Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Throughput Sequencing Reveals Principles of Adeno-Associated Virus Serotype 2 Integration

ABSTRACT Viral integrations are important in human biology, yet genome-wide integration profiles have not been determined for many viruses. Adeno-associated virus (AAV) infects most of the human population and is a prevalent gene therapy vector. AAV integrates into the human genome with preference for a single locus, termed AAVS1. However, the genome-wide integration of AAV has not been defined, and the principles underlying this recombination remain unclear. Using a novel high-throughput approach, integrant capture sequencing, nearly 12 million AAV junctions were recovered from a human cell line, providing five orders of magnitude more data than were previously available. Forty-five percent of integrations occurred near AAVS1, and several thousand novel integration hotspots were identified computationally. Most of these occurred in genes, with dozens of hotspots targeting known oncogenes. Viral replication protein binding sites (RBS) and transcriptional activity were major factors favoring integration. In a first for eukaryotic viruses, the data reveal a unique asymmetric integration profile with distinctive directional orientation of viral genomes. These studies provide a new understanding of AAV integration biology through the use of unbiased high-throughput data acquisition and bioinformatics.
Ischaemia/reperfusion induced cardiac stem cell homing to the injured myocardium by stimulating stem cell factor expression via NF‐κB pathway

Ischaemia/reperfusion (I/R) is a major cause of heart failure. Recently cardiac stem cells (CSCs) were proposed as the most appropriate cell type for heart disease therapy. However, it is still unclear whether I/R can stimulate the CSCs homing to the injured myocardium. Male Sprague–Dawley rats were subjected to a 30‐min ischaemia followed by reperfusion of different intervals. RT‐PCR, western blotting and immunohistochemistry were performed to detect stem cell factor (SCF) expression at mRNA and protein levels respectively. Activation of nuclear factor‐κB (NF‐κB) was determined by electrophoretic mobility shift assay. To assess the homing of CSCs in vivo, BrdU‐labelled CSCs were injected into AV‐groove before induction of ischaemia and examined by immunofluorescent staining in the injured myocardium after I/R. From day 3 to day 6 after reperfusion, the accumulation of CSCs was significantly elevated in the injured area, which was matched with the increased SCF expression during I/R. Pretreatment of rats with NF‐κB inhibitor, N‐acetyl‐l‐cysteine (NAC) not only suppressed NF‐κB activation induced by I/R but also attenuated SCF expression. Further analysis revealed that I/R induced phosphorylation of IκBα after 15 min of reperfusion, and the raised phosphor‐IκBα returned to the basal level at 2 h of reperfusion. In simulated I/R(SI/R) in vitro, it enhanced NF‐κB activation and SCF expression in cultured neonatal rat cardiomyocytes, which was markedly inhibited by NF‐κB decoy oligodeoxynucleotide or NAC. Taken together, our results demonstrated that I/R induced CSCs homing to the injured myocardium by stimulating myocardial SCF expression via activation of NF‐κB.
The Mediating Effects of Social Support and Coping on the Stress-Depression Relationship in Rural and Urban Adolescents

This study examined the relationship between potential risk and protective factors for depression among 167 girls and 343 boys in urban and rural areas of NSW, Australia. The risk and protective factors included social support, coping style, and perceived stress. The results indicated no significant differences in depression and risk and protective factors for rural and urban adolescents. Maladaptive coping (rumination and acting out) and social support (satisfaction and number of supporters) were partial mediators of the relationship between perceived stress and depression with the overall model explaining 66% of the variance in depression. Thus changes to coping and to social support network need to be addressed in any intervention aimed at reducing the impact of perceived stress on depression in adolescents.
Breathing Analysis Using Thermal and Depth Imaging Camera Video Records

The paper is devoted to the study of facial region temperature changes using a simple thermal imaging camera and to the comparison of their time evolution with the pectoral area motion recorded by the MS Kinect depth sensor. The goal of this research is to propose the use of video records as alternative diagnostics of breathing disorders allowing their analysis in the home environment as well. The methods proposed include (i) specific image processing algorithms for detecting facial parts with periodic temperature changes; (ii) computational intelligence tools for analysing the associated videosequences; and (iii) digital filters and spectral estimation tools for processing the depth matrices. Machine learning applied to thermal imaging camera calibration allowed the recognition of its digital information with an accuracy close to 100% for the classification of individual temperature values. The proposed detection of breathing features was used for monitoring of physical activities by the home exercise bike. The results include a decrease of breathing temperature and its frequency after a load, with mean values −0.16 °C/min and −0.72 bpm respectively, for the given set of experiments. The proposed methods verify that thermal and depth cameras can be used as additional tools for multimodal detection of breathing patterns.
Genetic and Functional Analyses of the Actinobacillusactinomycetemcomitans AfeABCD Siderophore-Independent Iron Acquisition System

ABSTRACT The ActinobacillusactinomycetemcomitansafeABCD iron transport system, the expression of which is controlled by iron and Fur, was identified in three different isolates. The protein products of this locus are related to bacterial ABC transporters involved in metal transport. Transformation of the Escherichiacoli 1017 iron acquisition mutant with a plasmid harboring afeABCD promoted cell growth under iron-chelated conditions. However, insertion disruption of each of the afeABCD coding regions abolished this growth-relieving effect. The replacement of the parental afeA allele with the derivative afeA::EZ::TN drastically reduced the ability of A. actinomycetemcomitans cells to grow under iron-chelated conditions.
Web Impact Factors for Iranian Universities

This study investigates the Web Impact Factors (WIFs) for Iranian universities and introduces a new system of measurement. Counts of links to the web sites of Iranian universities were calculated from the output of AltaVista search engine. The WIFs for Iranian universities were calculated by dividing link page counts by the number of pages found in AltaVista for each university at a given point in time. These WIFs were then compared, to study the impact, visibility, and influence of Iranian university web sites. Overall, Iranian university web sites have a low inlink WIF. While specific features of sites may affect an institution's Web Impact Factor, there is a significant correlation between the proportion of English-language pages at an institution's site and the institution's backlink counts. This indicates that for linguistic reasons, Iranian (Persian-language) web sites may not receive and attract the attention that they deserve from the World Wide Web. This raises the possibility that information may be ignored due to linguistic and geographic barriers, and this should be taken into account in the development of the global Web.
Efficient coherent population transfer in NO molecules using pulsed lasers.

Highly efficient and selective population transfer in NO molecules in the electronic ground state (X 2 Π 1/2 ) from the vibrational level υ''=0 to the level υ''=6 is demonstrated. It shows, for the first time with pulsed lasers, that a rather generally applicable scheme for complete control over the level population in atoms and molecules is now available. The efficiency relies on a counterintuitive interaction sequence of two lasers with the molecule in a process of stimulated Raman scattering involving adiabatic passage
A Vision Recognition Based Method for Web Data Extraction

This paper proposes a data extraction method based on visual recognition and Document Object Model(DOM) tree for Deep Pages to extract a large number of Deep Web data in-formation. By utilizing the characteristics of the presentation of Deep Web data and the characteristics of the visual information of the web page, the data region of multiple targets is located, and the data of the data region is extracted accurately by DOM analysis. Experiments were conducted on several travel websites, and test results show that efficiency and accuracy of the extraction are higher than those of the traditional methods.
An end-to-end QoS and security joint management for IPTV service delivery

Today, the IPTV technology is emerging as a new concept for delivering and accessing audiovisual services over IP networks. To allow the transmission of IPTV services on wired and wireless networks, different issues should be overcome regarding scalability, quality of service (QoS) provisioning, security guaranty and terminals heterogeneity. In the IPTV architecture, QoS and security constitute two needs that have to be tightly managed. In this paper, we propose a complete end-to-end architecture for providing IPTV services. This architecture enables managing end-to-end QoS and security, while addressing other issues like the terminal heterogeneity. At first, we describe the architecture which is composed of two segments: the core network and the access network. Then, we detail the different mechanisms which allow managing simultaneously QoS and security for the IPTV streams delivered to heterogeneous mobile terminals. Performances evaluation demonstrates the importance of the joint management of security and QoS.
Endothelial nitric oxide synthase Glu298Asp, 4b/a, and −786T>C gene polymorphisms and the risk of ischemic stroke

Saidi S, Mallat SG, Almawi WY, Mahjoub T. Endothelial nitric oxide synthase Glu298Asp, 4b/a, and −786T>C gene polymorphisms and the risk of ischemic stroke Acta Neurol Scand: 2010: 121: 114–119. © 2009 The Authors Journal compilation © 2009 Blackwell Munksgaard.
Structural and functional analysis of the YAP-binding domain of human TEAD 2

The Hippo pathway controls organ size and suppresses tumorigenesis in metazoans by blocking cell proliferation and promoting apoptosis. The TEAD1-4 proteins (which contain a DNA-binding domain but lack an activation domain) interact with YAP (which lacks a DNA-binding domain but contains an activation domain) to form functional heterodimeric transcription factors that activate proliferative and prosurvival gene expression programs. The Hippo pathway inhibits the YAP-TEAD hybrid transcription factors by phosphorylating and promoting cytoplasmic retention of YAP. Here we report the crystal structure of the YAP-binding domain (YBD) of human TEAD2. TEAD2 YBD adopts an immunoglobulin-like β-sandwich fold with two extra helix-turn-helix inserts. NMR studies reveal that the TEAD-binding domain of YAP is natively unfolded and that TEAD binding causes localized conformational changes in YAP. In vitro binding and in vivo functional assays define an extensive conserved surface of TEAD2 YBD as the YAP-binding site. Therefore, our studies suggest that a short segment of YAP adopts an extended conformation and forms extensive contacts with a rigid surface of TEAD. Targeting a surface-exposed pocket of TEAD might be an effective strategy to disrupt the YAP-TEAD interaction and to reduce the oncogenic potential of YAP.
Certainty-equivalence based super-twisting control using continuous adaptation laws

The certainty-equivalence super-twisting controller (CESTA) combines approaches from variable structure and adaptive control. In this paper, an improved variant of this algorithm is presented that resorts to a recently introduced Lyapunov function for the super twisting algorithm, establishing a novel continuous adaptation law. These controllers are beneficial for systems that are affected by structured and unstructured uncertainties. It is demonstrated that the combination of sliding-mode and adaptive control methodologies allows to relax the boundedness condition, known from the super twisting algorithm. In comparison to earlier work, asymptotic stability of the system states may be shown while requiring relaxed conditions on the structured uncertainty. The effectiveness of the proposed algorithm is shown with a simulation example.
On conditions of signal reception in short wave channels

Short wave or high-frequency (HF) radios are currently used for international broadcasting, various types of communications, over-the-horizon radar, and some scientific experiments. In the future, they can also be employed for communications among unmanned and manned stations on other planets with ionospheres. The reception conditions in the HF range are determined mainly by the short wave propagation and narrowband interference (NBI). Oblique sounding systems provide the most complete information on these conditions, thus greatly improving the reception quality. This paper presents background materials on the short wave propagation and NBI prior to introducing the first oblique sounding system that satisfied modern requirements. The system was developed in the USSR in 1966 and was the most advanced system then. It has influenced the progress of both all-purpose and built-in sounding systems. It also stimulated several theoretical findings that are still of interest to researchers and engineers. Despite that, most materials related to the system have never been published in English. This paper concisely explains theoretical and experimental results most important for future systems and provides information on the signal reception conditions in the HF range.
Promoting wound healing activity using indian costus (Saussurea lappa)

The plant Saussurea lappa (costus) was used in the traditional medicine to treat wounds. Although, there are no scientific reports on wound healing activity of Saussurea lappa in the literature, the present study was suggested to evaluate its scientific validity. This investigation was undertaken to determine the efficacy of Saussurea lappa on wound healing. Wound healing is the process of repair that follows injury of the skin and other soft tissues. It has three phases including inflammation, proliferative and remodeling phases. This study used the roots of Saussurea lappa to evaluate wound healing activity using tissue culture model as in vitro and excision wound model in rats as in vivo. In tissue culture, the fibroblast cells were used to investigate the effect of Saussure lappa on healing activity via their ability to stimulate fibroblast proliferation. In animal model, Excision wounds were made on the back of rats and Saussurea lappa was administered topically. Two groups of animals were used: a treated group which was treated topically with Saussurea lappa (6g/100ml water) and a control group which was left untreated. Healing was assessed by the rate of wound contraction, period of epithelialization, protein, hexosamine and hydroxyproline concentrations. The in vitro results showed that Saussurea lappa increase proliferation of fibroblasts and thus accelerate wound healing. Application of Saussurea lappa to a wound performed in rats showed that the healing process was faster than control group with out appearance of any infection. Wound contraction increased significantly in treated group compared to the control group (P<0.01). Also, the period of epithelialization decreased significantly (p<0.001). The results revealed that protein and hexosamine content in healed tissues were increased significantly in treated group compared to the control group. Increase in collagen content was observed, but not significant. As conclusion, Saussurea lappa may be reveal as safe and effective topical medicine for accelerating wound healing.
Geometry-driven feature detection

Changchang Wu: Geometry-driven Feature Detection. (Under the direction of Marc Pollefeys.) Matching images taken from different viewpoints is a fundamental step for many computer vision applications including 3D reconstruction, scene recognition, virtual reality, robot localization, etc. The typical approaches detect feature keypoints based on local properties to achieve robustness to viewpoint changes, and establish correspondences between keypoints to recover the 3D geometry or determine the similarity between images. The complexity of perspective distortion challenges the detection of viewpoint invariant features; the lack of 3D geometric information about local features makes their matching inefficient. In this thesis, I explore feature detection based on 3D geometric information for improved projective invariance. The main novel research contributions of this thesis are as follows. First, I give a projective invariant feature detection method that exploits 3D structures recovered from simple stereo matching. By leveraging the rich geometric information of the detected features, I present an efficient 3D matching algorithm to handle large viewpoint changes. Second, I propose a compact high-level feature detector that robustly extracts repetitive structures in urban scenes, which allows efficient widebaseline matching. I further introduce a novel single-view reconstruction approach to recover the 3D dense geometry of the repetition-based features.
Platelet Concentrates in an Additive Solution Prepared from Pooled Buffy Coats.

Abstract. A new method for the preparation of platelet concentrates (PCs) is described. The source material is buffy coat (BC), prepared after keeping standard CPD whole‐blood units at room temperature for 6–12 h, followed by centrifugation at 3,500 rpm for 10 min (first series) or 4,000 rpm for 12.5 min (second series). BC, separated from plasma and red cells, was kept at room temperature for a further 8–12 h without agitation. Pools of 6 (first series) and 4 (second series) BCs were prepared using a sterile docking device and suspended in a platelet‐additive solution (PAS) containing sodium/potassium chloride, citrate, phosphate, and mannitol. After gentle centrifugation, the platelet‐rich supernatant was expressed to and stored in one (first series) or two (second series) 1‐liter polyolefine (PL‐732) containers. In the first series, the total number of platelets was 316 ± 59 times 109 per PC (yield 65%). However, when the method was applied at a routine scale, the yield varied considerably and was shown to be strongly dependent on the hematocrit of the BCs. A number of steps were taken to standardize the technique which resulted in an improved yield (77.3 ± 8.7%) with 316 ± 52 times 109 platelets (mean ±SD, range 203–490, n = 134), obtained from 4 BC pools and lower leukocyte contamination than before, 18 ±17 times 106 per preparation (range 1–73, microscopic counting, n = 38). The storage medium consisted of a mixture of plasma and PAS. Standardization of the hematocrit and volume of the BCs is essential, both for improvement of the yield and for providing a sufficient amount of glucose and bicarbonate to the platelets throughout storage. The method is particularly suitable in combination with automated techniques for blood component preparation which include BC removal. Blood gases, pH and adenosine triphosphate were maintained at satisfactory levels; the release of platelet factor 4 and lactate dehydrogenase was not different from traditional PC preparation and storage. However, the content of glucose was exhausted in many PC units towards the end of a storage of 6 days. When whole blood and BC are stored for such a long period, and when the gas permeability of their containers is poor, it is important, in order to avoid early loss of swirling, that the surface‐to‐volume ratio and the gas permeability of the PC containers is sufficiently large to allow good gas exchange.
In vivo optic nerve head biomechanics: performance testing of a three-dimensional tracking algorithm

Measurement of optic nerve head (ONH) deformations could be useful in the clinical management of glaucoma. Here, we propose a novel three-dimensional tissue-tracking algorithm designed to be used in vivo. We carry out preliminary verification of the algorithm by testing its accuracy and its robustness. An algorithm based on digital volume correlation was developed to extract ONH tissue displacements from two optical coherence tomography (OCT) volumes of the ONH (undeformed and deformed). The algorithm was tested by applying artificial deformations to a baseline OCT scan while manipulating speckle noise, illumination and contrast enhancement. Tissue deformations determined by our algorithm were compared with the known (imposed) values. Errors in displacement magnitude, orientation and strain decreased with signal averaging and were 0.15 µm, 0.15° and 0.0019, respectively (for optimized algorithm parameters). Previous computational work suggests that these errors are acceptable to provide in vivo characterization of ONH biomechanics. Our algorithm is robust to OCT speckle noise as well as to changes in illumination conditions, and increasing signal averaging can produce better results. This algorithm has potential be used to quantify ONH three-dimensional strains in vivo, of benefit in the diagnosis and identification of risk factors in glaucoma.
Radiologic evaluations affecting surgical technique in ureteropelvic junction obstruction

Ureteropelvic junction obstructions can be explored by radiographic methods including ultrasonography, intravenous pyelography, radionuclide scanning, magnetic resonance imaging and computerized tomography. The decision to operate on an ureteropelvic stricture is best given by the results of a radionuclide scan, which can demonstrate the obstruction. The operative technique is influenced by the presence of a polar artery, as this presence represents a danger when endopyelotomy is performed. The presence of a polar artery may be demonstrated by computerized tomography using helicoidal reconstruction. Magnetic resonance imaging with injection of gadolinium is also useful when available. The outcome and the results of the surgical procedure are also evaluated by radionuclide scanning.
Suspenseful design: Engaging emotionally with complex applications through compelling narratives

Although story is a critical component of many games, stories and storytelling techniques are rarely used in other kinds of applications. In this paper, we introduce a framework for constructing suspenseful, narrative-based software applications. While many interface designs aim to reduce confusion and complexity, we introduce an alternative for inherently complex software by engaging people through narrative. We describe a framework for incorporating suspenseful elements into an interface and apply it to a proto-type of a suspenseful tutorial. We conducted a controlled experiment that compared this suspenseful tutorial to two more traditional tutorial designs. Participants who used the narrative-based tutorial reported greater feelings of hopeful suspense, which previous studies have found to be correlated with enjoyment and interest.