Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient backsplicing produces translatable circular mRNAs

While the human transcriptome contains a large number of circular RNAs (circRNAs), the functions of most circRNAs remain unclear. Sequence annotation suggests that most circRNAs are generated from splicing in reversed orders across exons. However, the mechanisms of this backsplicing are largely unknown. Here we constructed a single exon minigene containing split GFP, and found that the pre-mRNA indeed produces circRNA through efficient backsplicing in human and Drosophila cells. The backsplicing is enhanced by complementary introns that form double-stranded RNA structure to bring splice sites in proximity, but such structure is not required. Moreover, backsplicing is regulated by general splicing factors and cis-elements, but with regulatory rules distinct from canonical splicing. The resulting circRNA can be translated to generate functional proteins. Unlike linear mRNA, poly-adenosine or poly-thymidine in 3′ UTR can inhibit circular mRNA translation. This study revealed that backsplicing can occur efficiently in diverse eukaryotes to generate circular mRNAs.
Motivation zur Interaktivität: Usability Herausforderung für die Gestaltung von iTV Plattformen

In Deutschland bzw. im deutschsprachigen Markt findet interaktives Fernsehen bis jetzt so gut wie nicht statt. Die Gründe hierfür sind vielfältig und sind wirtschaftlicher, technischer Natur aber auch im Bereich der Usability angesiedelt. Im Sommer dieses Jahres wird Premiere voraussichtlich auf einigen 100.000 Receivern eine auf MediaHighway basierende interaktive Plattform starten. Ein solcher Launch bringt verschiedenste Problemfelder mit sich, u.a. auch verschiedene Herausforderungen an die Usability. Da ist zum einen die Frage, wie Applikationen auf dem TV gestaltet werden müssen, damit sie die Zuschauer unterschiedlichster Altersund Bildungsstufen, die interaktives Fernsehen nicht kennen, nicht überfordern. Auf der anderen Seite stellt der Anschluss der Receiver an den Rückkanal der über DSL realisiert werden soll große Herausforderungen, die zum großen Teil auch von der verwendeten Hardware abhängen. Dieser Artikel wird lediglich auf die Usability Probleme eingehen, die bei der Entwicklung auftraten und die bei bei der Einführung erwartet werden. In der dazugehörigen Präsentation sollen dagegen die Probleme geschildert werden, die dann tatsächlich im Feld auftreten.
Homology Search and Choice of Homologous Partner during Mitotic Recombination

ABSTRACT Homologous recombination is an important DNA repair mechanism in vegetative cells. During the repair of double-strand breaks, genetic information is transferred between the interacting DNA sequences (gene conversion). This event is often accompanied by a reciprocal exchange between the homologous molecules, resulting in crossing over. The repair of DNA damage by homologous recombination with repeated sequences dispersed throughout the genome might result in chromosomal aberrations or in the inactivation of genes. It is therefore important to understand how the suitable homologous partner for recombination is chosen. We have developed a system in the yeast Saccharomyces cerevisiae that can monitor the fate of a chromosomal double-strand break without the need to select for recombinants. The broken chromosome is efficiently repaired by recombination with one of two potential partners located elsewhere in the genome. One of the partners has homology to the broken ends of the chromosome, whereas the other is homologous to sequences distant from the break. Surprisingly, a large proportion of the repair is carried out by recombination involving the sequences distant from the broken ends. This repair is very efficient, despite the fact that it requires the processing of a large chromosomal region flanking the break. Our results imply that the homology search involves extensive regions of the broken chromosome and is not carried out exclusively by sequences adjacent to the double-strand break. We show that the mechanism that governs the choice of homologous partners is affected by the length and sequence divergence of the interacting partners, as well as by mutations in the mismatch repair genes. We present a model to explain how the suitable homologous partner is chosen during recombinational repair. The model provides a mechanism that may guard the integrity of the genome by preventing recombination between dispersed repeated sequences.
Tree Species Identification in Mixed Baltic Forest Using LiDAR and Multispectral Data

This work describes the task of inventorying Baltic mixed forests at an individual tree level. The development of a practicable methodology for semi-automated identification of tree species was targeted. Data acquisition equipment and preprocessing software, explored forest area, processing approaches, obtained classification results as well as newly developed software are described. To resolve the core problem - tree species identification - a classification approach is proposed for processing multi-spectral imagery data from the vicinity of tree tops. A multi-class classifier is designed from multi-spectral data of interactively selected trees included in initial design (training) sets for two conifer and three deciduous species of interest. An approach for the stabilization of the classification results is proposed, based on improving the representativeness of the design sets by selection of trees from different locations, dismissing trees with overlapping crowns and anomalies, followed by the calculation of a spectral dissimilarity parameter of the design sets and dismissing the sets of trees of any species which are too similar. The best classification results were obtained using a two-stage procedure. In the first stage, species clusters were created by adding randomly selected trees from the whole analyzed forest area. Final classification of all trees was done by using a Bayes classifier designed on the basis of cluster properties. A procedure for increasing robustness of the clustering stage is proposed, based on performing multiple clustering attempts, each using a randomly sampled subset of a chosen design set for the classifier design, and making a decision about the class of each tree by the majority vote from the results of these attempts. This classification algorithm was tested against the set of trees, for which information was available from field work. It is shown that a mean classification error below 3% can be achieved and the maximum error rate was decreased substantially by applying the proposed approach for selection of representative design sets.
Time dependent changes in the concentration and type of bacterial sequences found in cholesterol gallstones

The role of bacteria in gallstone formation could not be conclusively evaluated until bacterial presence or absence in a stone was consistently shown. Cultural bacteriologic investigations at the time of cholecystectomy, however, led to the assumption that cholesterol gallstones were free of bacteria. In this study, we used a culture independent, molecular genetic approach to detect, quantify, and identify bacteria in cholesterol gallstones from 100 patients at the time of cholecystectomy and 6 months following. Bacterial growth was recorded in the culture in 9 of 100 gallstones; bacterial DNA, however, was detected in 82 of 91 sterile gallstones. High concentrations corresponding to between 106 to 107 bacteria/g were detected in 11 stones and low concentrations of 105 bacteria/g were detected in 71 sterile stones. The infection in stones with a positive bacterial culture was characterized by the predominance of single bacterial sequence(s) of the bacteria cultured. A similar predominance, indicating a recent infection, was found in sterile gallstones with low DNA concentrations. A high diversity of non‐repeating bacterial sequences, possibly arising from previous overlapping infections, was found in sterile gallstones with high concentrations of bacterial DNA. After 6 months concentrations of bacterial DNA fell significantly in all groups of gallstones. As bacterial DNA is quickly destroyed upon storage, but is nevertheless readily found in most gallstones at the time of cholecystectomy, there must be a mechanism by which it is replenished. One such mechanism is the frequently reoccurring, possibly self‐terminating infection and another one is the permanent colonization of the gallstone with bacteria at low concentrations. Both can promote cholecystolithiasis.
Flame Furnace in Thermal Power Plant Condition Monitoring Using SVM

This paper presents a support vector machine algorithm to use to monitor the state of the furnace flame method. Through the comparison of several methods of monitoring found that the flame images, the basic brightness from the flame (through digital image processing methods will be broken down into its R, G, B RGB images), the flame area (camera video of the burning flame pixels area) in several aspects, such as extraction of data to analyze and eventually the state of the monitoring results of the flame. Support Vector Machine in the analysis algorithm based on the use of MATLAB language applications to achieve the classification of image analysis of raw data. Intensity in the furnace flame monitoring, the first application of digital image processing method to get the furnace burning flame of raw data (flame brightness R, G, B RGB data), and then use SVM classification algorithm to find the best possible image data plane (the largest interval hyper-plane), the original image data to identify the classification for flame intensity monitoring results. Flame of the furnace through the analysis of raw data, extract images combustion data points, and the total combustion flame image pixels are compared, can be more accurate analysis of the burning effect, that is, the results are divided into complete combustion, which are mostly full combustion and a small portion of the full combustion, and then classified by observing and analyzing the results to take appropriate measures. Simulation results show that the analysis of the use of this method flame images, can be effective, real-time to determine the brightness of the flame and combustion analysis of the status and accuracy of its combustion state.
Intrinsically disordered proteins as drug targets

Intrinsically disordered proteins (IDPs) are characterized by a lack of folded structure. Since their identification more than a decade ago, they were designed as potential drug targets. However, nowadays, only few therapeutic molecules have been designed against them. Due to the nature of these proteins bioinformatics methods could have a key role disentangling IDPs related issues, which is key to design new therapeutic agents against them
A Novel Approach to Minimize Sealing Defects: EndoAnchors Reduce Gutter Size in an in Vitro Chimney Graft Model

During the past 25 years, many evolutionary devices and techniques have been invented to improve early and late outcomes related to endovascular aneurysm repair (EVAR). Unfortunately, imperfect proximal seal and fixation is still the major drawback of this technique. The chimney graft technique (Ch-EVAR) is a novel approach to deal with unfavorable infrarenal, juxtarenal, pararenal, and, rarely, thoracoabdominal (TAAA) or arch aneurysms. This technique was invented to overcome the drawbacks of the fenestrated and branched approach (F-EVAR), mainly cost and the lack of off-the-shelf availability. Unfortunately, proximal seal is imperfect due to gutters (type Ia endoleak pathways) alongside the chimney grafts that may persist over time, jeopardizing permanent sac exclusion. In this issue of the JEVT, Niepoth et al. describe the effect of adding Aptus EndoAnchors to chimney grafts in a silicone juxtarenal aortic aneurysm model to reduce the size of gutters produced between these parallel grafts and the main body stent-graft. To appreciate the magnitude of their experiment and the potential applicability to everyday clinical practice, we review the current status of proximal sealing and fixation in EVAR, as well as the techniques available to deal with complex landing zones. PROXIMAL STENT-GRAFT SEALING AND FIXATION
DISRUPTIVE SELECTION AND ASSORTATIVE MATING IN TRIBOLIUM CASTANEUM

Disruptive selection (sometimes called diversifying selection) has been defined as simultaneous selection for more than one optimum phenotype within a single population (Mather, 1955). It is usually interpreted to mean favoring the extreme phenotypes of a quantitative character at the expense of those near the mean; however, the term can also apply to selection for qualitatively different phenotypes, e.g., alternative color patterns in insects (Tauber and Tauber, 1977). There have been many experimental studies of disruptive selection, and much speculation about its importance in natural populations (review in Thoday, 1972). These experiments have shown that disruptive selection can increase phenotypic and genetic variability. One unanswered question is, under what circumstances can disruptive selection lead to prezygotic reproductive isolation. If the extreme values of a quantitative character are favored at the expense of those individuals near the mean, will this promote positive assortative mating based on the character under selection? The reasoning is that matings between opposite extreme types will usually produce progeny near the mean, as-
Multidisciplinary management of adult anaplastic oligodendrogliomas and anaplastic mixed oligo-astrocytomas.

Once thought to be rare, oligodendroglial tumors might actually represent up to 25% of primary glial neoplasms. In recent years, the histologic criteria for the diagnosis of oligodendroglioma have been broadened to include most small cell, monomorphic glial neoplasms. These refinements have led to an increased recognition of oligodendroglial neoplasms, but uniform definitions of pure versus mixed oligodendroglioma as well as the criteria for high-grade (anaplastic) versus low-grade tumors remain elusive. From a prognostic standpoint, the presence of an oligodendroglial component in a malignant glioma predicts longer survivals times for patients treated with surgery, and radiation therapy with or without chemotherapy. High rates of response to PCV (procarbazine, CCNU and Vincristine) chemotherapy also have been noted among patients with anaplastic oligodendroglial neoplasms. Ongoing prospective trials seek to clarify the role of PCV chemotherapy when added to radiation therapy and surgery. In addition, the role of molecular markers as diagnostic aides and guides to therapy and prognosis are being explored for patients with pure and mixed anaplastic oligodendroglial tumors.
Diabetes Susceptibility of BALB/cBOM Mice Treated with Streptozotocin: Inhibition by Lethal Irradiation and Restoration by Splenic Lymphocytes

In genetically susceptible strains of mice, repeated injections of a subdiabetogenic dose of streptozotocin induces the development of progressive insulin-dependent hyperglycemia. We showed previously that host T-cell functions play an obligatory etiologic role in this experimental disease by demonstrating that the athymic nude mouse is resistant to diabetes induction unless its T-cell functions are reconstituted by thymus graft (Paik et al., Proc. Natl. Acad. Sci. USA 77:6129–33, 1980). Here we show that lethal irradiation of euthymic (+/nu) mice of BALB/cBOM background causes selective resistance of the mice to the diabetogenic effects of the multiple low doses of streptozotocin without affecting their sensitivity to a high pharmacologic dose of the toxin. We also show that reconstitution of the irradiated mice with splenic lymphocytes causes the restoration of diabetes susceptibility. Lethally irradiated mice thus represent a useful experimental model for analyzing the host functions involved in the development of this disease. These results provide an additional support for the hypothesis that the induction of diabetes in this model system is mediated by an autoimmune amplification mechanism.
Demand Forecasting by Using Support Vector Machine

Demand forecasting plays a crucial role for supply chain management of retail industry. The future demand for a certain product constructs the basis of its relevant replenishment system. In this research, the technique of support vector machine (SVM) is employed for demand forecasting. Various factors that affect the product demand such as seasonal and promotional factors have been taken into consideration in the model. Meanwhile, different other approaches such as statistical model, Winter model and radius basis function neural network (RBFNN) are also used for comparison and evaluation. The experiment results show that the performance of SVM is superior to other models, which will lead simultaneously to fewer sales failure and lower inventory levels.
Optimal Targeting of HER 2 – PI 3 K Signaling in Breast Cancer : Mechanistic Insights and Clinical Implications

The combination of a PI3K inhibitor with trastuzumab has been shown to be effective at overcoming trastuzumab resistance in models of HER2þ breast cancer by inhibiting HER2–PI3K–FOXO–survivin signaling. In this review the potential clinical implications of these findings are discussed. Cancer Res; 73(13); 1–4. 2013
Algorithmic Accountability

Every day automated algorithms make decisions that can amplify the power of businesses and governments. Yet as algorithms come to regulate more aspects of our lives, the contours of their power can remain difficult to grasp. This paper studies the notion of algorithmic accountability reporting as a mechanism for elucidating and articulating the power structures, biases, and influences that computational artifacts exercise in society. A framework for algorithmic power based on autonomous decision-making is proffered and motivates specific questions about algorithmic influence. Five cases of algorithmic accountability reporting involving the use of reverse engineering methods in journalism are then studied and analyzed to provide insight into the method and its application in a journalism context. The applicability of transparency policies for algorithms is discussed alongside challenges to implementing algorithmic accountability as a broadly viable investigative method.
Molecular mechanisms of drug addiction [published erratum appears in J Neurosci 1992 Aug;12(8):following table of contents]

Regulation of gene expression is one mechanism by which drugs of abuse can induce relatively long-lasting changes in the brain to cause a state of addiction. Here, we focus on two transcription factors, CREB (cAMP response element binding protein) and DeltaFosB, which contribute to drug-induced changes in gene expression. Both are activated in the nucleus accumbens, a major brain reward region, but mediate different aspects of the addicted state. CREB mediates a form of tolerance and dependence, which dampens an individual's sensitivity to subsequent drug exposure and contributes to a negative emotional state during early phases of withdrawal. In contrast, DeltaFosB mediates a state of relatively prolonged sensitization to drug exposure and may contribute to the increased drive and motivation for drug, which is a core symptom of addictive disorders. A major goal of current research is to identify the many target genes through which CREB and DeltaFosB mediate these behavioral states. In addition, future work needs to understand how CREB and DeltaFosB, acting in concert with numerous other drug-induced molecular changes in nucleus accumbens and many other brain regions, interact with one another to produce the complex behavioral phenotype that defines addiction.
Impact of Avoiding Non-functional Requirements in Software Development Stage

Non-functional requirements such as security, performance, usability, scalability and maintenance define the quality attributes or constraints of software to be developed. During the development of software, they are as critical as their counterpart functional requirements because they ensure the quality of software product. Avoiding non-functional requirements or constraints during the requirements engineering process could lead to the failure of software projects. In order to investigate this problem, we have reviewed several published research papers. Based on the study of previously published research this paper gives an overview of impact of avoiding nonfunctional requirements of software project during requirements engineering process. In this research we will also give our recommendations for the improvement of requirements engineering practices.
Preferential sensitization of anoxic bacteria to x-rays by organic nitroxide-free radicals.

Living organisms are generally sensitized to the lethal effects of ionizing radiation if either oxygen (1, 2) or nitric oxide (3, 4) is present during irradiation. They are also sensitized by pretreatment with N-ethylmaleimide (5), a sulfhydryl-binding agent, presumably as the result of the reduction in the level of free sulfhydryls in the cell. The sensitizing action of oxygen and nitric oxide, however, seems to be due to the high reactivity of these compounds with radiation-induced free radicals produced in vital molecules within the cell. It has been pointed out that anoxic protection may be a cause of the failure of the treatment of some forms of cancer by ionizing radiation. Oxygen, because of its high metabolic turnover, cannot diffuse far from circulating blood, and, since neoplastic growth tends to cause congestion and interference with the local blood supply, islands of malignant cells can become anoxic and therefore more resistant to damage by ionizing radiation. Some of these cells may therefore survive and serve as foci for regrowth (6, 7). In a search for other suitable substances that might sensitize anoxic cells, we were guided by the following requirements. For clinical application, a sensitizing agent would have to be chemically unreactive, stable in oxygen, nontoxic at concentrations at which it sensitized significantly, not rapidly metabolized, not pharmacologically active, and highly water-soluble rather than fat-soluble. Moreover, since nitric oxide and oxygen are both free radicals (in so far as they contain unpaired electrons), it seemed that an additional requirement would be that the compound should be a free radical. Since the organic nitroxide-free radicals (7-10) appeared to fulfill many of these requirements, we have studied the radiosensitizing action of three of these compounds. A preliminary account of the sensitizing action of the nitroxides on anoxic bacteria has been published (11). We report here a further investigation of their effects on both aerobic and anoxic bacteria and review the possible mechanisms involved.