Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining Mammalian Transcript Data for Functional Long Non-Coding RNAs

Background The role of long non-coding RNAs (lncRNAs) in controlling gene expression has garnered increased interest in recent years. Sequencing projects, such as Fantom3 for mouse and H-InvDB for human, have generated abundant data on transcribed components of mammalian cells, the majority of which appear not to be protein-coding. However, much of the non-protein-coding transcriptome could merely be a consequence of ‘transcription noise’. It is therefore essential to use bioinformatic approaches to identify the likely functional candidates in a high throughput manner. Principal Findings We derived a scheme for classifying and annotating likely functional lncRNAs in mammals. Using the available experimental full-length cDNA data sets for human and mouse, we identified 78 lncRNAs that are either syntenically conserved between human and mouse, or that originate from the same protein-coding genes. Of these, 11 have significant sequence homology. We found that these lncRNAs exhibit: (i) patterns of codon substitution typical of non-coding transcripts; (ii) preservation of sequences in distant mammals such as dog and cow, (iii) significant sequence conservation relative to their corresponding flanking regions (in 50% cases, flanking regions do not have homology at all; and in the remaining, the degree of conservation is significantly less); (iv) existence mostly as single-exon forms (8/11); and, (v) presence of conserved and stable secondary structure motifs within them. We further identified orthologous protein-coding genes that are contributing to the pool of lncRNAs; of which, genes implicated in carcinogenesis are significantly over-represented. Conclusion Our comparative mammalian genomics approach coupled with evolutionary analysis identified a small population of conserved long non-protein-coding RNAs (lncRNAs) that are potentially functional across Mammalia. Additionally, our analysis indicates that amongst the orthologous protein-coding genes that produce lncRNAs, those implicated in cancer pathogenesis are significantly over-represented, suggesting that these lncRNAs could play an important role in cancer pathomechanisms.
From p-branes to fluxbranes and back

In this note we study aspects of the interplay between ∞uxbranes and p-branes. We describe how a ∞uxbrane can be physically realized as a limit of a brane-antibrane conflguration, in a manner similar to the way a uniform electric fleld appears in between the plates of a capacitor. We also study the evolution of a ∞uxbrane after nucleation of p-branes. We flnd that Kaluza-Klein ∞uxbranes do relax by forming brane-antibrane pairs or spherical branes, but we also flnd that for ∞uxtubes with dilaton coupling in a difierent range, the fleld strength does not relax, instead it becomes stronger after each nucleation bounce. We speculate on a possible runaway instability of such ∞uxtubes and an eventual breakdown of their classical description.
F ¨ Ur Mathematik in Den Naturwissenschaften Leipzig Approximate Iterations for Structured Matrices Approximate Iterations for Structured Matrices

Important matrix-valued functions f (A) are, e.g., the inverse A −1 , the square root √ A, the sign function and the exponent. Their evaluation for large matrices arising from pdes is not an easy task and needs techniques exploiting appropriate structures of the matrices A and f (A) (often f (A) possesses this structure only approximately). However, intermediate matrices arising during the evaluation may lose the structure of the initial matrix. This would make the computations inefficient and even infeasible. However, the main result of this paper is that an iterative fixed-point like process for the evaluation of f (A) can be transformed, under certain general assumptions, into another process which preserves the convergence rate and benefits from the underlying structure. It is shown how this result applies to matrices in a tensor format with a bounded tensor rank and to the structure of the hierarchical matrix technique. We demonstrate our results by verifying all requirements in the case of the iterative computation of A −1 and √ A.
FDTD Analysis of Rectangular Waveguide in Receiving Mode as EMI Sensors

Testing electronic equipment for radiated emissions requires the accurate calibration of EMI sensor. The performance of the sensor depends on its Antenna Factor (AF), which is the ratio of the incident electric field on the antenna surface to the received voltage at the load end across 50Ω resistance. The theoretical prediction of the AF of EMI sensors is a very attractive alternative if one takes into consideration the enormous expenditure and time required for calibrating a sensor experimentally. In this work, FDTD is developed to predict the performance of rectangular waveguide for EMI sensors.
A statistical analysis of hip scores.

Thirteen methods of hip scoring were applied in the postoperative assessment of 47 hip arthroplasties. Their results were found to be inconsistent, often giving contrary measures of success in the same patient. Ten variables were measured during the postoperative review of 256 hip arthroplasties and the data were submitted to multivariate factor analysis. This revealed that the ten variables could be reduced to three factors: pain, which correlated poorly with any other variable (Spearman correlation, r < 0.02); functional activity (distance walked, use of walking aids, stair climbing, use of public transport, limp, sitting and tying shoelaces); and deformity and range of movement. The range of hip flexion correlated closely with the sum of the arcs of movement and with Gade's index (Spearman correlation, r > 0.9). We suggest that, for outcome assessment, only three variables need to be recorded: pain, walking distance and range of hip flexion. The combination of these three measures into a single hip score is misleading.
The Forecast Performance of Alternative Models of Inflation

It is inappropriate to ignore the behavior of money in explaining the generation and evolution of aggregate inflation over time. It is shown that over the period 1977 to 1987 an inflation model based on M2 demand describes more accurately the actual behavior of inflation than an expectations-augmented version of the Phillips curve.
Conservation Tillage: The Role of Farm and Operator Characteristics and the Perception of Soil Erosion

For more than half a century, the use of grassed waterways, terraces, contour plowing, strip cropping, and the raising of closely seeded crops have been used in Wisconsin to control soil erosion. Under the traditional farming system, farmers have used the moldboard plow as the primary tillage implement. Because of the degree to which the soil is lifted and turned over, the resulting field conditions are susceptible to wind and water erosion. Recently, new technologies have been developed which reduce soil erosion through the reduction in the number of primary tillage operations and the intensity of soil displacement. Given the social costs associated with soil erosion, the question remains as to how state and Federal governments can most effectively motivate producers to adopt such soil conserving tillage practices. The least controversial would be the use of voluntary education programs. If such voluntary policies were enacted, it would be important to understand the relationship between producer characteristics and the adoption and use of these alternative tillage practices (Uchtmann and Seitz 1979). For example, do farmers who face increased demands on their time because of an off-farm job use reduced tillage practices at a different rate than full-time farmers? If a relationship between off-farm work and the use of timesaving cultivation practices can be established, then the increasing trend of off-farm employment and policies that assist in such activities may have an impact on the use of soil conservation practices. Over the last decade the use of alternatives to moldboard plow tillage practices as a means of controlling soil erosion and soil degradation has been the focus of considerable economic research (Rahm and Huffman 1984; Young and Shortle 1984; Korsching et al. 1983; Lee and Stewart 1983, 1985; Heimlich 1985). The issues addressed have included the role of operator, farm, land tenure, and institutional characteristics as well as the farm level economic impacts. A distinction has been made between the
Microwave quantum logic spectroscopy and control of molecular ions

A general method for rotational microwave spectroscopy and control of polar molecular ions via direct microwave addressing is considered. Our method makes use of spatially varying ac Stark shifts, induced by far off-resonant, focused laser beams to achieve an effective coupling between the rotational state of a molecular ion and the electronic state of an atomic ion. In this setting, the atomic ion is used for read-out of the molecular ion state, in a manner analogous to quantum logic spectroscopy based on Raman transitions. In addition to high-precision spectroscopy, this setting allows for rotational ground state cooling, and can be considered as a candidate for the quantum information processing with polar molecular ions. All elements of our proposal can be realized with currently available technology.
Clarifying Evidence-Based Medicine in Educational and Therapeutic Experiences of Clinical Faculty Members: A Qualitative Study in Iran

Introduction: Although evidence-based medicine has been a significant part of recent research efforts to reform the health care system, it requires an assessment of real life community and patient. The present study strives to clarify the concept of evidence-based medicine in educational and therapeutic experiences of clinical faculty members of Kermanshah University of Medical Sciences (2014). Materials and Methods: It was a qualitative study of phenomenology. The population consists of 12 clinical faculty members of Kermanshah University Medical Sciences. Sampling was carried out using a purposeful method. Sample volume was determined using adequacy of samples’ law. Data gathering occurred through semi-structured interviews. Collaizzi pattern was employed for data interpretation concurrent with data gathering. Results: interpreting the data, three main themes were extracted. They include: 1. Unawareness and disuse (unaware of the concept, disuse, referral to colleagues, experiment prescription) 2. Conscious or unconscious use (using journals and scientific websites, aware of the process). 3. Beliefs (belief or disbelief in necessity). Conclusion: It sounds essential to change the behavior of clinical faculty members from passive to active with respect to employing evidence-based medicine as well as to alter negative attitudes into positive ones. In so doing, systematic training program aiming at behavior changing is necessary. Also, providing dissent facilities and infrastructures and removing barriers to the use of EBM can be effective.
RF benchmark tests for compact MOS models

Next to accurate fits of measurements, smoothness, and robustness, compact MOSFET models should ideally meet a large number of additional requirements. In this paper, we collect and derive a number of such demands that are important for RF-circuit applications. We present, for the first time, a derivation for the required reciprocity of capacitances at zero bias. We also derive from first principles the expected non-quasi-static behavior of a MOSFET at VDS = 0 as well as its thermal noise. This leads to a number of benchmark tests that a compact model needs to pass to ensure its suitability for RF-circuit applications. Finally, it is shown that the CMC standard model PSP satisfies all presented requirements.
Conflicting measures of hospital quality: ratings from "Hospital Compare" versus "Best Hospitals".

BACKGROUND In April 2005 the Centers for Medicare and Medicaid Services launched "Hospital Compare," the first government-sponsored hospital quality scorecard. We compared the ranking of U.S. News and World Report's "Best Hospitals" with Hospital Compare performance ratings. METHODS We examined Hospital Compare scores for core measures related to care for acute myocardial infarction (AMI), congestive heart failure (CHF), and community-acquired pneumonia (CAP). We calculated composite scores for the disease-specific sets of core measures and a composite combined score for the 14 core measures (across 3 diseases) and determined national score quartile cut points for each set. We then characterized the quartile distribution of Hospital Compare scores for the Best Hospitals for care of cardiac conditions and respiratory disorders in each year, as well as for the Best Hospital "Honor Roll" institutions. RESULTS AMI scores were available for 2165 hospitals, CHF scores for 3130, and CAP scores for 3462. In both 2004 and 2005, fewer than 50% of the Best Hospitals for cardiac care rated in the top quartile of Hospital Compare scores for AMI and CHF. Among the Best Hospitals for care of respiratory disorders, fewer than 15% scored in the top Hospital Compare quartile for CAP. Among Honor Roll institutions, only 5 (of 14 hospitals in 2004; of 16 in 2005) ranked in the top quartile for the combined core measure score. CONCLUSIONS Hospital Compare scores are frequently discordant with Best Hospital rankings, which is likely attributable to the markedly different methods each rating approach employs. Such discordance between major quality rating systems paints a conflicting picture of institutional performance for the public to interpret.
Change of Guard: The Next Generation of Social Graph De-anonymization Attacks

Past decade has seen active research in social graph de-anonymization with a variety of algorithms proposed. Previous algorithms used handcrafted tricks and were locked in a co-evolution of attack and defense with design of anonymization systems. We present a radically improved algorithm for re-identifying social network data. We use a machine learning system based on random forests to identify nodes using their structural features. The algorithm can handle a variety of threat models and is agnostic to the de-anonymization scheme employed. This is substantiated by our evaluation using three real-world social graph datasets under four threat models. Our algorithm is consistently better than the previous generation of algorithms as confirmed by comparison with seven seed-based and seedless attacks based on two real-world social networks. It is time for attacks based on heuristics to be replaced by learning models.
A Multicultural Society in the Making : How Norwegian Muslims challenge a white nation

This doctoral thesis explores the current process of Norway becoming a multicultural society, more specifically when Norwegian Muslims challenge ‘white’ perceptions of the nation. I apply Tariq Modood’s theory of political multiculturalism to analyze this process in terms of public sphere negotiations between a politically mobilized assertive minority, the majority population and state policy responses. I analyze four empirical cases from the ‘integration debate’ in national newspapers between 2006 and 2010; the cartoon affair, the hijab debates and debates on secularism and the role of ‘native informants’. I theorize these as ‘discursive struggles’ and identify four competing ideological positions; a confrontational and a dialogical liberalism on the majority side, and a dialogic antiracist multiculturalism and forms of communitarianism among the minority. The two dialogue positions correspond to the distinction between state multiculturalism as diversity management and a bottom-up multiculturalism that starts with critical minority perspectives on racism. Both see liberal and Muslim values as open to interpretation and thus compatible, but the antiracist perspective combines dialogue with resistance against dominant anti-Muslim discourses. The thesis combines detailed empirical data from Norwegian public debate, comparisons with similar debates in other European countries, and a comprehensive theoretical discussion of multiculturalism, postcolonial perspectives on anti-Muslim racism, politicized Islam and Muslim feminism, and secularism and the public sphere.
Reproducibility of Electrical Caries Measurements: A Technical Problem?

The currently available instrument for electrical detection of occlusal caries lesions [Electronic Caries Monitor (ECM)] uses a site-specific measurement with co-axial air drying. The reproducibility of this method has been reported to be fair to good. It was noticed that the measurement variation of this technique appeared to be non-random. It was the aim of this study to analyse how such a non-random reproducibility pattern arises and whether it could be observed for other operators and ECM models. Analysis of hypothetical measurement pairs showed that the pattern was related to measurements at the high and low end of the measurement range for the instrument. Data sets supplied by other researchers to a varying degree showed signs of a similar non-random pattern. These data sets were acquired at different locations, by different operators and using 3 different ECM models. The frequency distribution of measurements in all cases showed a single or double end-peaked distribution shape. It was concluded that the pattern was a general feature of the measurement method. It was tentatively attributed to several characteristics such as a high value censoring, insufficient probe contact and unpredictable probe contact. A different measurement technique, with an improved probe contact, appears to be advisable.
Arabidopsis thaliana AUCSIA-1 Regulates Auxin Biology and Physically Interacts with a Kinesin-Related Protein

Aucsia is a green plant gene family encoding 44–54 amino acids long miniproteins. The sequenced genomes of most land plants contain two Aucsia genes. RNA interference of both tomato (Solanum lycopersicum) Aucsia genes (SlAucsia-1 and SlAucsia-2) altered auxin sensitivity, auxin transport and distribution; it caused parthenocarpic development of the fruit and other auxin-related morphological changes. Here we present data showing that the Aucsia-1 gene of Arabidopsis thaliana alters, by itself, root auxin biology and that the AtAUCSIA-1 miniprotein physically interacts with a kinesin-related protein. The AtAucsia-1 gene is ubiquitously expressed, although its expression is higher in roots and inflorescences in comparison to stems and leaves. Two allelic mutants for AtAucsia-1 gene did not display visible root morphological alterations; however both basipetal and acropetal indole-3-acetic acid (IAA) root transport was reduced as compared with wild-type plants. The transcript steady state levels of the auxin efflux transporters ATP BINDING CASSETTE subfamily B (ABCB) ABCB1, ABCB4 and ABCB19 were reduced in ataucsia-1 plants. In ataucsia-1 mutant, lateral root growth showed an altered response to i) exogenous auxin, ii) an inhibitor of polar auxin transport and iii) ethylene. Overexpression of AtAucsia-1 inhibited primary root growth. In vitro and in vivo protein-protein interaction experiments showed that AtAUCSIA-1 interacts with a 185 amino acids long fragment belonging to a 2712 amino acids long protein of unknown function (At4g31570). Bioinformatics analysis indicates that the AtAUCSIA-1 interacting protein (AtAUCSIA-1IP) clusters with a group of CENP-E kinesin-related proteins. Gene ontology predictions for the two proteins are consistent with the hypothesis that the AtAUCSIA-1/AtAUCSIA-1IP complex is involved in the regulation of the cytoskeleton dynamics underlying auxin biology.
MicroRNA-153 Inhibits Osteosarcoma Cells Proliferation and Invasion by Targeting TGF-β2

Increasing evidence indicates that microRNAs (miRNAs), a class of small noncoding RNAs, participate in almost every step of cellular processes. MiRNAs are aberrantly expressed in human cancers and contribute to cancer development and progression. Study of miRNAs may provide a new clue for understanding the mechanism of carcinogenesis and a new tool for cancer treatment. In the present study, miR-153 was downregulated in human osteosarcoma tissues and cell lines. Introduction of miR-153 mimics into the MG-63 cells inhibited cell proliferation and invasion. Our results further revealed that transforming growth factor beta 2 (TGF-β2) was negatively regulated by miR-153. Furthermore, overexpression of miR-153 decreased p-SMAD2, p-SMAD3, epidermal growth factor receptor (EGFR) and insulin-like growth factor binding protein-3 (IGFBP-3) expressions, which were the downstream signaling molecules of TGF-β. Furthermore, miRNA-153 suppressed TGF-β-mediated MG-63 proliferation and migration. Therefore, our results suggest that miR-153 may act as a tumor suppressor in osteosarcoma through targeting TGF-β2.
Visual Reasoning as a critical attribute in design creativity

A visual reasoning ability is a fundamental attribute in a creative design process. This research investigates how the visual reasoning ability is measured and explained through experiment and visual reasoning model. The experiments consist of four visual reasoning tasks such as missing view problem, constructive perception task, plan-perspective view matching task, and emergent shape task. We could observe different performances between experiment participants with different design experiences, and meaningful correlation between tasks. These results suggest that our devised visual reasoning task is valid and that visual reasoning ability is potentially related to design creativity. We explain visual reasoning abilities found from the tasks through visual reasoning model.
Use of an Activity Monitor and GPS Device to Assess Community Activity and Participation in Transtibial Amputees

This study characterized measures of community activity and participation of transtibial amputees based on combined data from separate accelerometer and GPS devices. The relationship between community activity and participation and standard clinical measures was assessed. Forty-seven participants were recruited (78% male, mean age 60.5 years). Participants wore the accelerometer and GPS devices for seven consecutive days. Data were linked to assess community activity (community based step counts) and community participation (number of community visits). Community activity and participation were compared across amputee K-level groups. Forty-six participants completed the study. On average each participant completed 16,645 (standard deviation (SD) 13,274) community steps and 16 (SD 10.9) community visits over seven days. There were differences between K-level groups for measures of community activity (F(2,45) = 9.4, p < 0.001) and participation (F(2,45) = 6.9, p = 0.002) with lower functioning K1/2 amputees demonstrating lower levels of community activity and participation than K3 and K4 amputees. There was no significant difference between K3 and K4 for community activity (p = 0.28) or participation (p = 0.43). This study demonstrated methodology to link accelerometer and GPS data to assess community activity and participation in a group of transtibial amputees. Differences in K-levels do not appear to accurately reflect actual community activity or participation in higher functioning transtibial amputees.