Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Measurements of RNA Structure Conservation with Generalized Centroid Estimators

Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the minimum free energy (MFE) structure of an RNA sequence is regarded as the most stable structure, MFE alone could not be an appropriate measure for identifying ncRNAs since the free energy is heavily biased by the nucleotide composition. Therefore, instead of MFE itself, several alternative measures for identifying ncRNAs have been proposed such as the structure conservation index (SCI) and the base pair distance (BPD), both of which employ MFE structures. However, these measurements are unfortunately not suitable for identifying ncRNAs in some cases including the genome-wide search and incur high false discovery rate. In this study, we propose improved measurements based on SCI and BPD, applying generalized centroid estimators to incorporate the robustness against low quality multiple alignments. Our experiments show that our proposed methods achieve higher accuracy than the original SCI and BPD for not only human-curated structural alignments but also low quality alignments produced by CLUSTAL W. Furthermore, the centroid-based SCI on CLUSTAL W alignments is more accurate than or comparable with that of the original SCI on structural alignments generated with RAF, a high quality structural aligner, for which twofold expensive computational time is required on average. We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD.
Soft vector quantization and the EM algorithm 1

The relation between hard c-means (HCM), fuzzyc-means (FCM), fuzzy learning vector quantization (FLVQ), soft competition scheme (SCS) of Yair et al. (1992) and probabilistic Gaussian mixtures (GM) have been pointed out recently by Bezdek and Pal (1995). We extend this relation to their training, showing that learning rules by these models to estimate the cluster centers can be seen as approximations to the expectation–maximization (EM) method as applied to Gaussian mixtures. HCM and unsupervised, LVQ use 1-ofc type competition. In FCM and FLVQ, membership is the 12/(m 1 1)th power of the distance. In SCS and GM, Gaussian function is used. If the Gaussian membership function is used, the weighted within-groups sum of squared errors used as the fuzzy objective function corresponds to the maximum likelihood estimate in Gaussian mixtures with equal priors and covariances. The fuzzy clustering method named fuzzy c-means alternating optimization procedure (FCM-AO) proposed to optimize the former is then equivalent to batch EM and SCS’s update rule is a variant of the online version of EM. The advantages of the probabilistic framework are: (i) we no longer have spurious spread parameters that needs fine tuning as m in fuzzy vector quantization or b in SCS; instead we have a variance term that has a sound interpretation and that can be estimated from the sample; (ii) EM guarantees that the likelihood does not decrease, thus it converges to the nearest local optimum; (iii) EM also allows us to estimate the underlying distance norm and the cluster priors which we could not with the other approaches. We compare Gaussian mixtures trained with EM with LVQ (HCM), SCS and FLVQ on the IRIS dataset and see that it is more accurate due to its being able to take into account the covariance information. We finally note that vector quantization is generally an intermediate step before finding a final output for which supervision may be possible. Thus, instead of an uncoupled approach where an unsupervised method is used first to find the cluster parameters followed by supervised training of the mapping based on the memberships, we advocate a coupled approach where the cluster parameters and mapping are trained supervised in a coupled way. The uncoupled approach ignores the error at the outputs which may not be ideal. q 1998 Elsevier Science Ltd. All rights reserved.
Under Technology's Thumb

From the introduction: "Standing at the threshold of modern times, Francis Bacon saw in experimental science and technological innovation the keys to humanity's future. Human history to that point, he thought, was an endlessly repeated cycle of despair and false hopes. The false hopes were fed by the old illusion that a few cheap tricks and the right magical formulas would unlock nature's treasury where unlimited wealth and power lay. The despair arose from humanity's seeming inability to escape from subjection to the natural forces that periodically visited famine, disease, pestilence, and destruction upon it. "
A Framework for Effective Alert Visualization

Any organization/department that provides security typically deals with a large volume of alerts and logs generated from a variety of sources. These could be from firewalls, intrusion detection/prevention devices and agents, vulnerability scanners, etc. It would seem like a good idea to apply as much correlation as possible to this data in order to be able to see things from a bird’s eye perspective. Even at this point, a human could use some additional help in deciphering the situation. The authors believe that visualization is a key component to this end. This paper describes general methods and principles that allow the use of visualization as an efficient tool for alert analysis
A metabolic perturbation by U0126 identifies a role for glutamine in resveratrol-induced cell death

Recent evidence has identified substantial overlap between metabolic and oncogenic biochemical pathways, suggesting novel approaches to cancer intervention. For example, cholesterol lowering statins and the antidiabetes medication metformin both act as chemopreventive agents in prostate and other cancers. The natural compound resveratrol has similar properties: increasing insulin sensitivity, suppressing adipogenesis, and inducing apoptotic death of cancer cells in vitro. However, in vivo tumor xenografts acquire resistance to resveratrol by an unknown mechanism, while mouse models of metabolic disorders respond more consistently to the compound. Here we demonstrate that castration-resistant human prostate cancer C4-2 cells are more sensitive to resveratrol-induced apoptosis than isogenic androgen-dependent LNCaP cells. The MEK inhibitor U0126 antagonized resveratrol-induced apoptosis in C4-2 cells, but this effect was not seen with other MEK inhibitors. U0126 was found to inhibit mitochondrial function and shift cells to aerobic glycolysis independently of MEK. Mitochondrial activity of U0126 arose through decomposition, producing both mitochondrial fluorescence and cyanide, a known inhibitor of complex IV. Applying U0126 mitochondrial inhibition to C4-2 cell apoptosis, we tested the possibility that glutamine supplementation of citric acid cycle intermediate α-ketoglutarate may be involved. Suppression of the conversion of glutamate to α-ketoglutarate antagonized resveratrol-induced death in C4-2 cells. A similar effect was also seen by reducing extracellular glutamine concentration in the culture medium, suggesting that resveratrol-induced death is dependent on glutamine metabolism, a process frequently dysregulated in cancer. Further work on resveratrol and metabolism in cancer is warranted to ascertain if the glutamine dependence has clinical implications.
Outcome measurement in forensic mental health research: an evaluation

Abstract Measuring change resulting from healthcare interventions is critical to evaluating their usefulness. The choice of outcome measure is an important part of such evaluations and is driven by assumptions about what is likely to change and how best to capture this. Despite its importance, forensic mental health has paid little attention to determining which are the best measures of outcome. This study used a panel of relevant professionals to (i) assess the relative importance of different areas of potential outcome measurement and (ii) evaluate specific instruments used currently as outcome measures in forensic mental health research. Although a wide range of potential outcomes were endorsed as appropriate, few corresponding instruments have been used consistently. Only three psychiatric instruments deemed by our panel as feasible, relevant and psychometrically adequate have been used in five or more studies (the Beck Depression Inventory; the Brief Psychiatric Rating Scale, and the Symptom Checklist-90–Revised). Significant measurement gaps were noted in areas such as social and emotional functioning. Although instruments exist that could capture most areas, none were sufficiently developed for routine use as outcomes. Further research to develop robust, sensitive and diverse outcome measures is needed. This is an essential precursor to extending the evidence base for forensic mental health interventions.
X-ray monitoring of classical novae in the central region of M 31 I. June 2006 - March 2007 ?

Context. Classical novae (CNe) have recently been reported to represent the major class of supersoft X-ray sources (SSSs) in the central region of our neighbour galaxy M 31. Aims. We carried out a dedicated monitoring of the M 31 central region with XMM-Newton and Chandra in order to find SSS counterparts of CNe, determine the duration of their SSS phase and derive physical outburst parameters. Methods. We systematically searched our data for X-ray counterparts of CNe and determined their X-ray light curves and spectral properties. Additionally, we determined luminosity upper limits for all novae from previous studies which are not detected anymore and for all CNe in our field of view with optical outbursts between May 2005 and March 2007. Results. We detected eight X-ray counterparts of CNe in M 31, four of which were not previously known. Seven sources can be classified as SSSs, one is a candidate SSS. Two SSSs are still visible more than nine years after the nova outburst, whereas two other nova counterparts show a short SSS phase of less than 150 days. Of the latter sources, M31N 2006-04a exhibits a short-time variable X-ray light curve with an apparent period of (1.6 ± 0.3) h. This periodicity could indicate the binary period of the system. There is no X-ray detection for 23 out of 25 CNe which were within the field of view of our observations and had their outburst from about one year before the start of the monitoring until its end. From the 14 SSS nova counterparts known from previous studies, ten are not detected anymore. Additionally, we found four SSSs in our XMM-Newton data without a nova counterpart, one of which is a new source. Conclusions. Out of eleven SSSs detected in our monitoring, seven are counterparts of CNe. We therefore confirm the earlier finding that CNe are the major class of SSSs in the central region of M 31. We use the measured SSS turn-on and turn-off times to estimate the mass ejected in the nova outburst and the mass burned on the white dwarf. Classical novae with short SSS phases seem to be an important contributor to the overall population.
Extracting Policy Positions from Political Texts Using Words as Data

We present a new way of extracting policy positions from political texts that treats texts not as discourses to be understood and interpreted but rather, as data in the form of words. We compare this approach to previous methods of text analysis and use it to replicate published estimates of the policy positions of political parties in Britain and Ireland, on both economic and social policy dimensions. We “export” the method to a non-English-language environment, analyzing the policy positions of German parties, including the PDS as it entered the former West German party system. Finally, we extend its application beyond the analysis of party manifestos, to the estimation of political positions from legislative speeches. Our “language-blind” word scoring technique successfully replicates published policy estimates without the substantial costs of time and labor that these require. Furthermore, unlike in any previous method for extracting policy positions from political texts, we provide uncertainty measures for our estimates, allowing analysts to make informed judgments of the extent to which differences between two estimated policy positions can be viewed as significant or merely as products of measurement error.We thank Raj Chari, Gary King, Michael McDonald, Gail McElroy, and three anonymous reviewers for comments on drafts of this paper.
Expanding the Health Action and Process Approach to Predict Physical Activity in African Americans With HIV/AIDS

The current study investigated an expanded Health Action and Process Approach (HAPA) as a health-promotion model of physical activity/exercise behavior for African Americans living with HIV/AIDS. Predictions of physical activity/exercise participation were investigated among 110 African Americans living with HIV/AIDS. Results indicate the expanded HAPA model accounts for 35% of the variance in physical activity/exercise participation. The most significant predictor variables were symptom severity, outcome expectancy, and action and coping planning. Action and coping planning also partially mediated the relationship between physical activity/exercise intention and behavior. Results of the study provide partial support for the use of this expanded HAPA model in the design and implementation of health-promotion behavioral interventions targeting physical activity/exercise for Africana Americans with HIV/AIDS.
Die modifizierte Sprechangst-Anordnung

Zusammenfassung. Die Erforschung des Konstrukts Angst erfordert Untersuchungsanordnungen, die Angst induzieren und sie zu messen gestatten. Wie bei anderen Konstrukten existieren keine Anordnungen, die als paradigmatisch angesehen werden konnten. Der Beitrag bezieht sich auf eine in der Angstforschung haufig verwendete Untersuchungsanordnung, bekannt als “Offentliches Sprechen“ bzw. als “Sprechangst-Paradigma“. Er zeigt Wege und Irrwege auf, die mit dieser Anordnung seit ihrer ersten Erprobung in den 70iger Jahren innerhalb unseres Dusseldorfer Streslabors (Janke, Debus, Erdmann, Kallus, Bisping) beschritten wurden. “Irrwege“ betreffen die Auswahl und Interpretation der unabhangigen und der abhangigen Variablen als angstinduzierend bzw. angstdeterminiert wegen ihrer Konfundierung mit anderen Konstrukten (mentale Belastung) bzw. der Unspezifitat oder “Distalitat“ der Messmethoden. “Wege“ beinhalten Modifikationen der Anordnung zur Eliminierung konfundierender Bedingungen und die Erganzung der Erfassungsmet.
Dimension reduction of the modulation spectrogram for speaker verification

A so-called modulation spectrogram is obtained from the conventional speech spectrogram by short-term spectral analysis along the temporal trajectories of the frequency bins. In its original definition, the modulation spectrogram is a highdimensional representation and it is not clear how to extract features from it. In this paper, we define a low-dimensional feature which captures the shape of the modulation spectra. The recognition accuracy of the modulation spectrogram based classifier is improved from our previous result of EER=25.1% to EER=17.4% on the NIST 2001 speaker recognition task.
Integrating Care and Justice Issues in Professional Moral Education: A Gender Perspective.

Abstract This study examines gender differences in professional school students’ ethical sensitivity and moral reasoning, two aspects of Rest's four‐component model of moral development. Results indicate that men and women dental students differ in general sensitivity to ethical issues, but not in recognition of issues of care or justice, nor in moral reasoning. Our results contribute to a re‐interpretation of Gilligan's gender‐difference arguments, and suggest new directions for research in moral development.
Asymptotic Analysis of Equivalences and Core-Structures in Kronecker-Style Graph Models

Growing interest in modeling large, complexnetworks has spurred significant research into generative graphmodels. Kronecker-style models (e.g. SKG and R-MAT) are oftenused due to their scalability and ability to mimic key propertiesof real-world networks. Although a few papers theoreticallyestablish these models' behavior for specific parameters, manyclaims used to justify their use are supported only empirically. In this work, we prove several results using asymptotic analysiswhich illustrate that empirical studies may not fully capture thetrue behavior of the models. Paramount to the widespread adoption of Kronecker-stylemodels was the introduction of a linear-time edge-samplingvariant (R-MAT), which existing literature typically treats asinterchangeable with SKG. We prove that although several R-MAT formulations are asymptotically equivalent, their behaviordiverges from that of SKG. Further, we show these resultsare observable even at relatively small graph sizes. Second, weconsider a case where asymptotic analysis reveals unexpectedbehavior within a given model.
A hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags

Water temperature is a primary driver of stream ecosystems and commonly forms the basis of stream classifications. Robust models of stream temperature are critical as the climate changes, but estimating daily stream temperature poses several important challenges. We developed a statistical model that accounts for many challenges that can make stream temperature estimation difficult. Our model identifies the yearly period when air and water temperature are synchronized, accommodates hysteresis, incorporates time lags, deals with missing data and autocorrelation and can include external drivers. In a small stream network, the model performed well (RMSE = 0.59°C), identified a clear warming trend (0.63 °C decade−1) and a widening of the synchronized period (29 d decade−1). We also carefully evaluated how missing data influenced predictions. Missing data within a year had a small effect on performance (∼0.05% average drop in RMSE with 10% fewer days with data). Missing all data for a year decreased performance (∼0.6 °C jump in RMSE), but this decrease was moderated when data were available from other streams in the network.
Evaluation of endodontic files in digital radiographs before and after employing three image processing algorithms.

OBJECTIVES Two digital image processing algorithms, one aimed at correction for exponential attenuation and one at correction for visual response, have been developed. The aims of the present study were to test whether digital radiographs processed with these algorithms improve determination of the length of endodontic files and whether such processed radiographs are comparable with the radiographs processed with a default image processing method employed by one commercially available digital intraoral system. METHODS A dried human skull embedded in an acrylic compound was used for exposing radiographs of the upper and lower premolars and molars with endodontic files (Kerr files size 10 and size 15) positioned to the full length of the roots or 1.5 mm short of it. Radiographs were then processed in three sets. In one set, the radiographs were processed to compensate for exponential attenuation and the response of the human visual system. In the second, the radiographs were processed with the same compensation but with an additional shift in grey levels so that the output luminance in dentin at root tips corresponds to the mean of the luminance range of a computer monitor. In the third, the radiographs were processed with the default processing method in the Sidexis program. Ten viewers evaluated all radiographs. Receiver operating characteristic (ROC) curves were obtained and areas under the curves were calculated. RESULTS For file size 10, ROC curves for processed radiographs were higher than that for originals, while for file size 15, ROC curves for processed and original radiographs were close to each other. Significant differences were found between processed and original radiographs regarding areas under ROC curves for file size 10 but not between the differently processed radiographs. For file size 15, no significant differences were found. CONCLUSION Radiographs processed to correct for attenuation and visual response may improve determination of the length of thin endodontic files. Such processed radiographs are comparable with the radiographs processed with the default processing method in the Sidexis program.
Optimal routing algorithms for rectilinear pin clusters in high-density multichip modules

As the circuit densities and transistor counts are increasing, the package routing problem is becoming more and more challenging. In this article, we study an important routing problem encountered in typical high-end MCM designs: routing within dense pin clusters. Pin clusters are often formed by pins that belong to the same functional unit or the same data bus, and can become bottlenecks in terms of overall routability. Typically, these clusters have irregular shapes, which can be approximated with rectilinear convex boundaries. Since such boundaries have often irregular shapes, a traditional escape routing algorithm may give unroutable solutions. In this article, we study how the positions of escape terminals on a convex boundary affect the overall routability. For this purpose, we propose a set of necessary and sufficient conditions to model routability outside a rectilinear convex boundary. Given an escape routing solution, we propose an optimal algorithm to select the maximal subset of nets that are routable outside the boundary. After that, we focus on an integrated approach to consider routability constraints (outside the boundary) during the actual escape routing algorithm. Here, we propose an optimal algorithm to find the best escape routing solution that satisfies all routability constraints. Our experiments demonstrate that we can reduce the number of layers by 17% on the average, by using this integrated methodology.
"Multiple chemical sensitivities:" immunologic critique of clinical ecology theories and practice.

The concept of multiple chemical hypersensitivities as a disease entity in which the patient experiences numerous symptoms from numerous chemicals and foods caused by a disturbance of the immune systems lacks a scientific foundation. Published reports of such cases are anecdotal and without proper controls. There is no convincing evidence for any immunologic abnormality in these cases. Diagnostic methods have been shown to be unreliable. Diagnosis, treatment, and theoretical concepts underlying the purported disease are not consistent with current immunologic knowledge and theory. As defined and presented by its proponents, multiple chemical hypersensitivities constitutes a belief and not a disease.
Bacterial flagella grow through an injection-diffusion mechanism

The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ∼1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell. DOI: http://dx.doi. org/10.7554/eLife.23136. 001