Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyper conserved elements in vertebrate mRNA 3′-UTRs reveal a translational network of RNA-binding proteins controlled by HuR

Little is known regarding the post-transcriptional networks that control gene expression in eukaryotes. Additionally, we still need to understand how these networks evolve, and the relative role played in them by their sequence-dependent regulatory factors, non-coding RNAs (ncRNAs) and RNA-binding proteins (RBPs). Here, we used an approach that relied on both phylogenetic sequence sharing and conservation in the whole mapped 3′-untranslated regions (3′-UTRs) of vertebrate species to gain knowledge on core post-transcriptional networks. The identified human hyper conserved elements (HCEs) were predicted to be preferred binding sites for RBPs and not for ncRNAs, namely microRNAs and long ncRNAs. We found that the HCE map identified a well-known network that post-transcriptionally regulates histone mRNAs. We were then able to discover and experimentally confirm a translational network composed of RNA Recognition Motif (RRM)-type RBP mRNAs that are positively controlled by HuR, another RRM-type RBP. HuR shows a preference for these RBP mRNAs bound in stem–loop motifs, confirming its role as a ‘regulator of regulators’. Analysis of the transcriptome-wide HCE distribution revealed a profile of prevalently small clusters separated by unconserved intercluster RNA stretches, which predicts the formation of discrete small ribonucleoprotein complexes in the 3′-UTRs.
WATER, O2, AND ICE IN MOLECULAR CLOUDS

We model the temperature and chemical structure of molecular clouds as a function of depth into the cloud, assuming a cloud of constant density n illuminated by an external far-ultraviolet (FUV; 6 eV <hν < 13.6 eV) flux G0 (scaling factor in multiples of the local interstellar field). Extending previous photodissociation region (PDR) models, we include the freezing of species, simple grain surface chemistry, and desorption (including FUV photodesorption) of ices. We also treat the opaque cloud interior with time-dependent chemistry. Here, under certain conditions, gas-phase elemental oxygen freezes out as water ice and the elemental C/O abundance ratio can exceed unity, leading to complex carbon chemistry. Gas-phase H2O and O2 peak in abundance at intermediate depth into the cloud, roughly AV∼ 3–8 from the surface, the depth proportional to ln(G0/n). Closer to the surface, molecules are photodissociated. Deeper into the cloud, molecules freeze to grain surfaces. At intermediate depths, PDRs are attenuated by dust extinction, but photodesorption prevents total freeze-out. For G0 < 500, abundances of H2O and O2 peak at values ∼10−7, producing columns ∼1015 cm−2, independent of G0 and n. The peak abundances depend primarily on the product of the photodesorption yield of water ice and the grain surface area per H nucleus. At higher values of G0, thermal desorption of O atoms from grains slightly enhances the gas-phase H2O peak abundance and column, whereas the gas-phase O2 peak abundance rises to ∼10−5 and the column to ∼2 × 1016 cm−2. We present simple analytical equations for the abundances as a function of depth, which clarify the dependence on parameters. The models are applied to observations of H2O, O2, and water ice in a number of sources, including B68, NGC 2024, and ρ Oph.
A Genetic Screen for Increased Loss of Heterozygosity in Saccharomyces cerevisiae

Loss of heterozygosity (LOH) can be a driving force in the evolution of mitotic/somatic diploid cells, and cellular changes that increase the rate of LOH have been proposed to facilitate this process. In the yeast Saccharomyces cerevisiae, spontaneous LOH occurs by a number of mechanisms including chromosome loss and reciprocal and nonreciprocal recombination. We performed a screen in diploid yeast to identify mutants with increased rates of LOH using the collection of homozygous deletion alleles of nonessential genes. Increased LOH was quantified at three loci (MET15, SAM2, and MAT) on three different chromosomes, and the LOH events were analyzed as to whether they were reciprocal or nonreciprocal in nature. Nonreciprocal LOH was further characterized as chromosome loss or truncation, a local mutational event (gene conversion or point mutation), or break-induced replication (BIR). The 61 mutants identified could be divided into several groups, including ones that had locus-specific effects. Mutations in genes involved in DNA replication and chromatin assembly led to LOH predominantly via reciprocal recombination. In contrast, nonreciprocal LOH events with increased chromosome loss largely resulted from mutations in genes implicated in kinetochore function, sister chromatid cohesion, or relatively late steps of DNA recombination. Mutants of genes normally involved in early steps of DNA damage repair and signaling produced nonreciprocal LOH without an increased proportion of chromosome loss. Altogether, this study defines a genetic landscape for the basis of increased LOH and the processes by which it occurs.
Resveratrol Specifically Kills Cancer Cells by a Devastating Increase in the Ca2+ Coupling Between the Greatly Tethered Endoplasmic Reticulum and Mitochondria

Background/Aims: Resveratrol and its derivate piceatannol are known to induce cancer cell-specific cell death. While multiple mechanisms of actions have been described including the inhibition of ATP synthase, changes in mitochondrial membrane potential and ROS levels, the exact mechanisms of cancer specificity of these polyphenols remain unclear. This paper is designed to reveal the molecular basis of the cancer-specific initiation of cell death by resveratrol and piceatannol. Methods: The two cancer cell lines EA.hy926 and HeLa, and somatic short-term cultured HUVEC were used. Cell viability and caspase 3/7 activity were tested. Mitochondrial, cytosolic and endoplasmic reticulum Ca2+ as well as cytosolic and mitochondrial ATP levels were measured using single cell fluorescence microscopy and respective genetically-encoded sensors. Mitochondria-ER junctions were analyzed applying super-resolution SIM and ImageJ-based image analysis. Results: Resveratrol and piceatannol selectively trigger death in cancer but not somatic cells. Hence, these polyphenols strongly enhanced mitochondrial Ca2+ uptake in cancer exclusively. Resveratrol and piceatannol predominantly affect mitochondrial but not cytosolic ATP content that yields in a reduced SERCA activity. Decreased SERCA activity and the strongly enriched tethering of the ER and mitochondria in cancer cells result in an enhanced MCU/Letm1-dependent mitochondrial Ca2+ uptake upon intracellular Ca2+ release exclusively in cancer cells. Accordingly, resveratrol/piceatannol-induced cancer cell death could be prevented by siRNA-mediated knock-down of MCU and Letm1. Conclusions: Because their greatly enriched ER-mitochondria tethering, cancer cells are highly susceptible for resveratrol/piceatannol-induced reduction of SERCA activity to yield mitochondrial Ca2+ overload and subsequent cancer cell death.
Recent Longitudinal Evidence of Size and Union Threat Effects Across Genders

Based on data from the National Longitudinal Surveys of Youth covering years 2000 through 2008, it is evident that both male and female workers in medium/larger establishments receive not only higher wages but also have a higher probability of participating in benefit programs than those in smaller establishments. This reinforces the well-documented 'size' effect. Further, the firm size wage effects are much larger for men than women. The union wage effect decreases with establishment size for both genders. This supports the argument that large nonunion firms pay higher wages to discourage the entrance of unions (i.e., the 'threat' effect argument). In addition, the union wage premium is higher for males for small and medium firm sizes relative to females. This implies that unions in the large establishments may have a role to play in achieving a narrowing of the gender union wage gap. In other words, the threat of unionization could reduce union wage premiums for both genders as firm size increases. Given the presence of noticeable gender differences in estimated union effects on the different components of the compensation structure, unions should not treat both genders similarly with respect to wages and benefits.
The Genetic Diversity and Differentiation of Haliotis Ovina by AFLP

Amplified fragment length polymorphism technique has been applied to detect the genetic diversity and differentiation of three wild Haliotis ovina populations in Hainan province, China. High level of genetic diversity was detected among the populations. The mean effective number of alleles per locus was from 1.2027+0.3090 to 1.3530+0.3404, with an average of 1.2969+0.3338. The percentage of polymorphic loci ranged from 66.54% to 60.36%, with an average of 76.18%. The mean of Shannon's Information index was 0.2870+0.2422, ranging from 0.2026+0.2403 to 0.3397+0.2440. And the average of gene diversity index was 0.1981+0.1767, ranging from 0.1306+0.1686 to 0.2276+0.1791. In general, the genetic differentiation among the three populations was insignificant, the average genetic distance among the three populations was 0.0201, ranging from 0.0087 to 0.0462. The UPGMA dendrogram showed that Yinzhou and Yalongwan first clustered into a group and then grouped with Anyou.
Neural Circuits of Motivation

Present paper investigates brain activity associated with reasoning required to identify necessities for achieving and maintaining desired goals and with motivation to act with such an intention. We used a 12 second video composed by 6 scenes of 2 seconds each shows a sleeping baby and a flying mosquito that may hurt the baby, creating the necessity to kill it and motivating a mother to think about possible ways of killing the mosquito. EEG was recorded while volunteers were seeing this video. We used LORETA analysis to identify the set of neurons enrolled in video analysis and comprehension, and correlation analysis to calculate the amount of information provided by each electrode about these. Principal Component Analysis of covariation was used to disclose how these neurons enroll themselves to solve each necessary task of treat recognition, motivation triggering and analysis of alternative choices of action. This analysis showed that 3 different components brain activity that provide distinct neural signatures for each scene analysis and comprehension and show that motivation is a very complex psychological concept supported by a widely distributed neural processing.Finally, results and discussion here pointed to some very new hypotheses about modularity of neural processing supporting reasoning that must be taken with the caution deserved to first ideas. Because of this, data used to support all discussions in this paper is available in EEG book named EEG_Motivation. xls and how use information in this EEG book is provided in file EEG_BOOK. doc. Both files are available from the author by request. The use of the EEG book allows any one to check results presented here to draw his/her conclusions, agreeing or disaccording with present propositions. Any one is free to use the provided data once their origin is acknowledged.
Do Cigarette Smoking and Obesity Affect Semen Abnormality in Idiopathic Infertile Males?

Purpose This study was conducted to find the relative risk of semen abnormality with respect to smoking history and obesity. Materials and Methods Subfertile or infertile men were enrolled in this study from July 2010 to June 2011. All participants provided their cigarette use information, self-reported weight, height, semen analysis, physical examination, and sexually transmitted disease status. None of the enrolled patients had any specific pathological reason for infertility. Semen abnormality was defined as a condition in which one or more parameters did not satisfy the World Health Organization's criteria. Results A total of 1,073 male patients were considered for this study. After the application of the inclusion criteria, 193 patients were finally analyzed. These patients were divided into two groups according to semen abnormality: the normal semen group (n=72) and the abnormal semen group (n=121). Baseline characteristics, except age and smoking history, were not significantly different between the two groups. Smoking history and age were risk factors for the semen abnormality of idiopathic infertile male patients. Conclusions Smoking and old age were risk factors for semen abnormality. However, obesity did not affect the semen abnormality. Smoking affected semen quality and is therefore expected to play a negative role in conception.
X- and Ku-band internally matched GaN amplifiers with more than 100W output power

In this paper, internally matched GaN-HEMT high power amplifiers operating at X- and Ku-bands are presented. For the X-band amplifier, small package is adopted to reduce the over all RF module size. For the Ku-band amplifier, 4 transistor power bars are combined to obtain 100W output power. To the best of our knowledge, this is the first report that more than 100W output power is obtained from single solid state device in Ku-band.
Visibility Analysis for New View Synthesis from Images

This work introduces a new analysis procedure to measure availability of information to render a new view, given a set of views from a camera in linear motion, or a linear array of cameras. The given set can be interpolated to generate a new view using a crossed-slit camera model. The analysis consists of finding regions in the neighborhood of the linear camera positions, where a full view, partial view, or no view can be generated. A visibility parameter, V, is introduced to quantitatively measure the amount of information that can be interpolated. The present work differs from previous methods which aim at minimizing the number of input viewpoints while ensuring full coverage of a specific object. Our work analyzes the visibility for a set of views captured by a linear camera array, and can be extended to a set of images from a 2D camera mesh. The result of this analysis, the visibility, V, is computed and verified with respect to the interpolated views. Visibility analysis helps in identifying blind areas while generating videos for a new camera trajectory. It is also useful in planning best scene capturing strategy for the purpose of generating new views, and finds application in virtual walkthroughs, special effects, the free viewpoint television, remote education, etc.
Free Riding on Gnutella Revisited: The Bell Tolls?

A new analysis of free riding on the Gnutella network updates data from 2000 and points to an increasing downgrade in the network's overall performance and the emergence of a "metatragedy" of the commons. Individuals who use peer-to-peer (P2P) file-sharing networks such as Gnutella face a social dilemma. They must decide whether to contribute to the common good by sharing files or maximize their personal experience by free riding, downloading files while not contributing any to the network. Individuals gain no personal benefits from uploading files (in fact, it's inconvenient), so it's "rational" for users to free ride. However, significant numbers of free riders degrade the entire system's utility, creating a "tragedy of the digital commons. "
Q Learning based Reinforcement Learning Approach to Bipedal Walking Control

Reinforcement learning has been active research area not only in machine learning but also in control engineering, operation research and robotics in recent years. It is a model free learning control method that can solve Markov decision problems. Q-learning is an incremental dynamic programming procedure that determines the optimal policy in a step-by-step manner. It is an online procedure for learning the optimal policy through experience gained solely on the basis of samples. A Q learning based reinforcement learning of a double inverted pendulum has been shown in this paper which reaches a limit cycle at the end of several learning cycles. The double inverted pendulum becomes stable, since the pole angle and pole angular velocity become zero. Stabilization of an equivalent double inverted pendulum representing a bipedal robot has been successfully implemented for balancing the pole angles in the required range using Q learning in Reinforcement Learning. Keywords—Q learning; Double inverted pendulum; Limit Cycle.
CLASSIFICATION OF DIABETIC RETINOPATHY PATIENTS USING SUPPORT VECTOR MACHINES ( SVM ) BASED ON DIGITAL RETINAL IMAGE 3

Diabetic retinopathy is a micro vascular complicati on which is characterized by several changes in the retina. Changes occur in the diameter of the blood vessel, microaneurysm, hemorrhage exudates, and the growth of new blood vessels. These changes need to be detected early so that steps for further handlin g and treatment can be determined. Laser therapy is one of the common therapies for pa tients with Diabetic Retinopathy. This therapy is a manual examination of the scanned results of the fu ndus retinal image. Manual examinations that genera te ophthalmologist sight differ from each other. To ov ercome this problem, a special program is needed to analyze the fundus image of the eye. To create a special program for analyzing the fundu s images of the eye required several stages of rese arch. The study begins by preprocessing eye fundus images , getting rid of the optic dick form the fundus of the eye and then separating the vascular tissue of the damaged area of the retina. Damaged areas of the re tina consist of dark and bright lesians . Mathematical m orphology methods are used to detect the presence o f dark lesian. To detect the presence of bright lesia n a combination of mathematical morphology, Estimat ed Background, Colour analysis, Max-tree and attribute filt rs are used by utilizing a branch filtering approach. Fundus image segmentation results are ext racted and classified using Support Vector Machines (SVM) based on microneurysm and exudates features. Eye fundus images are classified into, Mild NonProliferative Diabetic Retinopathy, Moderate Non-Pr oliferative Diabetic Retinopathy and Severe NonProliferative Diabetic Retinopathy. The novelty of this research using maxtree represen tatio and atribute filtering to enhance image qual ity for exudate segmentation. From the classification experiments on patients wit h diabetic retinopathy the following sensitivity le vel were obtained, specificity and AUC above 90%. This indicates that the research could help opthalmologi st in analyzing a retina that is affected by diabetic retinopathy. The results of the study showed 96.9% sensitivity, specificity 100%, positive predictive value(ppv) 100%, negative predictive value(npv) 88. 19 and AUC 0.985%.
Qualitative Spatial Reasoning Via 3-Valued Heterogeneous Logic

Systems for qualitative spatial reasoning (QSR) are usually formulated as relation algebras, and reasoning in such systems is performed by constraint-satisfaction techniques. While this is often adequate, it is a rather inexpressive framework that cannot model and solve many spatial reasoning problems; it can also complicate the combination of different spatial formalisms, e.g., the combination of topological with metric primitives, or absolute orientation with relative orientation. Here we suggest an alternative approach, whereby spatial information is expressed in a rich quantified 3-valued logic, equipped with a novel semantics for dealing with incomplete information. Decidability is ensured by a systematic compilation into propositional logic and the use of SAT solvers. To illustrate, we define and implement a new system for two-dimensional positional reasoning that combines Frank’s cardinal-direction calculus, the flip-flop calculus for reasoning about relative orientation, and various new positional primitives. Unlike previous work, the system uses diagrams as well as symbolic formulas. In particular, the logic we introduce is heterogeneous, meaning that it combines symbolic and diagrammatic representation and inference. 1 A Hybrid System For Reasoning
Real-time foot attitude estimation for a humanoid robot based on inertial sensors and force sensor

This paper proposes a real-time foot attitude estimation approach consists of a foot attitude acquisition and an auto-calibration method. First, overview of the foot attitude estimation system is presented, including a tri-axis MEMS accelerometer, three angular rate gyroscopes and a data acquisition and processing unit. Then, the arithmetic of data processing and attitude acquisition is introduced. FIR digital filter is proposed to reduce the influence of inherent noise of the sensors, and combination of acceleration and angular rate is adopted to calculate the foot attitude. Finally, a special auto-calibration method based on the force sensor equipped at the ankle of the humanoid robot is presented. The effectiveness of the foot attitude estimation system and the auto-calibration method is confirmed by experiments with our developed humanoid robot.
Fast adaptation using constrained affine transformations with hierarchical priors

In this paper we present an approach to transformation based model adaptation that combines a fast, closed form solution to the MAP estimation of our transforms with robust priors. The robust priors are found using the technique of hierarchical priors, and a closed form solution is achieved by choosing diagonally constrained affine transformations and a suitable family of prior distributions for these transformations. We show that the method gives results comparable to other algorithms, but with significantly reduced computational complexity and memory demands. Experiments are conducted on the SI Recognition Outlier task from the Wall Street Journal corpus, where speaker independent models have to be adapted to handle speech from non-native speakers.
Multi-column substring matching for database schema translation

We describe a method for discovering complex schema translations involving substrings from multiple database columns. The method does not require a training set of instances linked across databases and it is capable of dealing with both fixed-and variable-length field columns. We propose an iterative algorithm that deduces the correct sequence of concatenations of column substrings in order to translate from one database to another. We introduce the algorithm along with examples on common database data values and examine its performance on real-world and synthetic datasets.
300/spl deg/C operating junction temperature inverter leg investigations

A silicon carbide JFET cascade sample is characterized at temperatures up to 300degC with the design of a diode-less inverter in mind. The JFET is considered as a power switch, on-off gate voltages are applied during testing, conduction capability and blocking are measured, reverse conduction is investigated experimentally. Switching losses are considered and total losses of the inverter leg are estimated
Analysis of effort estimation based on software project models

This paper investigates the interrelationship among various measured characteristics of a software project, ranging from project model, size, and metrics used to govern the administration of the project. By analyzing various dimensions of project characteristics based on the underlying model, metrics and project technicality such as language and development paradigm, our findings reveal that certain metrics and models are not suitable for small project since they possess insufficient information to extract and analyze the inherent characteristics of the project. As such, project managers should pay attention to proper selection of project parameters that are conducive toward accurate estimations.