Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Supplementation With Methionine and Homocysteine Promotes Early Atherosclerosis but Not Plaque Rupture in ApoE-Deficient Mice

Hyperhomocysteinemia is an independent risk factor for atherothrombosis. However, causality is unproven, and it remains unknown whether hyperhomocysteinemia promotes atherosclerosis, plaque rupture, and/or thrombosis. We evaluated the short- and long-term effects of hyperhomocysteinemia on plaque size and structure in 99 atherosclerosis-prone apolipoprotein E-deficient mice. Hyperhomocysteinemia was induced by methionine (Met) or homocysteine (HcyH) supplementation: low Met (+11 g Met/kg food), high Met (+33 g Met/kg food), low HcyH (0.9 g HcyH/L drinking water), and high HcyH (1.8 g HcyH/L drinking water). Met and HcyH supplementation significantly raised plasma total homocysteine levels by 4- to 16-fold above those observed in mice fed a control diet (up to 146.1 &mgr;mol/L). Compared with controls, aortic root plaque size was significantly larger in supplemented groups after 3 months (56% and 173% larger in high-Met and high-HcyH, respectively) but not after 12 months. Hyperhomocysteinemia was associated with an increase in the amount of collagen in plaques after both 3 and 12 months. Mechanical testing of the tail tendons revealed no weakening of collagen after 12 months of hyperhomocysteinemia. Many plaques in both control and supplemented mice appeared rupture prone morphologically, but all aortic root plaques and all but 1 coronary plaque had an intact surface without rupture or thrombosis. Thus, diet-induced hyperhomocysteinemia promotes early atherosclerosis and plaque fibrosis but does not, even in the long term, weaken collagen or induce plaque rupture.
Does Trophic Status Enhance or Reduce the Thermal Tolerance of Scleractinian Corals? A Review, Experiment and Conceptual Framework

Global warming, and nutrient and sediment runoff from coastal development, both exert increasing pressures on coastal coral reefs. The objective of this study was to resolve the question of whether coastal eutrophication may protect corals from thermal stress by improving their nutritional status, or rather diminish their thermal tolerance through the synergy of dual stressors. A review of previous studies on the topic of combined trophic status and heat exposure on the thermal tolerance of corals reveals a broad range of outcomes, including synergistic, additive and antagonistic effects. We conducted a 90-day long experiment exposing corals to realistic levels of elevated nutrients and sediments, and heat stress. Colonies of two common scleractinian corals (Acropora millepora and Montipora tuberculosa) were kept in coastal seawater, or coastal seawater that was further organically and nutrient enriched (OE), and/or enriched with nitrate. Batches of OE were created daily, facilitating nutrient uptake, plankton succession and organic enrichment as observed in coastal waters. After 10 days of acclimation, 67% of the colonies had their temperature gradually increased from 27° to 31.2°C. After 3–7 weeks of heat stress, colonies of both species had significantly greater reductions in fluorescence yields and lower survival in OE than without addition of OE. Furthermore, photophysiological recovery was incomplete 31–38 days after ending the heat stress only in the OE treatments. Nitrate alone had no measurable effect on survival, bleaching and recovery in either species. Skeletal growth rates were reduced by 45% in heat-stressed A. millepora and by 24% in OE-exposed M. tuberculosa. We propose a conceptual trophic framework that resolves some of the apparently contradictory outcomes revealed by the review. Our study shows that management actions to reduce coastal eutrophication can improve the resistance and resilience of vulnerable coastal coral reefs to warming temperatures.
Direct Analytical Methods for Solving Poisson Equations in Computer Vision Problems

Direct analytical methods are discussed for solving Poisson equations of the general form Delta u=f on a rectangular domain. Some embedding techniques that may be useful when boundary conditions (obtained from stereo and occluding boundary) are defined on arbitrary contours are described. The suggested algorithms are computationally efficient owing to the use of fast orthogonal transforms. Applications to shape from shading, lightness and optical flow problems are also discussed. A proof for the existence and convergence of the flow estimates is given. Experiments using synthetic images indicate that results comparable to those using multigrid can be obtained in a very small number of iterations. >
Macromolecular Crowding Compacts Unfolded Apoflavodoxin and Causes Severe Aggregation of the Off-pathway Intermediate during Apoflavodoxin Folding*

To understand how proteins fold in vivo, it is important to investigate the effects of macromolecular crowding on protein folding. Here, the influence of crowding on in vitro apoflavodoxin folding, which involves a relatively stable off-pathway intermediate with molten globule characteristics, is reported. To mimic crowded conditions in cells, dextran 20 at 30% (w/v) is used, and its effects are measured by a diverse combination of optical spectroscopic techniques. Fluorescence correlation spectroscopy shows that unfolded apoflavodoxin has a hydrodynamic radius of 37 ± 3 Å at 3 m guanidine hydrochloride. Förster resonance energy transfer measurements reveal that subsequent addition of dextran 20 leads to a decrease in protein volume of about 29%, which corresponds to an increase in protein stability of maximally 1.1 kcal mol–1. The compaction observed is accompanied by increased secondary structure, as far-UV CD spectroscopy shows. Due to the addition of crowding agent, the midpoint of thermal unfolding of native apoflavodoxin rises by 2.9 °C. Although the stabilization observed is rather limited, concomitant compaction of unfolded apoflavodoxin restricts the conformational space sampled by the unfolded state, and this could affect kinetic folding of apoflavodoxin. Most importantly, crowding causes severe aggregation of the off-pathway folding intermediate during apoflavodoxin folding in vitro. However, apoflavodoxin can be over expressed in the cytoplasm of Escherichia coli, where it efficiently folds to its functional native form at high yield without noticeable problems. Apparently, in the cell, apoflavodoxin requires the help of chaperones like Trigger Factor and the DnaK system for efficient folding.
Affinity selection of DNA-binding protein complexes using mRNA display

Comprehensive analysis of DNA–protein interactions is important for mapping transcriptional regulatory networks on a genome-wide level. Here we present a new application of mRNA display for in vitro selection of DNA-binding protein heterodimeric complexes. Under improved selection conditions using a TPA-responsive element (TRE) as a bait DNA, known interactors c-fos and c-jun were simultaneously enriched about 100-fold from a model library (a 1:1:20 000 mixture of c-fos, c-jun and gst genes) after one round of selection. Furthermore, almost all kinds of the AP-1 family genes including c-jun, c-fos, junD, junB, atf2 and b-atf were successfully selected from an mRNA display library constructed from a mouse brain poly A+ RNA after six rounds of selection. These results indicate that the mRNA display selection system can identify a variety of DNA-binding protein complexes in a single experiment. Since almost all transcription factors form heterooligomeric complexes to bind with their target DNA, this method should be most useful to search for DNA-binding transcription factor complexes.
Epipolar Plane Image Refocusing for Improved Depth Estimation and Occlusion Handling

In contrast to traditional imaging, the higher dimensionality of a light ﬁeld offers directional information about the captured intensity. This information can be leveraged to estimate the disparity of 3D points in the captured scene. A recent approach to estimate disparities analyzes the structure tensor and evaluates the orientation on epipolar plane images (EPIs). While the resulting disparity maps are generally satisfying, the allowed disparity range is small and occlusion boundaries can become smeared and noisy. In this paper, we ﬁrst introduce an approach to extend the total allowed disparity range. This allows for example the investigation of camera setups with a larger baseline, like in the Middlebury 3D light ﬁelds. Second, we introduce a method to handle the difﬁculties arising at boundaries between fore-and background objects to achieve sharper edge transitions.
Effects of four Ni-Ti preparation techniques on root canal geometry assessed by micro computed tomography.

AIM The aim of this study was to compare the effects of four preparation techniques on canal volume and surface area using three-dimensionally reconstructed root canals in extracted human maxillary molars. In addition, micro CT data was used to describe morphometric parameters related to the four preparation techniques. METHODOLOGY A micro computed tomography scanner was used to analyse root canals in extracted maxillary molars. Specimens were scanned before and after canals were prepared using Ni-Ti - K-Files, Lightspeed instruments, ProFile.04 and GT rotary instruments. Differences in dentine volume removed, canal straightening, the proportion of unchanged area and canal transportation were calculated using specially developed software. RESULTS Instrumentation of canals increased volume and surface area. Prepared canals were significantly more rounded, had greater diameters and were straighter than unprepared canals. However, all instrumentation techniques left 35% or more of the canals' surface area unchanged. Whilst there were significant differences between the three canal types investigated, very few differences were found with respect to instrument types. CONCLUSIONS Within the limitations of the micro CT system, there were few differences between the four canal instrumentation techniques used. By contrast, a strong impact of variations of canal anatomy was demonstrated. Further studies with 3D-techniques are required to fully understand the biomechanical aspects of root canal preparation.
Management of rheumatoid arthritis in Poland – where daily practice might not always meet evidence-based guidelines

Introduction International recommendations are intended to help rheumatologists in the effective management of rheumatoid arthritis (RA) through an evidence-based approach. This research aimed to evaluate management patterns and associated difficulties encountered by rheumatologists in daily practice. Material and methods Interviewers recruited 101 Polish rheumatologists in a random quota-based, nationwide sample of outpatient clinics. Quantitative data were input online using a computer-assisted web interview tool. Results Disease-modifying antirheumatic drugs (DMARDs) are not initiated at the time of diagnosis in 15% of RA patients, most often due to difficulties in patient-provider communication. The RA activity is assessed every 4 to 6 months by 30% of rheumatologists, and 64% of patients are reported to never achieve remission. Composite indices are the most reliable indicators of remission only for 38% of responders. Despite inadequate disease control with ≥ 2 treatment schedules with synthetic DMARDs, 34% of these patients are not considered for biological DMARDs (bDMARDs). Contraindications and reimbursement barriers are the most frequently stated reasons. Therapy with glucocorticoid (GC) lasting over 3 months is reported by 70% of rheumatologists. International recommendations are stated as the most common basis for treatment decisions. Conclusions Awareness of recommendations is not sufficient to ensure their application in clinical practice. Inadequate management of RA is quite prevalent, with a substantial contribution of non-medical factors. Daily practice mainly deviates from guidelines regarding frequency and mode of monitoring measures, time to DMARD initiation, and duration of GC treatment. Education programs and policy changes may significantly narrow the gap between evidence and practice.
Control delay in Reinforcement Learning for real-time dynamic systems: A memoryless approach

Robots controlled by Reinforcement Learning (RL) are still rare. A core challenge to the application of RL to robotic systems is to learn despite the existence of control delay - the delay between measuring a system's state and acting upon it. Control delay is always present in real systems. In this work, we present two novel temporal difference (TD) learning algorithms for problems with control delay. These algorithms improve learning performance by taking the control delay into account. We test our algorithms in a gridworld, where the delay is an integer multiple of the time step, as well as in the simulation of a robotic system, where the delay can have any value. In both tests, our proposed algorithms outperform classical TD learning algorithms, while maintaining low computational complexity.
Are IT interventions for girls a special case?

Over the past two decades, numerous interventions have been conducted to inform and inspire schoolgirls into studies and a career in computing and technology. Two successful intervention of this kind have been held over a number of years, and this paper presents the initial stages of a longitudinal study which evaluates the qualitative data from the survey from six Australian events in total. The paper explores the motivational aspects of the presentations in the context of the responses from students and teachers, and it highlights the importance of ensuring that presentation sessions at these events are fun, funny and interesting, and the importance of considering the age of the target audience. It concludes by raising a concern.
Kainate Receptors Regulate Unitary IPSCs Elicited in Pyramidal Cells by Fast-Spiking Interneurons in the Neocortex

Unitary IPSCs elicited by fast-spiking (FS) interneurons in layer V pyramidal cells of the neocortex were studied by means of dual whole-cell recordings in acute slices. FS to pyramidal cell unitary IPSCs were depressed by (RS)-S-amino-3-(3-hydroxy-5-tert-butylisoxazol-4-yl) (ATPA), a kainate (KA) receptor agonist, and by the endogenous agonist l-glutamate in the presence of AMPA, NMDA, mGluR, and GABAB receptor antagonists. This effect was accompanied by an increase in failure rate of synaptic transmission, in the coefficient of variation, and in the paired pulse ratio, indicating a presynaptic origin of the IPSC depression. Pairing the activation of the presynaptic neuron with a depolarization of the postsynaptic cell mimicked the decrease of unitary IPSCs, and this effect persisted when postsynaptic sodium action potentials were blocked with the local anesthetic QX314. The effects of ATPA, glutamate, and of the pairing protocol were almost totally blocked by CNQX. These data suggest that KA receptors located on presynaptic FS cell terminals decrease the release of GABA and can be activated by glutamate released from the somatodendritic compartment of the postsynaptic pyramidal cells.
PERCHLORIC ACID EXTRACTION OF DEOXYRIBONUCLEIC ACID FROM THIN SECTIONS OF EPON-ARALDITE-EMBEDDED MATERIAL

A method is presented for the extraction of deoxyribonucleic acid from thin sections of tissue fixed in glutaraldehyde and osmium tetroxide and embedded in water-insoluble epoxy resin. Incubation of thin sections in 20% perchloric acid at 60°C for 8 hr produced electron-transparent bands in the polytene chromosomes from Drosophila salivary glands. Chromosome bands were also rendered electron-transparent when hydroxypropylmethacrylate-embedded thin sections were digested with deoxyribonuclease or extracted with perchloric acid. Nucleolar ribonucleic acid was unaffected by the perchloric acid extraction.
Η δυναμική των τοπικών προϊόντων στις αστικές αγορές

Περίληψη Οι καταναλωτές στρέφονται ολοένα και περισσότερο στα τοπικά – παραδοσιακά ή ακόμα και ιδιότυπα προϊόντα, τα οποία θεωρούνται ανώτερης ποιότητας σε σύγκριση με τα βιομηχανοποιημένα. Αν και οι ακριβείς λόγοι που οδήγησαν σε αυτή τη στροφή δεν είναι απόλυτα σαφείς, οι διατροφικές κρίσεις των τελευταίων ετών, οι αυξανόμενες ανησυχίες για το περιβάλλον, αλλά και οι ανησυχίες των καταναλωτών για την ποιότητα και την ασφάλεια των τροφίμων, μπορούν να θεωρηθούν ως ενδεικτικές αιτίες (Renting κ.ά., 2003, Morris και Young, 2000). Σκοπός της παρούσας εργασίας είναι η διερεύνηση της δυναμικής των τοπικών προϊόντων μέσω των στάσεων των καταναλωτών. Πιο συγκεκριμένα, πραγματοποιήθηκε έρευνα στο πολεοδομικό συγκρότημα Θεσσαλονίκης, σε τυχαίο δείγμα 350 καταναλωτών με τη χρήση ερωτηματολογίου και μελετήθηκαν οι απόψεις των καταναλωτών για τα τοπικά προϊόντα, ο τρόπος με τον οποίο ενημερώνονται για αυτά και η προθυμία τους να πληρώσουν μία επιπλέον τιμή για την αγορά τους. Η εκτίμηση της ποιότητας των τελικών δεδομένων πραγματοποιήθηκε με τη χρήση του στατιστικού προγράμματος LISREL 8.54 και στη συνέχεια διαμορφώθηκε ένα υπόδειγμα η εκτίμηση του οποίου έγινε με την εφαρμογή ανάλυσης διαδρομών (Path Analysis). Τα αποτελέσματα που προέκυψαν δείχνουν ποια κοινωνικοδημογραφικά χαρακτηριστικά επηρεάζουν την αγορά τοπικών προϊόντων και ποιοι παράγοντες προσδιορίζουν τους λόγους αγοράς τοπικών προϊόντων. Λέξεις κλειδιά: τοπικά προϊόντα, LISREL, ανάλυση διαδρομών (Path Analysis), συμπεριφορά καταναλωτή
Attack Pattern Discovery in Forensic Investigation of Network Attacks

We mine the logs of network traffic data to find the contexts of attacks; we call them attack patterns. We propose an iterative algorithm for discovering attack patterns via a feedback mechanism, with the degrees of belief for attack instances propagated to the next iteration to further refine the search. Our simulations verify that the algorithm achieves accuracy in discovering attack patterns. Our attack pattern discovery has the additional advantage of being an unsupervised algorithm, e.g., it does not require a priori user-defined thresholds.
Racial/Ethnic Disparities in Primary Care: The Role of Physician-Patient Concordance

BackgroundResearch suggests that racial/ethnic concordance (matching) between patients and physicians improves quality of care for minority patients by reducing discrimination in the clinical encounter. ObjectiveExamine the impacts of patient and physician race/ethnicity, and racial/ethnic concordance, on primary care outcomes including blood pressure, tobacco use, and cholesterol screening and tobacco use counseling. Research DesignMultivariate regression analysis of 8160 visits by white and minority patients to 661 primary care physicians using the 2001 to 2003 National Ambulatory Medical Care Survey. I estimated models based on physicians who see both white and minority patients and include physician fixed-effects to correctly measure the contribution of concordance. ResultsConditional on accessing a primary care physician, patient race does not explain differences in rates of these guideline-recommended preventive screenings. Concordance is generally not an important predictor of outcomes, though it is associated with rates of cholesterol screening 2 to 3 times higher among black and Hispanic men compared with whites. In contrast, practice patterns vary quite markedly by physicians' race/ethnicity. ConclusionsGiven that physician race is a more powerful predictor of preventive screening than patient-physician concordance, minority patients may receive some guideline-recommended care at lower rates in concordant pairs. Addressing physician education and training to ensure practice that is consistent with preventive care guidelines may be important. Forms of discrimination in the clinical encounter thought to be modified by concordance do not appear to drive disparities in these outcomes.
Algorithmic Noise Tolerant (ANT) Architecture based Low Power Multiplier

In this paper, we propose a reliable low power multiplier using ANT architecture with compensation method to reduce the error of fixed-width multiplier for DSP applications. The input number based compensation method is carried out on array multiplier. The proposed architecture not only achieves low power consumption and area efficiency also involves in efficient precision reduction. By using the partial product terms of input correction vector and minor input correction vector, the truncation error is lowered and the hardware complexity of the fixed-width multiplier is simplified. The fixed width RPR is implemented using Xilinx in order to compare the number of Replica’s or Redundancy of the multiplier block. This gives a quite basic understanding of the difference between the proposed and the Fixed width RPR blocks. Finally the multipliers are used in low power FIR filters is implemented Xilinx software.
Searching human actions based on a multi-dimensional time series similarity calculation method

With the rapid performance improvement and popularization of sensor devices, a large amount of human action data can be captured in databases. Classification, recognition, searching, and mining of such human actions are promising applications. Although many of these applications have been developed, searching the large quantity of data, especially given the high dimensionality of the captured temporal data sequence is time-consuming. To reduce this time cost, we use a novel method for approximating a multi-dimensional time-series, named multi-dimensional time-series Approximation with use of Local features at Thinned-out Keypoints (A-LTK). With A-LTK applications for two human motion types, sign language and dancing, we found that the categorization of human action data and the search for the most similar human action became more accurate and reduced the time cost.
Dr aft V ers ion Automatic Segmentation in Concert Recordings

”. music is an art that exists in point of time”. Aaron Copland, What to Listen for in Music Few definitions are adequate to describe music, but a ”point of time” is a concept with which people are familiar. When musicians give concerts they try to create these points in a context, which allows the audience to observe each moment by itself. Concert practice has developed to define the edges of musical points, guided by cues such as clapping, pauses, and concert program notes. This masters thesis investigates how to analyze concert recordings of Western music and their program notes to produce segments, which best fit the boundaries of musical points. Modern segmentation techniques are reviewed and a new method specific to concert recordings is examined.
Malachite: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene

Background Researchers commonly use online tools such as ToppGene to conduct enrichment analyses on gene expression data. This process does not easily allow multiple gene data sets to be analyzed and compared at once. ToppGene requires the user to manually enter gene symbols or other gene identifiers into a text box and to manually sift through forms with many adjustable parameters in order to obtain a downloadable text file of results. This process makes the analysis of multiple sets of genes tedious, time-consuming, and error prone. To address this problem, we developed Malachite, a Python package that enables researchers to perform gene enrichment analyses on multiple gene lists and concatenate the resulting enrichment statistics. In this way, Malachite enables meta-enrichment analyses across multiple data sets. Results To illustrate its use, we applied Malachite to three data sets from the Gene Expression Omnibus comparing gene expression in the large airways of smokers and non-smokers. Biological processes enriched in all three data sets were related to xenobiotic stimulus; molecular functions typically involved nicotinamide adenine dinucleotide phosphate (NADP) activity. Conclusion Malachite enables researchers to automate gene enrichment metaanalyses using ToppGene. Malachite also enhances ToppGene’s gene set analysis of drug-gene relationships by further filtering for FDA approved drugs.