Miracle-dz/UniFAR-FTUs huggingface dataset:
The application of generalizability theory to reliability assessment: an illustration using isometric force measurements.

BACKGROUND AND PURPOSE The objective of this study was to examine the potential use of the generalizability theory for assessing reliability of muscle force measurements in clinical applications. Reliability is expressed in terms of standard error of measurement (SEM) and the indexes derived from the SEM. Using generalizability theory, potential sources of measurement error can be recognized and estimated. SUBJECTS Ten healthy women, aged 23 to 47 years (means = 29.5, SD = 7.1), participated in the study. METHODS The method is illustrated by presenting a pilot study. Repeated measurements of maximal isometric knee extension force were carried out by two therapists. The time interval between measurement occasions was 1 week. A functional prototype of a hand-held dynamometer was used, and measurements were carried out according to standardized test protocols. RESULTS Relatively important sources of measurement error were associated with interaction effects between subject and therapist as well as with interactions including the factor occasion. The SEM of the net knee moment was estimated for various hypothetical applications of the dynamometer. CONCLUSION AND DISCUSSION It is concluded that the SEM, the corresponding confidence interval, and the smallest detectable difference are practical measures for expressing reliability of measurements on an individual. Generalizability theory is a powerful tool for estimating the magnitude of multiple sources of measurement error and for assessing the reliability of measurements tailored to specific clinical applications.
GAknot: RNA secondary structures prediction with pseudoknots using genetic algorithm

Predicting RNA secondary structure is a significant challenge in Bioinformatics especially including pseudoknots. There are so many researches proposed that pseudoknots have their own biological functions inside human body, so it is important to predict this kind of RNA secondary structures. There are several methods to predict RNA secondary structure, and the most common one is using minimum free energy. However, finding the minimum free energy to predict secondary structure with pseudoknots has been proven to be an NP-complete problem, so there are many heuristic approaches trying to solve this kind of problems. In this paper, we propose GAknot, a computational method using genetic algorithm (GA), to predict RNA secondary structure with pseudoknots. GAknot first generates a set of maximal stems, and then it tries to generate several individuals by different combinations of stems. After halting condition is reached, GAknot will output the best solution as the output of predicted secondary structure. By using two commonly used validation data sets, GAknot is shown to be a better prediction method in terms of accuracy and speed comparing to several competitive prediction methods. Source code and datasets can be downloaded.
Teacher -child interaction in the preschool classroom: Gender equity in context

TEACHER-CHILD INTERACTION IN THE PRESCHOOL CLASSROOM: GENDER EQUITY IN CONTEXT MAY 2000 HIND R. MARI, B.A., AN-NAJAH NATIONAL UNIVERSITY M.A., UNIVERSITY OF MASSACHUSETTS AMHERST Ed.D. , UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Grace J. Craig This study has investigated the quality and quantity of interactions between teachers and children at three preschool settings to fmd out whether these teachers interacted differently with girls and boys. The study aimed at understanding how teachers integrated gender equity as a value into their other values through curriculum, classroom management and discipline, conflict resolution, their use of language, discussions with children, and the rest of their daily interactions with the children. Three preschool classrooms were chosen to be studied in depth. The setting of the study was three schools in a rural college community in New England. The preschools included one that is privately owned, another run by a non-profit community organization, and a third that belongs to a prestigious private college. The qualitative data collection process included
The lattice of topologies: Structure and complementation

The family of all topologics on a set is a complete, bounded lattice. The purpose of this paper is to study the structure of the lattice of topologies, employing the notion of ultraspace introduced by Frohlich [7] and to show that this lattice is complemented. The set of ultraspaces may naturally be divided into two classes, each of which generates a sublattice. One of these sublattices is the lattice of Tl-topologies. The other, which is studied in ? 2, is the lattice of principal topologies. Principal topologies are defined in terms of ultraspaces and are then characterized by properties of open sets. Some topological properties of ultraspaces are investigated in ? 4 and maximal regular (maximal T1, maximal normal, etc.) topologies are characterized in terms of ultraspaces. The problem of complementation in the lattice of topologies has been outstanding for some time. However, several partial solutions have been provided. Hartmanis [11] first showed the lattice was complemented if the ground set was finite and asked whether this was true in the infinite case. Gaifman [8] gave a positive answer for denumerable sets and Berri [3], using this fact, was able to provide complements for certain special topologies such as a topological group with a dense, nonopen countable subgroup. It is shown in ? 5 that the lattice of principal topologies is complemented. Gaifman [9] established that the complementation problem can be reduced to verifying that each T1-topology has a complement. In ? 6, it is proved that if every T1-topology has a lattice complement which is a principal topology, then every topology does. In ? 7 it is shown that the lattice of topologies on an arbitrary set is complemented by proving that every topology in the sublattice of T,-topologies has a lattice complement which lies in the sublattice of principal topologies.
Heterogeneous nuclear ribonucleoprotein (hnRNP) L promotes DNA damage-induced cell apoptosis by enhancing the translation of p53

The tumor suppressor p53 is an essential gene in the induction of cell cycle arrest, DNA repair, and apoptosis. p53 protein is induced under cellular stress, blocking cell cycle progression and inducing DNA repair. Under DNA damage conditions, it has been reported that post-transcriptional regulation of p53 mRNA contributes to the increase in p53 protein level. Here we demonstrate that heterogeneous nuclear ribonucleoprotein (hnRNP) L enhances p53 mRNA translation. We found that hnRNP L is increased and binds to the 5’UTR of p53 mRNA in response to DNA damage. Increased hnRNP L caused enhancement of p53 mRNA translation. Conversely, p53 protein levels were decreased following hnRNP L knock-down, rendering them resistant to apoptosis and arrest in the G2/M phase after DNA damage. Thus, our findings suggest that hnRNP L functions as a positive regulator of p53 translation and promotes cell cycle arrest and apoptosis.
Self-selection and risk sharing in a modern world of life-long annuities

Abstract Communicating a pension product well is as important as optimising the financial value. In a recent study, we showed that up to 80% of the value of a pension lump sum could be lost if customer communication failed. In this paper, we extend the simple customer interaction of the earlier contribution to the more challenging lifetime annuity case. Using a simple mobile phone device, the pension customer can select the life-long optimal investment strategy within minutes. The financial risk trade-off is presented as a trade-off between the pension paid and the number of years the life-long annuity is guaranteed. The pension payment decreases when investment security increases. The necessary underlying mathematical financial hedging theory is included in the study.
Relationship among vaginal palpation, vaginal squeeze pressure, electromyographic and ultrasonographic variables of female pelvic floor muscles

Background: The proper evaluation of the pelvic floor muscles (PFM) is essential for choosing the correct treatment. Currently, there is no gold standard for the assessment of female PFM function. Objective: To determine the correlation between vaginal palpation, vaginal squeeze pressure, and electromyographic and ultrasonographic variables of the female PFM. Method: This cross-sectional study evaluated 80 women between 18 and 35 years of age who were nulliparous and had no pelvic floor dysfunction. PFM function was assessed based on digital palpation, vaginal squeeze pressure, electromyographic activity, bilateral diameter of the bulbocavernosus muscles and the amount of bladder neck movement during voluntary PFM contraction using transperineal bi-dimensional ultrasound. The Pearson correlation was used for statistical analysis (p<0.05). Results: There was a strong positive correlation between PFM function and PFM contraction pressure (0.90). In addition, there was a moderate positive correlation between these two variables and PFM electromyographic activity (0.59 and 0.63, respectively) and movement of the bladder neck in relation to the pubic symphysis (0.51 and 0.60, respectively). Conclusions: This study showed that there was a correlation between vaginal palpation, vaginal squeeze pressure, and electromyographic and ultrasonographic variables of the PFM in nulliparous women. The strong correlation between digital palpation and PFM contraction pressure indicated that perineometry could easily be replaced by PFM digital palpation in the absence of equipment.
Seasonal affective disorder: a clinical update.

BACKGROUND Seasonal affective disorder (SAD) consists of recurrent major depressive episodes in the fall/winter with remissions in spring/summer. METHOD A Medline search was conducted to identify studies relating to clinical management of SAD using the Medical Subject Heading, seasonal affective disorder, and key words, depress* and season*, focusing on studies published in the past 10 years. The Cochrane library of systematic reviews was also searched for relevant studies. RESULTS A careful history is important to make the diagnosis and differentiate SAD from other similar conditions such as subsyndromal SAD and atypical depression. Seasonal patterns with winter worsening are also recognized in "nonseasonal" depression as well as many other psychiatric conditions, and comorbidity with SAD is common. The pathophysiology of SAD seems to be heterogeneous as research on circadian, neurotransmitter function and genetic hypotheses have shown discrepant results. A dual vulnerability model with differential loading on separate seasonal and depression factors has been proposed to explain these findings. Recent systematic reviews have shown that light therapy is an efficacious and well-tolerated treatment for SAD. There is also evidence for efficacy of pharmacotherapy to treat and prevent SAD. Clinical studies show equal effectiveness with light and antidepressants, so patient preference should be considered in the selection of initial treatment. Dawn stimulation, negative air ions, exercise and cognitve behaviour therapy are under investigation and may also be helpful treatments for SAD. CONCLUSIONS SAD is a common condition with significant psychosocial impairment. Clinicians should be vigilant in recognizing seasonal patterns of depressive episodes because there are effective, evidence-based treatments for SAD.
Recovering Intrinsic Images with a Global Sparsity Prior on Reflectance

We address the challenging task of decoupling material properties from lighting properties given a single image. In the last two decades virtually all works have concentrated on exploiting edge information to address this problem. We take a different route by introducing a new prior on reflectance, that models reflectance values as being drawn from a sparse set of basis colors. This results in a Random Field model with global, latent variables (basis colors) and pixel-accurate output reflectance values. We show that without edge information high-quality results can be achieved, that are on par with methods exploiting this source of information. Finally, we are able to improve on state-of-the-art results by integrating edge information into our model. We believe that our new approach is an excellent starting point for future developments in this field.
Lawrence Berkeley National Laboratory Recent Work Title Structure of the catalytic domain of the colistin resistance enzyme MCR-1 Permalink

Background: Due to the paucity of novel antibiotics, colistin has become a last resort antibiotic for treating multidrug resistant bacteria. Colistin acts by binding the lipid A component of lipopolysaccharides and subsequently disrupting the bacterial membrane. The recently identified plasmid-encoded MCR-1 enzyme is the first transmissible colistin resistance determinant and is a cause for concern for the spread of this resistance trait. MCR-1 is a phosphoethanolamine transferase that catalyzes the addition of phosphoethanolamine to lipid A to decrease colistin affinity. Results: The structure of the catalytic domain of MCR-1 at 1.32 Å reveals the active site is similar to that of related phosphoethanolamine transferases. Conclusions: The putative nucleophile for catalysis, threonine 285, is phosphorylated in cMCR-1 and a zinc is present at a conserved site in addition to three zincs more peripherally located in the active site. As noted for catalytic domains of other phosphoethanolamine transferases, binding sites for the lipid A and phosphatidylethanolamine substrates are not apparent in the cMCR-1 structure, suggesting that they are present in the membrane domain.
Active Cache: caching dynamic contents on the Web

Dynamic documents constitute an increasing percentage of contents on the Web, and caching dynamic documents becomes an increasingly important issue that affects the scalability of the Web. In this paper, we propose the Active Cache scheme to support caching of dynamic contents at Web proxies. The scheme allows servers to supply cache applets to be attached with documents, and requires proxies to invoke cache applets upon cache hits to furnish the necessary processing without contacting the server. We describe the protocol, interface and security mechanisms of the Active Cache scheme, and illustrate its use via several examples. Through prototype implementation and performance measurements, we show that Active Cache is a feasible scheme that can result in significant network bandwidth savings at the expense of moderate CPU costs.
Genotyping and characterization of the geographical distribution of tick‐borne encephalitis virus variants with a set of molecular probes

A panel of deoxyoligonucleotide probes for studying the genetic variability and genotyping of Tick‐borne encephalitis virus (TBEV) strains by molecular hybridization of nucleic acids (MHNA) was created. This panel allows to estimate the genetic structure of individual TBEV strains, as the targets for probes are both variable and genotype (subtype)‐specific sequences of all TBEV genes. With the help of this panel using the method of molecular hybridization of nucleic acids 268 archived TBEV isolates were investigated and the distribution of its genotypes and subgenotypes of genotype 3 was made more precise in the territory of Eurasia. The conclusion made earlier has confirmed that five genotypes of TBEV co‐circulate in Eastern Siberia. It is generally recognized that the Far Eastern (TBE‐FE), European (TBE‐Eu), and Siberian (TBE‐Sib) genotypes are widespread and epidemiologically important. The fourth genotype is presented by only one isolate, TBE178‐79, originated from Irkutsk region, Russia. The fifth genotype includes 10 isolates, 1 of them, TBE886‐84, was found earlier and recognized as unique [Zlobin et al. (2001b): Vopr Virusol 1:12–16 (Russian)]. J. Med. Virol. 82:? –? , 2010. © 2010 Wiley‐Liss, Inc.
Gating of maxi K+ channels studied by Ca2+ concentration jumps in excised inside-out multi-channel patches (myocytes from guinea pig urinary bladder)

Currents through maxi K+ channels were recorded in inside-out macro- patches. Using a liquid filament switch (Franke, C., H. Hatt, and J. Dudel. 1987. Neurosci, Lett. 77:199-204) the Ca2+ concentration at the tip of the patch electrode ([Ca2+]i) was changed in less than 1 ms. Elevation of [Ca2+]i from less than 10 nM to 3, 6, 20, 50, 320, or 1,000 microM activated several maxi K+ channels in the patch, whereas return to less than 10 nM deactivated them. The time course of Ca(2+)- dependent activation and deactivation was evaluated from the mean of 10- 50 sweeps. The mean currents started a approximately 10-ms delay that was attributed to diffusion of Ca2+ from the tip to the K+ channel protein. The activation and deactivation time courses were fitted with the third power of exponential terms. The rate of activation increased with higher [Ca2+]i and with more positive potentials. The rate of deactivation was independent of preceding [Ca2+]i and was reduced at more positive potentials. The rate of deactivation was measured at five temperatures between 16 and 37 degrees C; fitting the results with the Arrhenius equation yielded an energy barrier of 16 kcal/mol for the Ca2+ dissociation at 0 mV. After 200 ms, the time-dependent processes were in a steady state, i.e., there was no sign of inactivation. In the steady state (200 ms), the dependence of channel openness, N.P(o), on [Ca2+]i yielded a Hill coefficient of approximately 3. The apparent dissociation constant, KD, decreased from 13 microM at -50 mV to 0.5 microM at +70 mV. The dependence of N.P(o) on voltage followed a Boltzmann distribution with a maximal P(o) of 0.8 and a slope factor of approximately 39 mV. The results were summarized by a model describing Ca2+- and voltage-dependent activation and deactivation, as well as steady-state open probability by the binding of Ca2+ to three equal and independent sites within the electrical field of the membrane at an electrical distance of 0.31 from the cytoplasmic side.
Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq

Obtaining high quality RNA from complex biological tissues, such as the brain, is needed for establishing high-fidelity cell-type specific transcriptomes. Although combining genetic labeling techniques with laser capture microdissection (LCM) is generally sufficient, concerns over RNA degradation and limited yields call into question results of many sequencing studies. Here we set out to address both of these issues by: (1) developing a fluorescence-assisted LCM protocol that yields high quality RNA from fresh-frozen tissues; and (2) determining a suitable RNA-Seq library generation method for limited amounts of RNA (1–5 ng total RNA). The latter focused on comparing commercially available kits able to produce libraries of sufficient concentration and complexity while limiting PCR amplification biases. We find that high quality RNA (RNA integrity number, RIN, >9) of sufficient concentration can be isolated from laser-captured material from thinly-sectioned tissues when digestion time and temperature are minimized. Furthermore, we found that library generation approaches that retain ribosomal RNA (rRNA) through cDNA library generation required fewer cycles of PCR, minimizing bias in the resulting libraries. Lastly, end stage depletion of rRNA prior to sequencing enriches for target RNAs, thereby increasing read depth and level of gene detection while decreasing sequencing costs. Here we describe our protocol for generating robust RNA-Seq libraries from laser-captured tissue and demonstrate that with this method, we obtain samples with RNA quality superior to the current standard in the LCM field, and show that low-input RNA-Seq kits that minimize PCR bias produce high fidelity sequencing metrics with less variability compared to current practices.
Prosodic word boundary detection using mora transition modeling of fundamental frequency contours -speaker independent experiments-

We have been developing a reliable method for prosodic word boundary detection for Japanese continuous speech based on the discrete hidden Markov modeling of fundamental frequency (F0) contours in mora unit. Although a favorable result was obtained for ATR continuous speech corpus as report-ed already, experiments were done only on closed conditions. This paper reports the results on open and speaker-independent cases using database by two speakers. On average, detection rate reached around 76.0% with insertion error rate of 18.4%. Degradation from the closed condition experiment was only a little, showing the validity of the method for open conditions.
Hardware-Software Codesign of a Large Vocabulary Continuous Speech Recognition system.

Modern real-time applications with increasing design complexity have revolutionized the embedded design procedure. Energy budget constraints and shortening time to market have led designers to consider cooperative design of hardware and software modules for a given embedded application. In hardware-software codesign the trade offs in both the domains are carefully analyzed and the processor intensive tasks are off-loaded to the hardware to meet the performance criteria while the rest is implemented in software to provide the required features and flexibility. Speech recognition systems used in real time applications involve complex algorithms for faithful recognition. The nature of these tasks restricts the implementation to large platforms and is not feasible to meet the performance constraints for smaller embedded mobile systems and battery operated devices. This thesis proposes an idea for hardware-software codesign of a Hidden Markov Model (HMM) based large vocabulary continuous speech recognition system. The entire procedure can be divided into three phases: the initial phase deals with the spectral analysis of the speech input, the second phase deals with learning of the sound units followed by the recognition phase. Studies have shown that the recognition phase consumes more than 50% of the processor time. Keeping this in mind, we partitioned our design to perform the spectral analysis and acoustic training in software using the front end executables and the acoustic trainers provided by the CMU SPHINX. The decoder implementing the phonetic detection and viterbi algorithm was designed in hardware. In this project we simulated different speech input files in software and the relevant input vector files required for hardware analysis were tapped from the SPHINX system
Lempel-Ziv complexity analysis for the evaluation of atrial fibrillation organization

The Lempel-Ziv (LZ) complexity is a non-linear time series analysis metric that reflects the arising rate of new patterns along with the sequence. Thus, it captures its temporal sequence and, quite conveniently, it can be computed with short data segments. In the present work, a detailed analysis on LZ complexity is presented within the context of atrial fibrillation (AF) organization estimation. As the analysed time series depend on the original sampling rate (fs), we evaluated the relationship between LZ complexity and fs. Furthermore, different implementations of LZ complexity were tested. Our results show the usefulness of LZ complexity to estimate AF organization and suggest that the signals from a terminating paroxysmal AF group are more organized (i.e. less complex) than those from the non-terminating paroxysmal AF group. However, the diagnostic accuracy was not as high as that obtained with sample entropy (SampEn), another non-linear metric, with the same database in a previous study (92% vs. 96%). Nevertheless, the LZ complexity analysis of AF organization with sampling frequencies higher than 2048 Hz, or even its combination with SampEn or other non-linear metrics, might improve the prediction of spontaneous AF termination.