO, taking these bids at face value, maximizes welfare subject to transmission constraints. We find that equilibrium outcomes are sensitive to firms’ strategy spaces: 1. In the presence of transmission congestion and loop flows, supply function equilibria (SFE) are not bounded from above by Cournot equilibria, so Cournot outcomes may be more effcient than SFE, a difference that can be accentuated by increasing the number of rivals at a given node; 2. Allocation of transmission rights to generators can reduce effciency; and 3. Countervailing power on the part of buyers can lower effciency.
Increasing trends of acute myocardial infarction in Spain: the MONICA-Catalonia Study.

AIMS To assess coronary mortality and morbidity secular trends in Spain. METHODS AND RESULTS Acute coronary events occurring in both sexes at ages 35-74 years between 1985 and 1997, were monitored in a geographical area of Catalonia, through a population-based registry. Information was collected from annual discharge lists of 78 hospitals and from death certificates, and validated following the methods and quality control of the World Health Organization MONItoring Trends and Determinants in CArdiovascular Disease Project (MONICA). Registration included 19 119 valid events (14 221 in men, 4898 in women) of which 30% were fatal and 41% were definite acute myocardial infarctions. Average attack rates were 315 per 100 000 (95% CI 300-329) and 80 (75-86) in men and women, respectively. Incidence (first-ever event) rates were 209 (194-224) and 56 (52-60) per 100 000. Attack rates increased annually by 2.1% (0.3-4.1) and 1.8% (-0.9 to +4.6). Average 28-day case fatality was 46% (44-47) in men decreasing significantly by 1.4 and 53% (51-55) in women with no change. Fatal trends remained stable. Nationwide morbidity statistics showed similar trends. CONCLUSION Acute coronary syndromes are rising in Spanish men.
Left ventricular systolic pressure-volume area correlates with oxygen consumption.

In 13 excised, cross-circulated canine hearts, we studied the correlation between left ventricular oxygen consumption per beat (MVO2) and the magnitude of a specific pressure-volume (P-V) area circumscribed by the end-systolic and end-diastolic P-V relationship curves and the systolic segment of the P-V trajectory of a left ventricular contraction. The pressure and volume load of the ventricle were changed with a volume servo pump in order to alter the P-V area, and MVO2 was measured (after each change in the pressure and volume load). In the data collected from both isovolumic and ejecting contractions of each left ventricle contracting with a stable inotropic background, we found a linear correlation between MVO2 and the P-V area. The average correlation coefficient was 0.92 +/- 0.016 (SE). Linear regression analysis yielded the formula: MVO2 (ml/beat) = alpha[P-V area (mmHg.ml/beat)] + b, where alpha, the slope coefficient, was (1.53 +/- 0.14) x 10(-5) and b, which probably represents the basal O2 consumption, was 0.019 +/- 0.003 ml/beta. We propose that the P-V area as defined above may be a good index of ventricular oxygen consumption under a given inotropic background.
Sexual Development in Plasmodium: Lessons from Functional Analyses

Malaria is a devastating global disease with several hundred million clinical cases and just under 1 million deaths each year (http://www.who.int/topics/malaria/). It is caused by protozoan parasites of the genus Plasmodium, which have a complex life cycle in a vertebrate host and a mosquito vector. Malaria parasites are haploid throughout most of this life cycle, replicating by asexual multiplication twice in a mammalian host: in liver hepatocytes (pre-erythrocytic schizogony) and within red blood cells (blood stage schizogony), and once in the mosquito (sporogony). The essential sexual stage occurs at the transmission from vertebrate to insect. Some asexual blood stage parasites develop into either male or female gametocytes (the precursor sex cells) and following ingestion in a mosquito blood meal differentiate further into gametes in the lumen of the mosquito's gut, where fertilization takes place. The core processes of gametocytogenesis, gamete activation, exflagellation, fertilization, and zygote formation are conserved across the species from the human parasite Plasmodium falciparum to the rodent parasite Plasmodium berghei, which is an attractive laboratory model, in part because of its ease of genetic manipulation and the shorter time for the maturation and differentiation of the sexual stages. Here, we focus largely on recent functional studies using reverse genetics that have uncovered many aspects of the parasite's sexual development.
Fast, realistic lighting and material design using nonlinear cut approximation

We present an efficient computational algorithm for functions represented by a nonlinear piecewise constant approximation called cuts. Our main contribution is a single traversal algorithm for merging cuts that allows for arbitrary pointwise computation, such as addition, multiplication, linear interpolation, and multi-product integration. A theoretical error bound of this approach can be proved using a statistical interpretation of cuts. Our algorithm extends naturally to computation with many cuts and maps easily to modern GPUs, leading to significant advantages over existing methods based on wavelet approximation. We apply this technique to the problem of realistic lighting and material design under complex illumination with arbitrary BRDFs. Our system smoothly integrates all-frequency relighting of shadows and reflections with dynamic per-pixel shading effects, such as bump mapping and spatially varying BRDFs. This combination of capabilities is typically missing in current systems. We represent illumination and precomputed visibility as nonlinear sparse vectors; we then use our cut merging algorithm to simultaneously interpolate visibility cuts at each pixel, and compute the triple product integral of the illumination, interpolated visibility, and dynamic BRDF samples. Finally, we present a two-pass, data-driven approach that exploits pilot visibility samples to optimize the construction of the light tree, leading to more efficient cuts and reduced datasets.
Perspectives of Cosmesis following Breast Conservation for Multifocal and Multicentric Breast Cancers

Background. Contemporary data suggest that breast conservation treatment (BCT) for multifocal and multicentric breast cancer (MFMCBC) may be appropriate with noninferior local control rates. However, there is a paucity of data to evaluate patient's satisfaction with cosmetic outcomes after BCT for MFMCBC. This study was performed to bridge this information gap. Methods. All patients treated at the authors' healthcare facility were included in the study. Patients with MFMCBC who were assessed to be eligible for BCT underwent tumour resection using standard surgical techniques with direct parenchymal closure through a single incision. After at least three years of follow-up, they were invited to participate in a survey regarding their cosmetic outcomes. Results. Of a total of 160 patients, 40 had MFMCBC, of whom 34 (85%) underwent successful BCT. Five-year cancer-specific survival and disease-free survival were 95.7%. Twenty of the 34 patients responded to the survey. No patient rated her cosmetic outcome as “poor. ” Analysis indicated low agreement between patients' self-assessment and clinician-directed evaluation of aesthetic results. Conclusion. BCT for MFMCBC is feasible with acceptable survival and cosmetic outcomes. However, there appears to be a disparity between patient and clinician-directed evaluation of cosmetic results which warrant further research.
Grasp analysis as linear matrix inequality problems

Three important problems in the study of grasping and manipulation by multi-fingered robotic hands are: 1) given a grasp characterised by a set of contact points and the associated contact models, determine if the grasp has force closure; 2) if the grasp does not have force closure, determine if the fingers are able to apply a specified resultant wrench on the object; and 3) compute "optimal" contact forces if the answer to problem (2) is affirmative. In this paper, based on an early result by Buss-Hashimoto-Moore (1996), which transforms the nonlinear friction cone constraints into positive definiteness of certain symmetric matrices, we further cast the friction cone constraints into linear matrix inequalities (LMIs) and formulate all three of the problems stated above as a set of convex optimization problems involving LMIs. We perform simulation studies to show the simplicity and efficiency of the LMI formulation to the three problems.
Generation and Functional Characterization of Mice with a Disrupted Glutathione S-Transferase, Theta 1 Gene

Glutathione S-transferase (GST) theta 1 (GSTT1) has been regarded as one of the key enzymes involved in phase II reactions because of its unique substrate specificity. In this study, we generated mice with the disrupted Gstt1 gene (Gstt1-null mice) by gene targeting and analyzed the metabolic properties in cytosolic and in vivo studies. The resulting Gstt1-null mice failed to express the Gstt1 mRNA and GSTT1 protein by reverse transcriptase-polymerase chain reaction analysis and two-dimensional fluorescence difference gel electrophoresis/mass spectrometry analysis, respectively. However, the Gstt1-null mice appeared to be normal and were fertile. In an enzymatic study using cytosolic samples from the liver and kidney, GST activity toward 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), dichloromethane (DCM), and 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) was markedly lower in Gstt1-null mice than in the wild-type controls, despite there being no difference in GST activity toward 1-choloro-2,4-dinitrobenzene between Gstt1-null mice and the wild-type controls. Gstt1-null mice had GST activity of only 8.7 to 42.1% of the wild-type controls to EPNP, less than 2.2% of the wild-type controls to DCM, and 13.2 to 23.9% of the wild-type controls to BCNU. Plasma BCNU concentrations after a single i.p. administration of BCNU to Gstt1-null mice were significantly higher, and there was a larger area under the curve5–60 min (male, 2.30 times; female, 2.28 times, versus the wild-type controls) based on the results. In conclusion, Gstt1-null mice would be useful as an animal model of humans with the GSTT1-null genotype.
Distributed Kalman filtering based on consensus strategies

In this paper, we consider the problem of estimating the state of a dynamical system from distributed noisy measurements. Each agent constructs a local estimate based on its own measurements and on the estimates from its neighbors. Estimation is performed via a two stage strategy, the first being a Kalman-like measurement update which does not require communication, and the second being an estimate fusion using a consensus matrix. In particular we study the interaction between the consensus matrix, the number of messages exchanged per sampling time, and the Kalman gain for scalar systems. We prove that optimizing the consensus matrix for fastest convergence and using the centralized optimal gain is not necessarily the optimal strategy if the number of exchanged messages per sampling time is small. Moreover, we show that although the joint optimization of the consensus matrix and the Kalman gain is in general a non-convex problem, it is possible to compute them under some relevant scenarios. We also provide some numerical examples to clarify some of the analytical results and compare them with alternative estimation strategies.
Serum levels of matrix metalloproteinase-3 in relation to the development of radiological damage in patients with early rheumatoid arthritis.

OBJECTIVE To evaluate the significance of serum matrix metalloproteinase-3 (MMP-3) levels in relation to the development of radiological damage (X-ray damage) in early rheumatoid arthritis (RA). METHODS Serum MMP-3 levels were measured in 46 healthy controls (CTRL), 19 osteoarthritis (OA) and 78 RA patients with joint symptoms for <1 yr at presentation (T0): 48 patients without and 30 with X-ray damage at T0. Serum MMP-3, measured by ELISA, and X-ray damage, scored according to Sharp's method, were assessed at 0, 6, 12 and 24 months. RESULTS MMP-3 levels in CTRL and OA were low or undetectable with no differences between the groups (P=0.19). Levels in RA were higher than in CTRL (P<0.01). Initial MMP-3 levels in patients with X-ray damage at T0 (n=30) were higher than the levels in patients without any X-ray damage during follow-up (n=19) (P<0.01), but were not different from those in patients who developed X-ray damage during the study (n=29) (P=0.11). In the patients without X-ray damage at T0, there was a significant correlation between MMP-3 at T0 and the total X-ray damage after 6 months (r=0.34, P=0.02) and 12 months (r=0.32, P=0.03). This correlation was almost exclusively determined by joint space narrowing in the Sharp score. CONCLUSION The serum MMP-3 level seems to be an indicator for the development of radiological damage in patients with early RA and appears to be particularly indicative of cartilage degradation.
IFN gamma-induced suppression of beta-catenin signaling: evidence for roles of Akt and 14.3.3 zeta

The proinflammatory cytokine interferon γ (IFNγ ) influences intestinal epithelial cell (IEC) homeostasis in a biphasic manner by acutely stimulating proliferation that is followed by sustained inhibition of proliferation despite continued mucosal injury. β-Catenin activation has been classically associated with increased IEC proliferation. However, we observed that IFNγ inhibits IEC proliferation despite sustained activation of Akt/β-catenin signaling. Here we show that inhibition of Akt/β-catenin–mediated cell proliferation by IFNγ is associated with the formation of a protein complex containing phosphorylated β-catenin 552 (pβ-cat552) and 14.3. 3ζ. Akt1 served as a bimodal switch that promotes or inhibits βcatenin transactivation in response to IFNγ stimulation. IFNγ initially promotes β-catenin transactivation through Akt-dependent C-terminal phosphorylation of β-catenin to promote its association with 14.3. 3ζ. Augmented β-catenin transactivation leads to increased Akt1 protein levels, and active Akt1 accumulates in the nucleus, where it phosphorylates 14.3. 3ζ to translocate 14.3. 3ζ/β-catenin from the nucleus, thereby inhibiting β-catenin transactivation and IEC proliferation. These results outline a dual function of Akt1 that suppresses IEC proliferation during intestinal inflammation.
Exploring the molecular pathogenesis and biomarkers of high risk oral premalignant lesions on the basis of long noncoding RNA expression profiling by serial analysis of gene expression

Oral premalignant lesions (OPLs) have malignant transformation potential, with no reliable markers available. This study aimed to assess molecular events to identify biomarkers that can reflect high-risk lesions as predictive factors to tailor clinical decision for patients on the basis of long noncoding RNAs (lncRNA) expression profiling by serial analysis of gene expression. The GSE31021 and GSE8127 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs were identified using the LIMMA package in R language. The genes targeted by lncRNAs were predicted among screened DEGs using Pearson’s correlation. Gene ontology function and Kyoto Encyclopedia of Genes and Genomes pathway analyses were carried out for genes targeted by lncRNAs using the Database for Annotation, Visualization, and Integrated Discovery online tool. A total of 674 DEGs and differentially expressed lncRNAs were screened. Thirty-two interactions of 10 lncRNAs and 524 target genes were predicted. The lncRNA NEAT1 was among the top 10 lncRNAs. The coregulated target genes RP4-684O24, RP11-283I3, and RP11-350G8 were significantly enriched in the immune response and mannosyl-oligosaccharide mannosidase activity. The target genes coregulated by LINC00665 and MIR378D2 were significantly enriched in the ubiquitin-dependent protein catabolic process, ubiquitin-protein ligase activity, and neurotrophin signaling. The lncRNA NEAT1 may play an important role in high-risk lesions. The novel lncRNAs and DEGs identified in OPLs may mediate the immune response and neurotrophin signaling and show ubiquitin ligase activity. These results improve our understanding of the molecular pathogenesis of OPLs and identify some potential targets for early diagnosis of high risk OPLs.