Miracle-dz/UniFAR-FTUs huggingface dataset:
In search of lost introns

UNLABELLED Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution, require adequate computational tools. We describe novel computational methods for studying spliceosomal intron evolution. Our goal is to give a reliable characterization of the dynamics of intron evolution. Our algorithmic innovations address the identification of orthologous introns, and the likelihood-based analysis of intron data. We discuss a compression method for the evaluation of the likelihood function, which is noteworthy for phylogenetic likelihood problems in general. We prove that after O(n l) preprocessing time, subsequent evaluations take O(n l/log l) time almost surely in the Yule-Harding random model of n-taxon phylogenies, where l is the input sequence length. We illustrate the practicality of our methods by compiling and analyzing a data set involving 18 eukaryotes, which is more than in any other study to date. The study yields the surprising result that ancestral eukaryotes were fairly intron-rich. For example, the bilaterian ancestor is estimated to have had more than 90% as many introns as vertebrates do now. AVAILABILITY The Java implementations of the algorithms are publicly available from the corresponding author's site http://www.iro. umontreal.ca/~csuros/introns/. Data are available on request.
Three-dimensional ultrastructural analysis of the Saccharomyces cerevisiae mitotic spindle

The three dimensional organization of microtubules in mitotic spindles of the yeast Saccharomyces cerevisiae has been determined by computer- aided reconstruction from electron micrographs of serially cross- sectioned spindles. Fifteen spindles ranging in length from 0.6-9.4 microns have been analyzed. Ordered microtubule packing is absent in spindles up to 0.8 micron, but the total number of microtubules is sufficient to allow one microtubule per kinetochore with a few additional microtubules that may form an interpolar spindle. An obvious bundle of about eight interpolar microtubules was found in spindles 1.3- 1.6 microns long, and we suggest that the approximately 32 remaining microtubules act as kinetochore fibers. The relative lengths of the microtubules in these spindles suggest that they may be in an early stage of anaphase, even though these spindles are all situated in the mother cell, not in the isthmus between mother and bud. None of the reconstructed spindles exhibited the uniform populations of kinetochore microtubules characteristic of metaphase. Long spindles (2.7-9.4 microns), presumably in anaphase B, contained short remnants of a few presumed kinetochore microtubules clustered near the poles and a few long microtubules extending from each pole toward the spindle midplane, where they interdigitated with their counterparts from the other pole. Interpretation of these reconstructed spindles offers some insights into the mechanisms of mitosis in this yeast.
Prevalence of and factors associated with persistent pain following breast cancer surgery.

CONTEXT Persistent pain and sensory disturbances following surgical treatment for breast cancer is a significant clinical problem. The pathogenic mechanisms are complex and may be related to patient characteristics, surgical technique, and adjuvant therapy. OBJECTIVE To examine prevalence of and factors associated with persistent pain after surgical treatment for breast cancer. DESIGN, SETTING, AND PATIENTS A nationwide cross-sectional questionnaire study of 3754 women aged 18 to 70 years who received surgery and adjuvant therapy (if indicated) for primary breast cancer in Denmark between January 1, 2005, and December 31, 2006. A study questionnaire was sent to the women between January and April 2008. MAIN OUTCOME MEASURES Prevalence, location, and severity of persistent pain and sensory disturbances in 12 well-defined treatment groups assessed an average of 26 months after surgery, and adjusted odds ratio (OR) of reported pain and sensory disturbances with respect to age, surgical technique, chemotherapy, and radiotherapy. RESULTS By June 2008, 3253 of 3754 eligible women (87%) returned the questionnaire. A total of 1543 patients (47%) reported pain, of whom 201 (13%) had severe pain, 595 (39%) had moderate pain, and 733 (48%) had light pain. Factors associated with chronic pain included young age (18-39 years: OR, 3.62; 95% confidence interval [CI], 2.25-5.82; P < .001) and adjuvant radiotherapy (OR, 1.50; 95% CI, 1.08-2.07; P = .03), but not chemotherapy (OR, 1.01; 95% CI, 0.85-1.21; P = .91). Axillary lymph node dissection (ALND) was associated with increased likelihood of pain (OR, 1.77; 95% CI, 1.43-2.19; P < .001) compared with sentinel lymph node dissection. Risk of sensory disturbances was associated with young age (18-39 years: OR, 5.00; 95% CI, 2.87-8.69; P < .001) and ALND (OR, 4.97; 95% CI, 3.92-6.30; P < .001). Pain complaints from other parts of the body were associated with increased risk of pain in the surgical area (P < .001). A total of 306 patients (20%) with pain had contacted a physician within the prior 3 months for pain complaints in the surgical area. CONCLUSION Two to 3 years after breast cancer treatment, persistent pain and sensory disturbances remain clinically significant problems among Danish women who received surgery in 2005 and 2006.
Common frequency pattern for music preference identification using frontal EEG

In this paper, we investigate the use of 2-channel frontal EEG signal to classify two music preferences: like and dislike. The hypothesis for this investigation is that the frontal EEG signal contains sufficient information on the mental state of a subject for discriminating the preference of music of the subject. An experiment is performed to collect 2-channel frontal EEG data from 12 subjects by playing various types of music pieces and asking whether they like or dislike the music in order to obtain the true labels of their music preferences. We then propose a frequency band optimization method called common frequency pattern (CFP) for feature extraction and Linear SVM for classification to identify the music preference of the subjects from the 2-channel frontal EEG. The results of using the proposed method yield an average classification accuracy of 74.77% for a trial length of 30 s over the 12 subjects. Hence the experimental results show evidence that frontal EEG signal contains sufficient information to discriminate preference of music. Furthermore, the frequency band optimization results indicate that gamma band is essential for EEG-based music preference identification.
Intelligent Analysis of Genomic Measurements

In this paper we propose a methodology for intelligent analysis of genomic measurements. It is based on a sequential scheme of Support Vector Machines and it can be used for class prediction of multiclass genomic samples. The proposed methodology was evaluated using two lung cancer datasets. The results are comparable and in many cases higher to the accuracy of relevant methodologies that have been proposed in the literature.
Quasi-Orthogonal Time-Reversal Space–Time Block Coding for Frequency-Selective Fading Channels

Quasi-orthogonal space-time block codes (QO-STBCs) are a powerful code family designed for more than two transmit antennas. In contrast to their orthogonal counterparts designed for the same number of transmit antennas, QO-STBCs are able to provide full-rate transmission rate. While original QO-STBCs enjoy only a partial diversity, the recently proposed rotated versions of QO-STBCs achieve the maximum diversity order which is equal to the number of transmit antennas. Since QO-STBCs have been originally proposed for frequency-flat fading channels, it is a challenging design problem to apply them over frequency-selective channels. The dispersive nature of such channels results in intersymbol interference which needs to be carefully handled at the receiver. In this paper, we investigate time-domain equalization for QO-STBC, exploiting the embedded quasi-orthogonal structure to design low-complexity receivers. We also present diversity gains for the proposed scheme through pairwise error probability (PEP) derivation and analysis which are further confirmed by Monte Carlo simulations
Direct agglutination test for diagnosis of Toxoplasma infection: method for increasing sensitivity and specificity

A method that increases the sensitivity and specificity of the direct agglutination (AG) test for diagnosis of Toxoplasma gondii infection is described. Qualitative results in the Sabin-Feldman dye test (DT) and AG test were in excellent agreement (98%). Differences in titers between these two tests often related to the length of time the individual was infected. The AG test titer was most often lower than the DT titer during acute (recent) infection; the AG test titer was most often higher than the DT titer in older or chronic infection. If the AG test antigen described here can be made available, the AG test would be ideal for use as a screening test and would provide a simple and inexpensive means for the surveillance of seronegative women during pregnancy and for detection of seroconversions.
The 22q13.3 Deletion Syndrome (Phelan-McDermid Syndrome)

The 22q13.3 deletion syndrome, also known as Phelan-McDermid syndrome, is a contiguous gene disorder resulting from deletion of the distal long arm of chromosome 22. In addition to normal growth and a constellation of minor dysmorphic features, this syndrome is characterized by neurological deficits which include global developmental delay, moderate to severe intellectual impairment, absent or severely delayed speech, and neonatal hypotonia. In addition, more than 50% of patients show autism or autistic-like behavior, and therefore it can be classified as a syndromic form of autism spectrum disorders (ASD). The differential diagnosis includes Angelman syndrome, velocardiofacial syndrome, fragile X syndrome, and FG syndrome. Over 600 cases of 22q13.3 deletion syndrome have been documented. Most are terminal deletions of ∼100 kb to >9 Mb, resulting from simple deletions, ring chromosomes, and unbalanced translocations. Almost all of these deletions include the gene SHANK3 which encodes a scaffold protein in the postsynaptic densities of excitatory synapses, connecting membrane-bound receptors to the actin cytoskeleton. Two mouse knockout models and cell culture experiments show that SHANK3 is involved in the structure and function of synapses and support the hypothesis that the majority of 22q13.3 deletion syndrome neurological defects are due to haploinsufficiency of SHANK3, although other genes in the region may also play a role in the syndrome. The molecular connection to ASD suggests that potential future treatments may involve modulation of metabotropic glutamate receptors.
Combustion Properties of Maize Cobs - Results from Lab and Pilot-Scale Tests

In order to evaluate the fuel maize cobs regarding its combustion related properties a comprehensive fuel evaluation based on fuel analyses, lab-scale reactor tests as well as combustion trials at a pilot-scale grate-fired biomass combustion plant have been performed. The results and experiences gained from these investigations form an important basis for the development of combustion systems which are tailored to the demands of maize cob combustion. Maize cobs show a significantly lower energy density than wood fuels which has especially to be considered regarding fuel transport and storage as well as regarding the fuel feeding system and the grate design. Especially regarding their comparably high N, S and Cl contents as well as their unfavourable ash melting behaviour maize cobs distinguish themselves from conventional chemically untreated woody biomass fuels. Nevertheless, they could be utilised in the pilot-scale combustion plant at very low CO and OGC as well as acceptable NOx, HCl and SOx emissions which indicate that with the exception of HCl most probably no secondary emission control measures are needed for a real-scale plant. Fine PM emissions dominated the total dust emissions and due their high level (90.7 mg/Nm3, dry flue gas and 13 vol% O2) advanced filter concepts such as ESP or baghouse filters will be needed for PM emission control. Special respect must be regarded to boiler tube deposits since they most probably will contain considerable amounts of KCl thus increasing corrosion risks. Moreover, K-Si-phases in the bottom ash with melting temperatures in the range of 1,050°C were found which underlines the need for an optimised fuel bed temperature control by appropriate combustion air settings as well as flue gas recirculation below the grate in order to avoid severe slagging problems. Summing up, it can be concluded that if all measures proposed in this paper are implemented in a medium sized combustion plant, maize cobs represent an interesting alternative to traditional wood fuels especially for decentralised systems where the fuel is available within short transport distances.
Applying a Grammatical Structure to Practice Game Design on Non-Computer Games

In this paper, we propose a pedagogical approach based on the sentence grammar to teach an introductory game design course. Different from the conventional game design courses concentrated on developing computer games, we advocate exercising non-computer games. In our approach, we elucidate the importance of understanding the core idea of a game by executing the game analysis to extract an identical sentence of the game on the first stage. This notion is then progressively brought to other stages of the course. In the second stage, an exercise on activity games is introduced to exploit the students' ability in conceiving the game interaction in a face-to-face multiplayer environment. This interactive experience obtained is then transferred to the third stage to develop board games. The grammatical approach is introduced to interpret the idea of core sentence to help developing their board game projects. We illustrate specific examples of each stage and the progress made by students. A final evaluation on their projects is reported.
Nutrient status of soils and carnation ( Dianthus caryophyllus Linn.) Foliage under protected cultivation in the western Himachal Himalaya

A study was undertaken to obtain insight of soil nutrient status, under intensive carnation cultivation, of polyhouses located in low and mid hills of Himachal Pradesh. Studies reveal high soil organic carbon content (1.76-2.00 %) and available nitrogen, phosphorus and potassium ranged from 246.1 to 264.8, 49.5 to 61.9 and 587.1 to 682.5 kg ha-1, respectively. With the exception of nitrogen at some locations, all the soils were high in primary nutrient content. The exchangeable calcium and magnesium were found to be adequate and sulphur content (15.21 to 16.99 mg kg-1) was medium in the soils. Micronutrients Zn, Fe, Cu and Mn were medium to high in availability. Total N, P, K, Ca, Mg and S concentration in leaf were categorized as medium, medium, medium, high, high and low range, respectively. Foliage Zn, Cu, Fe, and Mn concentrations were found to be medium to high, high, medium to high and medium range, respectively. Thus, the crop is well supplied with the essential nutrients except sulphur.
Effect of thermospheric contraction on remediation of the near‐Earth space debris environment

[1] Historically, computer simulations of the near-Earth space debris environment have provided a basis for international debris mitigation guidelines and, today, continue to influence international debate on debris environment remediation and active debris removal. Approximately 22,500 objects larger than 10 cm are known to exist in Earth orbit, and less than 5% of these are operational payloads, with the remaining population classed as space debris. These objects represent a significant risk to satellite operations because of the possibility of damaging or catastrophic collisions, as demonstrated by the collision between Iridium 33 and Cosmos 2251 in February 2009. Indeed, recent computer simulations have suggested that the current population in low Earth orbit (LEO) has reached a sufficient density at some altitudes for collision activity there to continue even in the absence of new launches. Even with the widespread adoption of debris mitigation guidelines, the growth of the LEO population, in particular, is expected to result in eight or nine collisions among cataloged objects in the next 40 years. With a new study using the University of Southampton's space debris model, entitled DAMAGE, we show that the effectiveness of debris mitigation and removal strategies to constrain the growth of the LEO debris population could be more than halved because of a long-term future decline in global thermospheric density. However, increasing debris remediation efforts can reverse the impact of this negative density trend.
The influence of smoking on maternal serum AFP and free beta hCG levels and the impact on screening for Down syndrome

I have studied the impact of maternal smoking on the levels of maternal serum alpha‐fetoprotein (AFP) and free beta human chorionic gonadotrophin (hCG) during the second trimester in a large series (30 727) of self‐reported smokers and non‐smokers whose pregnancy resulted in the birth of a normal fetus. I have confirmed in a smaller subset of this population that self‐reporting is an accurate method of assessing smoking status as confirmed by biochemical (serum cotinine) assessment. In addition, I have investigated marker levels among 195 pregnancies affected by Down syndrome with smoking status confirmed by measurement of serum cotinine. In both unaffected and Down syndrome groups, the incidence of smoking was 19 per cent but a considerable variation was observed with maternal age when the incidence in younger women (under 25) was 32 per cent. AFP median levels in unaffected smokers were 3 per cent higher, whilst in the Down syndrome group smoker medians were increased by 10 per cent compared with the non‐smoker group. Free beta hCG levels in unaffected smokers were reduced by 14 per cent, whilst in the Down syndrome group smoker median levels were decreased by 16 per cent. In the smoker group, the Down syndrome detection rate was 10 per cent lower than in the non‐smoker group, whilst the false‐positive rate was also 2 per cent lower. Correcting for smoking status would redress this inequality and produce an overall 2 per cent increase in the detection rate for a 0·4 per cent increase in the false‐positive rate. This increase in screening performance may be worth building into screening programmes, particularly in populations with a high smoking incidence. © 1998 John Wiley & Sons, Ltd.
GABA shapes sensitivity to interaural intensity disparities in the mustache bat's inferior colliculus: implications for encoding sound location

This study examined how GABAergic inhibition affected binaural properties of neurons in the mustache bat's inferior colliculus. Evaluations were made by documenting changes in acoustically evoked inhibition that occurred when GABAergic inputs were reversibly blocked by iontophoretic application of the GABAA antagonist bicuculline. We studied neurons sensitive to interaural intensity disparities (IIDs), since these are the principal cues animals use to localize high- frequency sounds. Neurons sensitive to these cues receive excitation from one ear and inhibition from the other ear, and are called EI neurons. Recordings focused on the EI region in the hypertrophied 60 kHz isofrequency contour, where the sensitivities of the EI cells to IIDs are systematically ordered, thereby creating a map of IID sensitivity. EI neurons were classified on the basis of their IID functions, of which there were two principal types. Seventy percent of the cells had conventional IID functions where the firing rate evoked by a fixed intensity at the contralateral (excitatory) ear remained constant with low intensities at the ipsilateral (inhibitory) ear and then declined progressively as the intensity at the ipsilateral ear increased. We refer to cells that had this type of IID function simply as EI neurons. The IID functions in the remaining 30% of the cells showed binaural facilitation and were classified as EI/f neurons. In these cells, increasing sound intensity at the ipsilateral (inhibitory) ear when the intensity at the contralateral (excitatory) ear was fixed, initially caused the firing rate to increase by at least 25% above the rate evoked by the sound at the contralateral ear alone. Additional intensity increases at the ipsilateral ear then resulted in a marked decline in response rate. We examined the effects of bicuculline on three binaural properties: (1) the degree of inhibition evoked by the ipsilateral ear (the maximum inhibition), (2) the IID at which the unit's discharge rate declined by 50% (the 50% point), and (3) binaural facilitation. There are three main findings. First, bicuculline substantially reduced or eliminated the inhibition evoked by the ipsilateral ear in about 40% of the cells. In the other 60% of the cells, bicuculline had little or no effect on the magnitude of the ipsilaterally evoked inhibition. The second finding is that in more than half of the cells in which there was little or no reduction in the magnitude of the ipsilaterally evoked inhibition, bicuculline changed the IID at which the ipsilaterally evoked inhibition caused the discharge rate to decline by 50%. (ABSTRACT TRUNCATED AT 400 WORDS)
Safety, Correlative Markers, and Clinical Results of Adjuvant Nivolumab in Combination with Vaccine in Resected High-Risk Metastatic Melanoma

Purpose: The anti-programmed death-1 (PD-1) antibody nivolumab (BMS-936558) has clinical activity in patients with metastatic melanoma. Nivolumab plus vaccine was investigated as adjuvant therapy in resected stage IIIC and IV melanoma patients. Experimental Design: HLA-A*0201 positive patients with HMB-45, NY-ESO-1, and/or MART-1 positive resected tumors received nivolumab (1 mg/kg, 3 mg/kg, or 10 mg/kg i.v.) with a multi-peptide vaccine (gp100, MART-1, and NY-ESO-1 with Montanide ISA 51 VG) every 2 weeks for 12 doses followed by nivolumab maintenance every 12 weeks for 8 doses. Primary objective was safety and determination of a maximum tolerated dose (MTD). Secondary objectives included relapse-free survival (RFS), overall survival (OS), and immunologic correlative studies. Results: Thirty-three patients were enrolled. Median age was 47 years; 55% were male. Two patients had stage IIIC disease; 31 patients had stage IV disease. Median follow-up was 32.1 months. MTD was not reached. Most common related adverse events (>40%) were vaccine injection site reaction, fatigue, rash, pruritus, nausea, and arthralgias. Five related grade 3 adverse events [hypokalemia (1), rash (1), enteritis (1), and colitis (2)] were observed. Ten of 33 patients relapsed. Estimated median RFS was 47.1 months; median OS was not reached. Increases in CTLA-4+/CD4+, CD25+Treg/CD4+, and tetramer specific CD8+ T-cell populations were observed with treatment (P < 0.05). Trends for lower baseline myeloid-derived suppressor cell and CD25+Treg/CD4+ populations were seen in nonrelapsing patients; PD-L1 tumor status was not significantly associated with RFS. Conclusions: Nivolumab with vaccine is well tolerated as adjuvant therapy and demonstrates immunologic activity with promising survival in high-risk resected melanoma, justifying further study. Clin Cancer Res; 21(4); 712–20. ©2014 AACR.