Miracle-dz/UniFAR-FTUs huggingface dataset:
Submicroscopic genomic imbalances in burkitt lymphomas/leukemias: Association with age and further evidence that 8q24/MYC translocations are not sufficient for leukemogenesis

Chromosome banding analyses reveal secondary chromosome abnormalities in addition to the MYC translocations t(8;14)(q24;q32), t(8;22)(q24;q11), and t(2;8)(p11;q24) in 60%–80% of Burkitt lymphomas/leukemias (BL). The high incidence of such aberrations indicates that additional changes are important, perhaps necessary, for malignant transformation, i.e., the 8q24/MYC rearrangements may not be sufficient. To investigate this possibility, we performed single nucleotide polymorphism (SNP) array analysis on 20 cases of 8q24/MYC‐positive BL. Nineteen (95%) harbored genomic imbalances; the only case without such aberrations displayed secondary changes by chromosome banding analysis. Thus, all BL cases had abnormalities in addition to the 8q24 translocation. The adult cases harbored more changes (median 3; range 1–21) than did the childhood cases (median 1.5; range 0–5) (P = 0.034). Several recurrent aberrations were detected by SNP array analysis, in particular losses of 6q14.1‐q22.33, 9p21.3, and 13q14.2‐q14.3, gains of 1q23.3‐q31.3, chromosome 7, 13q31.3, and partial uniparental isodisomies for 6p12.2‐pter, 9p23‐pter, and 17p11.2‐pter. The molecular genetic consequences of these changes include deletions of the CDKN2A and TP53 genes, and gains/losses of several genes, such as MIR17HG and E2F2K, involved in the MYC pathway. Thus, deregulation of the MYC pathway, both directly through the 8q24/MYC translocation and indirectly through secondary genomic imbalances, may be essential not only for the initiation but also for the progression of BL. © 2012 Wiley Periodicals, Inc.
Tree-Child Cluster Networks

In general, a phylogenetic network is a graphical representation of an evolutionary history that involves reticulate events like recombinations, hybridizations, or lateral gene transfers. Tree-child reticulate networks (TC networks) are a special class of phylogenetic networks that allow to represent evolutionary histories where, despite the existence of such reticulate events, every ancestral species has some descendant through mutations. In this paper we establish two equivalent characterizations of the families of clusters of TC networks. These characterizations yield a simple, polynomial-time algorithm that decides whether a given family of clusters on a set of taxa is the family of clusters of some TC network or not, and, when the answer is positive, outputs a TC network that is a minimal reticulate network representing this family of clusters. This algorithm is based on the notion of cluster network introduced by Huson and Rupp, and it has been implemented in a Python package and a companion web tool, which are freely available on the web.
Updaies of relational views

We study the problem of translating updates of database views. View updates are disambiguated by requning that a specified view complement (i.e. a second view which contnms all the information omitted from the given view) remains constant during the translation. We study some of the computational problems related to the application of this general methodology in the context of relational databases. We restrict our attention to projective views of databases which consist of a single relation and satisfy functional dependencies. We first characterize complementary views and show that finding a minimum complement of a given view is NP-complete. We then study in detail the problem of translating the insertion of a tuple into a view and extend our results to the cases of deletion and replacement of a tuple. Finally we define and study a new kind of dependencies the explicit functional dependencies, which intuitively state that some part of the database information can be computed from the rest.
Improving website search with server log analysis and multiple evidence combination

Despite the success of global search engines, website search is still problematic in its retrieval accuracy. Server logs contain a rich source of information about how users actually access a website. In this paper, we propose a novel approach of using server log analysis to extract terms to build the web page representation, which is a new source of evidence for website search. Then, we use multiple evidence combination to combine this log-based evidence with text-based and anchor-based evidence. We test the performance of different combination approaches the combination of representations and of ranking scores, using linear combination and inference network models. We also consider different baseline retrieval models. Our experimental results have shown that the server log, when used in multiple evidence combination, can improve the effectiveness of website search, whereas the impact on different models is different.
Air exposure assessment of TDI and biological monitoring of TDA in urine in workers in polyurethane foam industry

Objectives Toluene diisocyanate (TDI) is used in the manufacturing process of polyurethane (PU) foams and is a potent inducer of occupational asthma. The objective of this study was to evaluate the correlation between the exposure to total TDI (2,4- and 2,6-TDI) in air and the corresponding biomarker concentration of total TDA (2,4- and 2,6-TDA) in hydrolysed urine. The aim was also to propose an appropriate biological exposure limit for total TDA in urine. Methods 9 workers from two production lines in a PU foam producing plant were studied. Personal exposure to TDI during four representative production shifts was monitored by an active air sampling method (filter impregnated with 1-(2-methoxyphenyl)piperazine) and quantified by high-performance liquid chromatography and diode array detection (NIOSH n° 2535, 5521). In parallel, pre-shift and post-shift urinary samples were collected from the exposed workers, and TDA concentrations were determined by gas chromatography–mass spectrometry after alkaline hydrolysis. All samples were collected on four measuring days: two Fridays (end of workweek) and two Mondays (start of workweek) separated by a weekend without exposure. Results Strong correlations between the personal air concentrations of total TDI and the corresponding biomarker levels of total TDA in urine (r=0.816) were observed. An increase of 18.12 μg TDA/l (post-shift minus pre-shift concentration) corresponds to an exposure of 5 ppb (37 μg/m3, the current American Conference of Governmental Industrial Hygienists threshold limit value) during the shift. Conclusions The increase in TDA during the shift is a suitable biomarker for exposure to TDI during the same shift. Further research is needed to evaluate the use of start of week or end of week post-shift TDA in urine as biomarker since TDA was found to accumulate during the working week and thus the moment of sampling will clearly influence the result.
Privacy or Security?: Take A Look And Then Decide

Big data paradigm is currently the leading paradigm for data production and management. As a matter of fact, new information are generated at high rates in specialized fields (e.g., cybersecurity scenario). This may cause that the events to be studied occur at rates that are too fast to be effectively analyzed in real time. For example, in order to detect possible security threats, millions of records in a high-speed flow stream must be screened. To ameliorate this problem, a viable solution is the use of data compression for reducing the amount of data to be analyzed. In this paper we propose the use of privacy-preserving histograms, that provide approximate answers to 'safe' queries, for analyzing data in the cybersecurity scenario without compromising individuals' privacy, and we describe our system that has been used in a real life scenario.
Novel Approach for Query Expansion Using Genetic Algorithm

This paper is focused towards query expansion, which is an important technique for improving retrieval efficiency of an Information Retrieval System. Specifically the paper proposes a novel evolutionary approach for improving efficiency of Pseudo Relevance Feedback (PRF) Based Query Expansion. In this method the candidate terms for query expansion are selected from an initially retrieved list of documents, ranked on the basis of co-occurrence measure of the terms with the query terms. Top n selected terms create a term pool. From this term pool, Genetic Algorithm is used to select a thematically rich combination of terms, which provide the terms for expanding the query. We call this method as Genetic Algorithm Based Query Expansion (GABQE). The experiments were performed on standard CISI dataset. The results are quite motivating and one can clearly observe the difference in the result when GA is not used and when GA is used. The paper uses GA for improving PRF based query expansion, but at the same time it can also be generalized and tested for other types of query expansions, where terms may be selected in a different way but a good combination of expansion terms can be obtained using GA.
Compressibility Effects On The Non-linear Receptivity Of Boundary Layers To Dielectric Barrier Discharges

COMPRESSIBILITY EFFECTS ON THE NON-LINEAR RECEPTIVITY OF BOUNDARY LAYERS TO DIELECTRIC BARRIER DISCHARGES Marie F.C. Denison, Ph.D. The University of Texas at Arlington, 2013 Supervising Professor: Luca Massa The reduction of drag and aerodynamic heating caused by boundary layer transition is of central interest for the development of hypersonic vehicles. Receptivity to flow perturbation in the form of Tollmien-Schlichting (TS) wave growth often determines the first stage of the transition process, which can be delayed by depositing specific excitations into the boundary layer. Weakly ionized Dielectric Barrier Discharge (DBD) actuators are being investigated as possible sources of such excitations, but little is known today about their interaction with high-speed flows. In this framework, the first part of the thesis is dedicated to a receptivity study of laminar compressible boundary layers over a flat plate by linear stability analysis following an adjoint operator formulation, under DBD representative excitations assumed independent of flow conditions. The second part of the work concentrates on the development of a coupled plasma-Navier and Stokes solver targeted at the study of supersonic flow and compressibility effects on DBD forcing and non-parallel receptivity. The linear receptivity study of quasi-parallel compressible flows reveals several interesting features such as a significant shift of the region of maximum receptivity
Accurate Prediction of Drug‐Induced Liver Injury Using Stem Cell‐Derived Populations

Despite major progress in the knowledge and management of human liver injury, there are millions of people suffering from chronic liver disease. Currently, the only cure for end‐stage liver disease is orthotopic liver transplantation; however, this approach is severely limited by organ donation. Alternative approaches to restoring liver function have therefore been pursued, including the use of somatic and stem cell populations. Although such approaches are essential in developing scalable treatments, there is also an imperative to develop predictive human systems that more effectively study and/or prevent the onset of liver disease and decompensated organ function. We used a renewable human stem cell resource, from defined genetic backgrounds, and drove them through developmental intermediates to yield highly active, drug‐inducible, and predictive human hepatocyte populations. Most importantly, stem cell‐derived hepatocytes displayed equivalence to primary adult hepatocytes, following incubation with known hepatotoxins. In summary, we have developed a serum‐free, scalable, and shippable cell‐based model that faithfully predicts the potential for human liver injury. Such a resource has direct application in human modeling and, in the future, could play an important role in developing renewable cell‐based therapies.
Adaptive Contextualization: Combating Bias During High-Dimensional Visualization and Data Selection

Large and high-dimensional real-world datasets are being gathered across a wide range of application disciplines to enable data-driven decision making. Interactive data visualization can play a critical role in allowing domain experts to select and analyze data from these large collections. However, there is a critical mismatch between the very large number of dimensions in complex real-world datasets and the much smaller number of dimensions that can be concurrently visualized using modern techniques. This gap in dimensionality can result in high levels of selection bias that go unnoticed by users. The bias can in turn threaten the very validity of any subsequent insights. In this paper, we present Adaptive Contextualization (AC), a novel approach to interactive visual data selection that is specifically designed to combat the invisible introduction of selection bias. Our approach (1) monitors and models a user's visual data selection activity, (2) computes metrics over that model to quantify the amount of selection bias after each step, (3) visualizes the metric results, and (4) provides interactive tools that help users assess and avoid bias-related problems. We also share results from a user study which demonstrate the effectiveness of our technique.
Control of Mesenchymal Lineage Progression by MicroRNAs Targeting Skeletal Gene Regulators Trps1 and Runx2*

Background: MicroRNAs control cell growth and differentiation in part by inhibiting transcription factor expression. Results: Specific microRNAs in mesenchymal cells block osteoblastic and chondrocytic but not adipocytic cell fate. Conclusion: Select microRNA-transcription factor networks control mesenchymal cell fate. Significance: MicroRNAs can be used to manipulate stem cells for musculoskeletal tissue regeneration. Multiple microRNAs (miRNAs) that target the osteogenic Runt-related transcription factor 2 (RUNX2) define an interrelated network of miRNAs that control osteoblastogenesis. We addressed whether these miRNAs have functional targets beyond RUNX2 that coregulate skeletal development. Here, we find that seven RUNX2-targeting miRNAs (miR-23a, miR-30c, miR-34c, miR-133a, miR-135a, miR-205, and miR-217) also regulate the chondrogenic GATA transcription factor tricho-rhino-phalangeal syndrome I (TRPS1). Although the efficacy of each miRNA to target RUNX2 or TRPS1 differs in osteoblasts and chondrocytes, each effectively blocks maturation of precommitted osteoblasts and chondrocytes. Furthermore, these miRNAs can redirect mesenchymal stem cells into adipogenic cell fate with concomitant up-regulation of key lineage-specific transcription factors. Thus, a program of multiple miRNAs controls mesenchymal lineage progression by selectively blocking differentiation of osteoblasts and chondrocytes to control skeletal development.
A METHOD OF DETERMINING THE ELASTIC PROPERTIES OF ALLOYS IN SELECTED CRYSTALLOGRAPHIC DIRECTIONS FOR X-RAY DIFFRACTION RESIDUAL STRESS MEASUREMENT

A technique and apparatus are described for obtaining the elastic constant E/(1 + ν) in selected crystallographic directions for the purpose of calibrating x-ray diffraction residual stress measurement methods. The preparation of a simple rectangular beam specimen with two active electrical resistance strain gages applied to the test surface is described. Samples are clamped in a diffractometer fixture designed to minimize displacement errors, and loaded in four-point bending to several stress levels below the proportional limit. A method is described for calculating E/(1 + ν) and an estimate of the experimental error. Values of E/(1 + ν) obtained for several alloy-(hkl) combinations are presented. The results indicate that several alloys of current commercial interest exhibit significant elastic anisotropy.
The Protective Effect of 3-Deoxysappanchalcone on In Vitro Influenza Virus-induced Apoptosis and Inflammation

Abstract Influenza virus is one of the most important causes of acute respiratory disease. Viral infection and viral replication activate multiple cell signalling pathways. Apoptosis of infected cells and immune response against viral replication, which are generally considered to be protective mechanisms, are also probably mediated by viruses, which lead to severe health problems. We previously reported that 3-deoxysappanchalcone (3-DSC), a compound that is isolated from Caesalpinia sappan, exhibited in vitro anti-influenza activity. In the present study, we further identified that 3-DSC inhibited viral genomic replication and transcription only at a relatively high concentration. We then evaluated the effect of 3-DSC on the regulation of virus-induced cellular apoptosis. 3-DSC ameliorated virus-induced DNA fragmentation in a concentration-dependent manner, which tends to be a consequence of its inhibition of upstream caspase activation. 3-DSC also protected host cells against influenza-induced inflammation by suppressing CCL5 and CXCL10 secretions in endothelial cells and reducing the production of IL-6 and IL-1β in monocytes/macrophages. In conclusion, our results demonstrate that anti-influenza virus mechanisms of 3-DSC involved anti-apoptosis and anti-inflammation activities in vitro. Moreover, 3-DSC could be a promising drug candidate for influenza treatment.
Methylenetetrahydrofolate Reductase (MTHFR) Gene Mutations in Patients with Idiopathic Scoliosis: A Clinical Chart Review

The effects of genetic variations of methylenetetrahydrofolate reductase (MTHFR) enzyme activity have been the discussion of many research papers. It has been associated with multiple neurological sequelae, and has been implicated in other chronic diseases. Although many genetic influences on the development and/or progression of idiopathic scoliosis have been reported, there has been no report of any relationship between MTHFR mutations and idiopathic scoliosis. This paper compared two groups of patients who received MTHFR genetic testing. One group had a history of idiopathic scoliosis, while the other served as a control group. The scoliosis group showed a positive MTHFR mutation in 23 out of 44 patients, while the control group showed 11/44 (P < 0.01). Given the increased incidence of MTHFR defects in scoliosis patients, this study warrants further investigation into how MTHFR variations may trigger the development or progression of idiopathic scoliosis.
Carrier Frequency Offset Estimation in MIMO-OFDM Systems

Orthogonal frequency division multiplexing (OFDM) is a popular method for high data rate wireless transmission. The performance of OFDM system is very sensitive to carrier frequency Offset (CFO), which introduces inter-carrier interference (ICI). Multi-input multi-output system used for increasing diversity gain and capacity of the system. Alamouti space time block code is used for MIMO transmission scheme. The basic method is used for Carrier Frequency Offset Estimation in OFDM system. In cyclic prefix (CP) based estimation, the CFO can be found from the phase angle of the product of the CP and corresponding rear part of the OFDM symbol. In CFO estimation using a training symbol, the CFO estimation range can be increased by reducing the distance between two blocks of samples for correlation. This was made possible by using training symbol that is repetitive with shorter period. An analytic expression in the form of mean square error (MSE) of frequency offset synchronization is reported, and simulation results verify theoretical analysis. Block-by-block CFO estimation is used in MIMO-OFDM system. In this algorithm we use block delay with other block and compare with the delay block. Analysis of the optimal size of block and minimization of the MSE of frequency estimator. We use S observation symbols they are grouped into two consecutive blocks with length A and S-A. The observation symbol, in each block is added sequentially and summed results are correlated block-wise.
Using cluster analysis to classify audiogram shapes

Abstract The purpose of this study was to design a statistical classification system of audiogram shapes in order to improve and integrate shape recognition across clinical settings. The study included 1633 adult subjects with normal hearing or symmetric sensorineural hearing impairment who underwent pure-tone audiometry between July 2007 and December 2008. K-means cluster analysis was employed to categorize audiometric shapes. Eleven audiogram shapes were identified: rising, flat, peaked 8-kHz dip, 4-kHz dip, 8-kHz dip, mild sloping, severe 8-kHz dip, sloping, abrupt loss, severe sloping, and profound abrupt loss. By using the classification system and nomenclature identified for audiogram shapes as outlined in this study, errors based on personal experiences can be reduced and a consistency can be developed across clinics. Sumario El propósito de este estudio fue diseñar un sistema de clasificación estadística de formas de audiogramas para mejorar e integrar el reconocimiento de formas en los diferentes contextos clínicos. El estudio incluyó 1633 sujetos adultos con audición normal o con hipoacusias sensorineurales simétricas, que se sometieron a una audiometría tonal entre julio del 2007 y diciembre del 2008. El análisis en grupo con medios K fue utilizado para organizar las formas audiométricas. Se identificaron once formas audiométricas: en ascenso, planas, con caída puntiaguda en 8 kHz, con caída en 4 kHz, con caída en 8 kHz, con pendiente suave, con caída severa en 8 kHz, con pendiente, pérdida abrupta, pendiente severa y pérdida profunda abrupta. Utilizando el sistema de clasificación y la nomenclatura identificada para las formas de audiograma conforme se delinea en este estudio, los errores basados en la experiencia personal pueden reducirse y puede desarrollarse consistencia entre las clínicas audiológicas.
A Model of Third-Party Integration Testing Process for Foundation Software Platform

FSP, short for foundation software platform, refers to the supporting foundation of application system. Third-party integration testing is the important method to ensure the quality of FSP. The integration testing of FSP would involve collaboration among many vendors, cover functionality testing, compatibility testing, performance testing etc. Furthermore, foundation software usually has very huge code size and is written in different languages. As a result, the integration testing of FSP is concerned with numerous and complicated testing objects, methods and processes. So there is an urgent need for an integration testing process model fitting for the properties of FSP to guide and organize all the testing tasks and the testing activities. Combined with the properties of FSP and the existed traditional software testing process, an integration testing process model for FSP is proposed, which can be summarized as "metadata-based, bug-driven, iterative improvement". The architecture of integration testing engineering environment for FSP is also presented. The model has been used in the integration testing and maintenance of domestic FSP in China.
The leopard (multiple lentigines) syndrome revisited

The Leopard syndrome, an acronym, consists of the following features: L-lentigines (multiple), E-electrocardiographic abnormalities, O-ocular hypertelorism, P-pulmonary stenosis, A-abnormalities of genitalia, R-retardation of growth and D-deafness (sensorineural). In addition to the lentigines a few large dark café-noir spots may be scattered over the trunk. Electrocardiographic abnormalities include the S1, S2, S3 pattern and frequently there is pulmonary valvular dysplasia characterized by a pulmonary systolic ejection murmur but no ejection click. Some patients have had subaortic or subpulmonic defects. Others have had atrial septal defect. Hypospadias, cryptorchidism or absence of one ovary has been found. The syndrome is inherited as an autosomal dominant trait.