Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of DNA-PKcs and Artemis in Opening Viral DNA Hairpin Termini in Various Tissues in Mice

ABSTRACT A subset of cellular DNA hairpins at double-strand breaks is processed by DNA-dependent protein kinase catalytic subunit (DNA-PKcs)- and Artemis-associated endonuclease. DNA hairpin termini of adeno-associated virus (AAV) are processed by DNA repair machinery; however, how and what cellular factors are involved in the process remain elusive. Here, we show that DNA-PKcs and Artemis open AAV inverted terminal repeat (ITR) hairpin loops in a tissue-dependent manner. We investigated recombinant AAV (rAAV) genome metabolism in various tissues of DNA-PKcs- or Artemis-proficient or -deficient mice. In the absence of either factor, ITR hairpin opening was impaired, resulting in accumulation of double-stranded linear rAAV genomes capped with covalently closed hairpins at termini. The 5′ end of 3-base hairpin loops of the ITR was the primary target for DNA-PKcs- and Artemis-mediated cleavage. In the muscle, heart, and kidney, DNA-PKcs- and Artemis-dependent hairpin opening constituted a significant pathway, while in the liver, undefined alternative pathways effectively processed hairpins. In addition, our study revealed a Holliday junction resolvase-like activity in the liver that cleaved T-shaped ITR hairpin shoulders by making nicks at diametrically opposed sites. Thus, our approach furthers our understanding of not only rAAV biology but also fundamental DNA repair systems in various tissues of living animals.
[Diagnostic application of serum protein pattern and artificial neural network software in breast cancer].

BACKGROUND & OBJECTIVE The progress in proteomics provides a novel platform for early diagnosis of cancer, and screening for new tumor biomarkers. This study was designed to develop and evaluate a diagnostic model of breast cancer with surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) ProteinChip array technology and artificial neural network software. METHODS SELDI-TOF-MS ProteinChip was used to detect serum protein patterns of 49 patients with breast cancer, and 33 healthy women. Diagnostic model was developed, and validated using artificial neural network software. RESULTS An intact diagnostic model from all 253 discrepant protein peaks, and a terse model from the top-scored 4 peaks were built. The diagnostic sensitivity, and specificity of the intact model were 83.33% (15/18), and 88.89% (8/9)u the detection rates of breast cancer of stage I, and stage II-IV using the intact model were 90.00% (9/10), and 75.00% (6/8). The diagnostic sensitivity, and specificity of the terse model were 76.47% (13/17), and 90.00% (9/10)u the detection rates of breast cancer of stage I, and stage II-IV using the terse model were 100.00% (3/3), and 71.43% (10/14). The diagnostic values of these 2 models were similar (P>0.05). Their diagnostic abilities to breast cancer of stage I were not worse than those to breast cancer of stage II-IV (P>0.05). CONCLUSION High sensitivity and specificity achieved by this method show great potential for early diagnosis of breast cancer, and screening for new tumor biomarkers.
Cardiovascular risk and events after liver transplantation. Experiences from 313 consecutive transplants with a follow‐up of 20 years

Cardiovascular diseases (CVD) are the third leading cause of late death after liver transplantation (LT). The old PROCAM score was described in males (aged 35–65 yr) to estimate cardiovascular events after LT. New PROCAM is now available to estimate risks for cardiovascular events in both genders and for a wider age range (25–75 yr). We tested old and new PROCAM in long‐term follow‐up (10 and 20 yr) and described CVD risk factors, kidney function, and immunosuppression over two decades.
Identification and Verification of Novel Rodent Postsynaptic Density Proteins*S

The postsynaptic density (PSD) is a cellular structure specialized in receiving and transducing synaptic information. Here we describe the identification of 452 proteins isolated from biochemically purified PSD fractions of rat and mouse brains using nanoflow HPLC coupled to electrospray tandem mass spectrometry (LC-MS/MS). Fluorescence microscopy and Western blotting were used to verify that many of the novel proteins identified exhibit subcellular distributions consistent with those of PSD-localized proteins. In addition to identifying most previously described PSD components, we also detected proteins involved in signaling to the nucleus as well as regulators of ADP-ribosylation factor signaling, ubiquitination, RNA trafficking, and protein translation. These results suggest new mechanisms by which the PSD helps regulate synaptic strength and transmission.
Collaborative problem solving: integrating theory and practice in the classroom

This report describes our experience in teaching an experimental graduate-level course employing collaborative teaching and learning. It was co-taught by four instructors with various backgrounds in computer science, including mecha-tronics and computational geometry. The course was designed to attract students with either systems or theory backgrounds and during the semester, they identified cooperative robotics problems in active areas of research. The course culminated in collaborative projects where teams of students designed, built and programmed teams of autonomous robots out of Lego MindStorms to solve one of the problems identified earlier. We review our experience with this course, both as teachers and as students. Three of us were the instructors and four of us were the students.
Cardiovascular reactivity during hypnosis and hypnotic susceptibility: Three studies of heart rate variability

Abstract This paper was designed to examine the relationship between hypnotic susceptibility and cardiovascular measures, especially parasympathetic activity, in 3 separate studies. In these studies, neither heart rate nor heart rate variability differed between the high and low hypnotically susceptible individuals at the initial baseline. Furthermore, in the first study, experimental tasks designed to elicit differential sympathetic and parasympathetic cardiac responses demonstrated no interaction with hypnotic susceptibility. Overall, these 3 studies suggest that hypnotic susceptibility in itself is not associated with parasympathetic aspects of either basal cardiac states or cardiac responses. In addition, a hypnotic induction itself did not differentially influence parasympathetic activity for the high versus low susceptible individuals.
D02.04 -communication Network Design (rel.2) Information and Communication Technologies Communication Network Design (rel. 2) -d02.04 Communication Network Design (rel. 2) -d02.04

SUMMARY In this report, divided into 4 chapters, we report the final advances on WP2 and in particular on the task 3.2, " Communication network design ". It corresponds to an extended version of Deliverable 2.1 since it includes some novel contributes, namely Section 2.3. Chapter one introduces the developed arguments and presents parts of the literature review. Chapter two is devoted to network topology design, and offers recent studies on the influence of network topologies on the performance of distributed systems, i.e. systems constituted by many interacting units. Concerning this topic, the paper [9] analyses the performance of the consensus algorithm, which is largely proposed as an efficient and low complexity tool for distributed control, estimation and optimization. The optimal topology for this algorithm, yielding fastest convergence time, is proposed. This topo-logy is described by the de Bruijn graphs. In [27, 15] the properties of the Cayley graphs (again in relation with the consensus algorithm) are analyzed. These graphs are often used as a simple paradigm of geometric graphs, namely graphs in which the nodes are deployed in a geometric space. For this kind of graph topologies quadratic type performance indexes are often considered. Those performance indexes come into the picture when applying consensus algorithms to distributed estimation or control and yield completely different evaluation of the possible choices of the network topologies. In [35, 34] we extend the result for Cayley graphs taking into consideration a special class of geometric graphs, characterized by four purely geometric parameters. The extension is done for the particular class of reversible Markov chains due to the strong analogy they show with resistive electrical networks. Chapter three deals with control applications, and more generally with real-time applications running over wireless sensor networks (WSNs). These systems require the design of dedicated routing protocols and control strategies to cope with the potential random delays and packet losses due to the wireless nature of the WSNs. In this chapter we then address this problem from two points of view. In the first we focus on the design of special routing strategies, namely Unicast Path Diversity (UDP) and Directed Staged Flooding (DSF), that are specifically designed for real-time application: in fact they can trade off lower end-to-end delays with higher packet loss. These two strategies, however, cannot completely remove delays randomness or packet losses. Therefore, for linear dynamical systems, we designed opportune time-varying Kalman filters that compensate …
Restless legs syndrome enhances cardiovascular risk and mortality in patients with end-stage kidney disease undergoing long-term haemodialysis treatment.

BACKGROUND Restless legs syndrome (RLS) is a sensorimotor neurological disorder characterized by paraesthesia, dysaesthesia and the irresistible urge to move the legs especially at night. Its prevalence is much higher among dialysis patients at 12 to 62% compared to 3 to 9% in the general population. Here, we investigated the association between RLS and cardiovascular events risk and laboratory parameters in end-stage kidney disease (ESKD) patients on dialysis. METHODS One hundred ESKD patients undergoing haemodialysis were enrolled in an 18-month prospective observational study. The main outcomes were the associations of RLS with new cardiovascular events and cardiovascular mortality. RESULTS RLS affected 31% of the study population. It was associated with female gender, gradual reduction in residual diuresis, lower albumin (P = 0.039) and inflammation, but not the dialysis parameters Kt/V and URR. During observation, 47% of patients experienced new cardiovascular events (64.5% with and 39.1% without RLS; P = 0.019). New cardiovascular events increased with severity of RLS [intermittent (I-RLS) vs continuous (C-RLS)]. Mortality was 20.0% in all patients, 32.3% in those with and 14.5% in patients without RLS (P = 0.04). In patients with I-RLS, mortality was 23.8% compared to 55.6% in patients with C-RLS (P = 0.014). Multivariate analysis confirmed the relationship between RLS and mortality. CONCLUSIONS This study confirmed the high prevalence of RLS among dialysis patients and the associations between the severity of RLS and the risk of new cardiovascular events and higher short-term mortality.
Pathways between socioeconomic determinants of health

Study objective: Many previous studies on socioeconomic inequalities in health have neglected the causal interdependencies between different socioeconomic indicators. This study examines the pathways between three socioeconomic determinants of ill health. Design, setting, and participants: Cross sectional survey data from the Helsinki health study in 2000 and 2001 were used. Each year employees of the City of Helsinki, reaching 40, 45, 50, 55, and 60 years received a mailed questionnaire. Altogether 6243 employees responded (80% women, response rate 68%). Socioeconomic indicators were education, occupational class, and household income. Health indicators were limiting longstanding illness and self rated health. Inequality indices were calculated based on logistic regression analysis. Main results: Each socioeconomic indicator showed a clear gradient with health. Among women half of inequalities in limiting longstanding illness by education were mediated through occupational class and household income. Inequalities by occupational class were largely explained by education. A small part of inequalities for income were explained by education and occupational class. For self rated health the pathways were broadly similar. Among men most of the inequalities in limiting longstanding illness by education were mediated through occupational class and income. Part of occupational class inequalities were explained by education. Two thirds of inequalities by income were explained by education and occupational class. Conclusions: Parts of the effects of each socioeconomic indicator on health are either explained by or mediated through other socioeconomic indicators. Analyses of the predictive power of socioeconomic indicators on health run the risk of being fruitless, if interrelations between various indicators are neglected.
Efficient Prestressed Concrete-Steel Composite Girder for Medium-Span Bridges

AbstractIn this paper, finite-element analysis (FEA) of the prestressed concrete-steel composite (PCSC) girder is performed to investigate strain and stress distributions in the girder sections and determine the influence of stud distribution on stresses in the concrete bottom flange. Approaches of FEA are discussed for the material and element models of steel, concrete, and strands, and element models of the bond between the concrete and strand and the shear studs, loading and boundary conditions, and convergence issues. A PCSC girder specimen is fabricated and instrumented in the structural laboratory to validate the proposed fabrication and design procedures. FEA and service design using the age-adjusted elasticity modulus method (AEMM) are both validated using the strain profiles at different sections and values of concrete surface strains and camber/deflection. Test results indicate that the cracking moment, ultimate moment, and ultimate shear of the PCSC girder can be well predicted using the AEMM a.
Molecular analysis of human forearm superficial skin bacterial biota

The microbial ecology of human skin is complex, but little is known about its species composition. We examined the diversity of the skin biota from the superficial volar left and right forearms in six healthy subjects using broad-range small subunit rRNA genes (16S rDNA) PCR-based sequencing of randomly selected clones. For the initial 1,221 clones analyzed, 182 species-level operational taxonomic units (SLOTUs) belonging to eight phyla were identified, estimated as 74.0% [95% confidence interval (C.I.), ≈64.8–77.9%] of the SLOTUs in this ecosystem; 48.0 ± 12.2 SLOTUs were found in each subject. Three phyla (Actinobacteria, Firmicutes, and Proteobacteria) accounted for 94.6% of the clones. Most (85.3%) of the bacterial sequences corresponded to known and cultivated species, but 98 (8.0%) clones, comprising 30 phylotypes, had <97% similarity to prior database sequences. Only 6 (6.6%) of the 91 genera and 4 (2.2%) of the 182 SLOTUs, respectively, were found in all six subjects. Analysis of 817 clones obtained 8–10 months later from four subjects showed additional phyla (numbering 2), genera (numbering 28), and SLOTUs (numbering 65). Only four (3.4%) of the 119 genera (Propionibacteria, Corynebacteria, Staphylococcus, and Streptococcus) were observed in each subject tested twice, but these genera represented 54.4% of all clones. These results show that the bacterial biota in normal superficial skin is highly diverse, with few well conserved and well represented genera, but otherwise low-level interpersonal consensus.
Intelligent Dynamic Load Balancing Approach for Computational Cloud

Cloud computing is a new technology, which enables provisioning of resources on demand. It caters anything as service. Clients can scale up or scale down their requirements as per their demand. Load balancing is essentially, complex problem in computational cloud. A computational cloud differs from traditional high performance computing systems because of its heterogeneity among the computing nodes. In order to realize the full potential of cloud computing virtualization is widely used. Through virtualization, it is possible to meet the demands from multiple tenants, without switching on many physical nodes. In this paper, we propose Intelligent Dynamic Load Balancing(IDLB) algorithm for computational cloud. IDLB uses cloud machines, when the local processor becomes overloaded. The objective of IDLB is to provide fairness to all the jobs in the cloud by balancing the load between the virtual machines(VM). In this respect our algorithm uses ram size, bandwidth and image size in determining a balance threshold value of each VM for scheduling the jobs. The IDLB distributes the load evenly to all the virtual machines thus it solves the problem of load imbalance and high migration cost incurred by traditional algorithms.
An Alternative Extension of the FCM Algorithm for Clustering Fuzzy Databases

Several real applications need to manage fuzzy information. Among the languages proposed for this type of data, the Fuzzy SQL (FSQL) language had a great success, seen its great power of modeling and it’s an extension of the well-known SQL language. In this paper, we propose an alternative for FCM algorithm For Fuzzy Database describe with FSQL. The conventional fuzzy clustering algorithms form fuzzy clusters so as to minimize the total distance from cluster centers to data points. However, they cannot be applied in the case where the data vectors are described with FSQL is given. To concretize our approach we used the BDRF described with the GEFRED model, which is supporting the FSQL language.
Effect of Lactose and Dried Whey Supplementation on Growth Performance and Histology of the Immune System in Broilers

The objective of this study was to evaluate the effect of lactose and dried whey supplementation as dietary component on growth performance and histology of lymphoid organs and ileum in broilers. A total of 480 day-old chicks were utilised for 42 days. Animals were assigned randomly to one of three treatments: control, lactose (2.5%), and dried whey (3.85%). Body weight was greater for animals supplemented with lactose or dried whey than for those not supplemented. There were no effects of treatments on feed intake and feed efficiency. In general, the effects of lactose or dried whey supplementation on histology of lymphoid organs and ileum were variable. Plasma cell counts were lower for animals supplemented with lactose than for those supplemented with dried whey. However, the length of intestinal villi during the starter period was greater for experimental groups than for control group.
First trimester tricuspid regurgitation and fetal abnormalities

Abstract Background: Tricuspid regurgitation (TR) is a common sonographic finding during the fetal life. It has been reported in 7% of normal fetuses. It may be associated with aneuploidy and with both cardiac and extracardiac defects. Objectives: In this study, we have looked at the characteristics of fetuses with and without TR at 11+0 to 13+6 weeks’ gestation. Groups were compared with respect to the following variables: prevalence of chromosomal defects; other markers of aneuploidy; fetal cardiac; and extracardiac anomalies. Methods: The study group included women, who underwent an ultrasound examination at 11–13+6 weeks’ gestation between 2009 and 2012. The inclusion criteria were singleton pregnancies with crown-rump length measurements of 45–84 mm where the pregnancy outcome was known. Results: Some 1075 patients met our inclusion criteria including 979 fetuses without TR and 96 with TR. There were 72 cases of aneuploidy diagnosed (6.7%). Isolated TR was found in 53 euploid fetuses (5.2%). All of the TR(+) aneuploid fetuses (n=40) had additional ultrasound markers present. Extracardiac anatomy showed a higher prevalence of abnormalities in the group of TR positives (12.5%) vs. TR negatives (1.6%). Abnormal cardiac findings were more frequent in the TR-positive group independently of chromosomal status and were found in 18.8% of fetuses with TR and in 1.9% with a normal tricuspid flow. Conclusions: TR in combination with other markers is the strongest predictor for aneuploidy. TR, as an isolated parameter, is a poor screening tool both for all and for each individual chromosomal abnormality and congenital cardiac defects.
Color image denoising in wavelet domain using adaptive thresholding incorporating the Human Visual System model

This paper utilizes the characteristics of the Human Visual System (HVS) for obtaining better results in denoising color images corrupted by Gaussian noise. Implementation of the Contrast Sensitivity Function (CSF) of the HVS is done in each of the sub-bands in the wavelet domain. In this paper, an 11-weight Invariant Single Factor (ISF) system is proposed and implemented which outperforms the generally used 6-weight ISF system. The major strength of the incorporation of this vision model is the optimum way in which the scales are distributed among the luminance and chrominance components to achieve better image quality without color degradation. Two adaptive thresholding schemes in the wavelet domain have been used in the denoising process. To evaluate the performance of the algorithm universal image quality index (Q) and Peak Signal-to-Noise Ratio (PSNR) have been used.
Yapay sinir ağları ile finansal tahmin

Bu tez calismasinda Turk Finansal Piyasalarindaki gelismelerin hisse senedi bazindaki degerlendirmesi yapilmaya calisilmistir. Bu sirada Yapay Sinir aglari temel hareket noktasi olarak kabul edilerek, cozume bu yoldan ulasilmaya calisilmistir.Temel olarak bakildiginda yapay sinir aglari Turk finansal piyasalarinda cok basarili sonuclar vermektedir ve bu tez calismasinda Turk finansal piyasalari icin gerekli olan ag yapisi ve parametreleri tespit edilmistir. Bundan sonraki arastirmacilar bu cikarimlari referans olarak kabul edebilirler. Calismamizda 2005 yili kapanis verileri icin 4-5-1 siniraginin cok basarili performans gosterdigi gorulmustur. Uc katmanli yapidan daha fazla katman kullanmak sinir aginin performansini dusurmustur. Yine ayni sekilde ortakatmandaki sinir hucresi sayisini arttirmak herhangi bir fayda saglamamistir. Sinir aginin ogrenim algoritmasi olarak en iyi sonucu verdigi gorulen geriye dogru yayilim algoritmasi secilmis, en onemli ogrenim parametrelerinden olan alpha ve beta degerlerinin her ikisininde 0.1 degerini aldiginda sinir aginin performansinin en iyi sonuca ulastigigorulmustur. Ogrenim fonksiyonlari arasinda ise geriye dogru turevlenebilirligi acisindan diger ogrenim fonksiyonlarindan ayrilan 'sigmoid' fonksiyonu ustun bir performans gostermistir. Girdi degerlerinin normalizasyonu yapilirken de borsa kapanis degerlerinin 0ila 0,9 arasina cekilmesi gerektigi tespit edilmistir. Yine agin performansinin artmasi icin eldeki verilen girdi seti ile test seti arasinda 80'e 20 oraninda paylastirilmasi gerektigi sonucuna varilmistir. Bir diger onemli bulguda agin ilk yaratildigi anda agin agirliklarinin sonuca etkisi ile ilgilidir. Bu noktada agin rastgele degerleri yuzde bir oraninda sonucuzerinde bir etki yaratmaktadir.