Miracle-dz/UniFAR-FTUs huggingface dataset:
A diminutive and specific RNA binding site for L-tryptophan

Selection for amino acid affinity by elution of RNAs from tryptophan–Sepharose using free L-tryptophan evokes one sequence predominantly (KD = 12 µM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in randomized tracts of 70, 60, 40, 20 and 17 nt show that this internal loop is the simplest sequence that can meet the column affinity selection. From sequence variation in ∼50 independent isolates, only 26 bits of information are required to describe this loop (equivalent to only 13 fully conserved nucleotides). Thus, it is among the simplest amino acid binding sites known, as well as selective among hydrophobic side chains. Among site sequences defined as essential to affinity by conservation, protection and modification-interference, there is a recurring CCA sequence (a tryptophan anticodon triplet) which apparently forms one side of the binding site. Such conserved juxtaposition of tryptophan with a cognate coding triplet supports a stereochemical origin for the genetic code.
Information Consistency of Nonparametric Gaussian Process Methods

Bayesian nonparametric models are widely and successfully used for statistical prediction. While posterior consistency properties are well studied in quite general settings, results have been proved using abstract concepts such as metric entropy, and they come with subtle conditions which are hard to validate and not intuitive when applied to concrete models. Furthermore, convergence rates are difficult to obtain. By focussing on the concept of information consistency for Bayesian Gaussian process (GP)models, consistency results and convergence rates are obtained via a regret bound on cumulative log loss. These results depend strongly on the covariance function of the prior process, thereby giving a novel interpretation to penalization with reproducing kernel Hilbert space norms and to commonly used covariance function classes and their parameters. The proof of the main result employs elementary convexity arguments only. A theorem of Widom is used in order to obtain precise convergence rates for several covariance functions widely used in practice.
A numerical study of the wrinkling evolution of an elastic film on a viscous layer

The wrinkling phenomenon of a compressed elastic thin film bonded to a viscous layer is studied. Linear stability analysis (LSA) shows that, for materials with cubic crystalline symmetry, the sign of the degree of elastic anisotropy ζ = ((C12 + 2C44)/C11) − 1 plays an important role in the anisotropy of the buckling instability of the thin film system. More precisely, the growth rate of the fastest growing wave number, taken as a function of directions, reaches a peak in the ⟨1 0 0⟩ directions for ζ > 0 and in the ⟨1 1 0⟩ directions for ζ < 0. A highly efficient semi-implicit spectral method is established. The numerical experiments of long time wrinkling evolution processes of a 1 + 2-dimensional system verified the LSA results, successfully simulated anisotropic wrinkling pattern formation and coarsening, produced a power law scaling and reproduced certain featured phenomena observed in physical experiments.
A Trust-Based Geographical Routing Scheme in Sensor Networks

Devices in a sensor network need to work in a hostile environment and they are usually powered by batteries. Yet the whole purpose of deploying a sensor network is to perform distributed collaborative computing, possibly in a massive scale. In a hostile computing environment, the sensor devices might be routinely tampered with. Together with the possibility of faulty devices due to extreme conditions or low power, the trustworthiness of a device varies. Specifically, a device should only communicate with another device which has a trust level above a certain threshold. However, setting up trusted communication channels among sensor devices remains a major challenge. In this paper, we propose a trust-based routing scheme in sensor networks for providing a high level of robustness in node selection based on packet trust requirement with lifetime consideration. Our protocol allows messages to be routed through malicious and faulty devices with the selection of trusted neighbors. On the other hand, the network lifetime can also be prolonged by selecting those with their sensing functions covered by some existing nodes. Simulation results show that our scheme is possible to prolong the lifetime of sensor networks and maintain certain satisfactory delivery ratio.
Identification of known and novel germ cell cancer‐specific (embryonic) miRs in serum by high‐throughput profiling

microRNAs (miRs) are short non‐coding RNA molecules (≈21 nucleotides) involved in regulation of translation. As such they are crucial for normal cell development and differentiation as well as cellular maintenance. Dysregulation of miRs has been reported in various diseases, including cancer. Interestingly, miRs can be informative as tumor classifiers and disease biomarkers. Recent studies demonstrated the presence of miRs in body fluids like serum, thus providing a putative non‐invasive tool to study and monitor disease state. Earlier targeted studies by several independent groups identified specific embryonic miRs as characteristic for germ cell tumors (GCT) (miR‐371‐2‐3 & miR‐302/367 clusters). This study reports a high‐throughput miR profiling (≈750 miRs) approach on serum from testicular germ cell tumor patients (14 seminoma and 10 non‐seminoma) and controls (n = 11), aiming at independent identification of miRs as candidate biomarkers for testicular GCT. A magnetic bead capture system was used to isolate miRs from serum. Subsequently, the TaqMan Array Card 3.0 platform was used for profiling. The previously identified miRs 371 and 372 were confirmed to be specifically elevated in serum from germ cell tumor patients. In addition, several novels miRs were identified that were discriminative between germ cell cancer and controls: miR‐511, ‐26b, ‐769, ‐23a, ‐106b, ‐365, ‐598, ‐340, and let‐7a. In conclusion, this study validates the power of the embryonic miRs 371 and 372 in detecting malignant GCT (SE and NS) based on serum miR levels and identifies several potential novel miR targets.
Extremal Numbers for Odd Cycles

We describe the C2k+1-free graphs on n vertices with maximum number of edges. The extremal graphs are unique for n ∉ {3k − 1, 3k, 4k − 2, 4k − 1}. The value of ex(n, C2k+1) can be read out from the works of Bondy [3], Woodall [14], and Bollobás [1], but here we give a new streamlined proof. The complete determination of the extremal graphs is also new. We obtain that the bound for n0(C2k+1) is 4k in the classical theorem of Simonovits, from which the unique extremal graph is the bipartite Turán graph.
Terrestrial Ecosystem Carbon Fluxes Predicted from MODIS Satellite Data and Large-Scale Disturbance Modeling

The CASA (Carnegie-Ames-Stanford) ecosystem model based on satellite greenness observations has been used to estimate monthly carbon fluxes in terrestrial ecosystems from 2000 to 2009. The CASA model was driven by NASA Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation cover properties and large-scale (1-km resolution) disturbance events detected in biweekly time series data. This modeling framework has been implemented to estimate historical as well as current monthly patterns in plant carbon fixation, living biomass increments, and long-term decay of woody (slash) pools before, during, and after land cover disturbance events. Results showed that CASA model predictions closely followed the seasonal timing of Ameriflux tower measurements. At a global level, predicting net ecosystem production (NEP) flux for atmospheric CO2 from 2000 through 2005 showed a roughly balanced terrestrial biosphere carbon cycle. Beginning in 2006, global NEP fluxes became increasingly imbalanced, starting from -0.9 Pg C yr-1 to the largest negative (total net terrestrial source) flux of -2.2 Pg C yr-1 in 2009. In addition, the global sum of CO2 emissions from forest disturbance and biomass burning for 2009 was predicted at 0.51 Pg C yr-1. These results demonstrate the potential to monitor and validate terrestrial carbon fluxes using NASA satellite data as inputs to ecosystem models.
Combined association of clinical and lifestyle factors with non-restorative sleep: The Nagahama Study

Background Non-restorative sleep (NRS) was suggested to be associated with cardiovascular outcomes. However, causative factors for NRS have not been fully elucidated. This study aimed to clarify factors and their relationships with NRS to better understand the clinical and epidemiological implications of NRS and to develop a score that can objectively evaluate NRS status. Methods Study subjects consisted of 9,788 community residents (age 53.6 ± 13.4 y). Subjective NRS as well as possible clinical and lifestyle factors for NRS were investigated by questionnaires. Other clinical parameters were obtained from personal records of information obtained at the baseline examination. Results A total of 3,261 participants complained of NRS. Factors independently associated with subjective NRS were younger age (odds ratio = 1.43), use of a hypnotic drug (2.04), irregular sleep schedule (2.02), short sleep duration (<5 h, 11.7; 5–6 h, 4.81; 6–7 h, 2.40), frequent sleepiness (2.33), routine stress (4.63), no habitual exercise (1.61), nocturia symptoms (1.43), symptoms of gastroesophageal reflux disease (1.44), and depression (1.46) (all P <0.001). The NRS score comprised of these 10 factors was linearly associated with the frequency of subjective NRS (Ptrend <0.001). Frequency of individuals with a high NRS score was greater in women (52.3%) than in men (42.1%, P<0.001), while no clear association was observed with common risk factors for cardiovascular diseases. Conclusions NRS was a phenomenon representing various clinical and lifestyle features. Careful attention should be paid to individuals with a high NRS score who might be at risk for mental fatigue and have unfavorable lifestyle factors.
Magnitude and Duration of Thermal Stress Determine Kinetics of hsp Gene Regulation in the Goby Gillichthys mirabilis

The stress‐induced transcription of heat shock genes is controlled by heat shock transcription factor 1 (HSF1), which becomes activated in response to heat and other protein denaturants. In previous research on the eurythermal goby Gillichthys mirabilis, thermal activation of HSF1 was shown to vary as a function of acclimation temperature, suggesting the mechanistic importance of HSF1 activation to the plasticity of heat shock protein (Hsp) induction temperature. We examined the effect of season on the thermal activation of HSF1 in G. mirabilis, as well as the relative kinetics of HSF1 activation and Hsp70 mRNA production at ecologically relevant temperatures. There was no predictable seasonality in the thermal activation of HSF1, perhaps due to the existence of stressors, in addition to heat, acting in the field. Concentrations of Hsp70, a negative regulator of HSF1, as well as those of HSF1, varied with collection date. The rapidity of HSF1 activation and of Hsp70 mRNA synthesis increased with laboratory exposure temperature. Furthermore, Hsp70 mRNA production was more sustained at 35°C than at 30°C. Therefore, both the magnitude and the duration of a heat shock are important in determining the intensity of heat shock gene induction.
Highlights of the Third International Conference on Immunotherapy in Pediatric Oncology

The third International Conference on Immunotherapy in Pediatric Oncology was held in Frankfurt/Main, Germany, October 1–2, 2012. Major topics of the conference included (i) cellular therapies using antigen-specific and gene-modified T cells for targeting leukemia and pediatric solid tumors; (ii) overcoming hurdles and barriers with regard to immunogenicity, immune escape, and the role of tumor microenvironment; (iii) vaccine strategies and antigen presentation; (iv) haploidentical transplantation and innate immunity; (v) the role of immune cells in allogeneic transplantation; and (vi) current antibody/immunoconjugate approaches for the treatment of pediatric malignancies. During the past decade, major advances have been made in improving the efficacy of these modalities and regulatory hurdles have been taken. Nevertheless, there is still a long way to go to fully exploit the potential of immunotherapeutic strategies to improve the cure of children and adolescents with malignancies. This and future meetings will support new collaborations and insights for further translational and clinical immunotherapy studies.
Kernel‐Machine Testing Coupled with a Rank‐Truncation Method for Genetic Pathway Analysis

Traditional genome‐wide association studies (GWASs) usually focus on single‐marker analysis, which only accesses marginal effects. Pathway analysis, on the other hand, considers biological pathway gene marker hierarchical structure and therefore provides additional insights into the genetic architecture underlining complex diseases. Recently, a number of methods for pathway analysis have been proposed to assess the significance of a biological pathway from a collection of single‐nucleotide polymorphisms. In this study, we propose a novel approach for pathway analysis that assesses the effects of genes using the sequence kernel association test and the effects of pathways using an extended adaptive rank truncated product statistic. It has been increasingly recognized that complex diseases are caused by both common and rare variants. We propose a new weighting scheme for genetic variants across the whole allelic frequency spectrum to be analyzed together without any form of frequency cutoff for defining rare variants. The proposed approach is flexible. It is applicable to both binary and continuous traits, and incorporating covariates is easy. Furthermore, it can be readily applied to GWAS data, exome‐sequencing data, and deep resequencing data. We evaluate the new approach on data simulated under comprehensive scenarios and show that it has the highest power in most of the scenarios while maintaining the correct type I error rate. We also apply our proposed methodology to data from a study of the association between bipolar disorder and candidate pathways from Wellcome Trust Case Control Consortium (WTCCC) to show its utility.
A Communication-Centric Approach To Instruction Steering For Future Clustered Processors

In any clustered processor, there is a mechanism that determines the assignment of instructions to clusters. One key goal of this instruction steering mechanism is to minimize inter-cluster communication. As feature size decreases and the number of clusters increases, the relative cost of inter-cluster communication will increase, requiring even greater focus on optimizing inter-cluster communication. To this end, we propose the CSPAN (Communication Span) instruction steering algorithm that controls the communication cost by controlling the distance that values must traverse to reach dependent instructions. This is done without imposing absolute constraints on resource utilization. The scheme dynamically adapts to the characteristics of the program, imposing communication locality only to the extent that it is beneficial to performance. Experimental results demonstrate that CSPAN is able to outperform the best known Advanced RMBS steering algorithm by around 13% over a set of SPEC2000 and MediaBench applications. This improvement comes from a reduction of 28% in the inter-cluster communication penalty without any noticeable change in resource contention. Also, CSPAN is able to improve performance by 10% compared to prior work on dynamic communication/parallelism tradeoff.
Characterization of the Existing Soil Management Groups in terms of their Physical and Hydraulic Properties at Metahara Sugarcane Plantation

Ninety eight disturbed and undisturbed samples were taken from surface and subsurface layers of Metahara sugarcane plantation soils in order to characterize them in terms of their physical and hydraulic properties, and develop pedotransfer functions for estimating water contents at field capacity (FC) and permanent wilting point (PWP). The mean values of the measured soil properties indicated that bulk density, particle density, total porosity, sand content, silt content, clay content and organic matter content varied from 1.01 to 1.43 g cm-3, 2.23 to 2.76 g cm -3 , 40.91 to 61.42 9.3 to 40 %, 12.8 to 35.3 %, 33 to 76.3 %, and 0.84 to 2.69 %, respectively. Moreover, the available water holding capacity, the mean saturated hydraulic conductivity, the basic infiltration rate varied from 99.71 to 212.01 mm m -1 , 0.96 to 5.95 m s -1 , and 0.43 to 3.68 cm hr -1 , respectively. In addition, the soil water retention characteristic curves (SWRCC) indicated the presence of three distinct groups of soils in the plantation unlike the previous characterization, i.e. six groups. Furthermore, the equation developed using clay content and bulk density as predictor variables was found to be the best equation for predicting gravimetric water content at field capacity and permanent wilting point with reasonable accuracy. Therefore, the existing irrigation scheduling should be revised based on the three soil groups.
A fuzzy object query language (FOQL) for image databases

Content based retrieval systems have been developed for querying image data in which the users can pose queries based on visual properties such as color and texture. These systems, which have advanced the state of the art in image database systems, remarkably lack formal query languages. The traditional query languages are unable to capture the inherent fuzzy nature of the image data and content based querying. The fuzzy object query language (FOQL) presented in this paper addresses the need to support fuzzy values and fuzzy collections required for image databases. It can be used for defining schemas and high level concepts, and for querying image databases. It captures the inherent fuzzy nature of content based retrieval by keeping the query results fuzzy as against other query languages. The users can interactively refine their queries and high level concept definitions using recursive and named query definition constructs in FOQL. Being an extension of ODMG-OQL, FOQL can be easily mapped to ODMG-compliant visual query languages.
Damage behavior of 200-nm thin copper films under cyclic loading

Fatigue damage in 200-nm-thick Cu films was investigated and compared with the damage in thicker Cu films. The fatigued 200-nm-thick Cu films exhibited only a few, small extrusions and extensive cracking along twin and grain boundaries, whereas the thicker films showed many extrusions/intrusions and cracks lying along the extrusions rather than along the boundaries. This change in fatigue damage behavior with film thickness is attributed to the inhibition of dislocation mobility and the limited availability and activation of dislocation sources on the small length scale. It is argued that the decrease in film thickness and grain size inhibits the localized accumulation of plastic strain within grains, such as at extrusions/intrusions and in extended dislocation structures, and promotes the formation of damage such as cracks at twin and grain boundaries during fatigue. This effect is suggested as the likely cause for the increase in fatigue life with decreasing specimen dimensions.
Primosome assembly site in Bacillus subtilis.

A single‐strand initiation site was detected on the Enterococcus faecalis plasmid pAM beta 1 by its ability to prevent accumulation of single stranded DNA of a rolling circle plasmid, both in Bacillus subtilis and Staphylococcus aureus. This site, designated ssiA, is located on the lagging strand template, approximately 150 bp downstream from the replication origin. ssiA priming activity requires the DnaE primase, the DnaC replication fork helicase, as well as the products of the dnaB, dnaD and dnaI genes of B.subtilis, but not the RNA polymerase. The primase and the replication fork helicase requirements indicate that ssiA is a primosome assembly site. Interestingly, the pAM beta 1 lagging strand synthesis is inefficient when any of the proteins involved in ssiA activity is mutated, but occurs efficiently in the absence of ssiA. This suggests that normal plasmid replication requires primosome assembly and that the primosome can assemble not only at ssiA but also elsewhere on the plasmid. This work for the first time describes a primosome in a Gram‐positive bacterium. Involvement of the B.subtilis proteins DnaB, DnaD and DnaI, which do not have any known analogue in Escherichia coli, raises the possibility that primosome assembly and/or function in B.subtilis differs from that in E.coli.
MaxCut in ${\bm H)$-Free Graphs

For a graph G, let f(G) denote the maximum number of edges in a cut of G. For an integer m and for a fixed graph H, let $f(m,H)$ denote the minimum possible cardinality of $f(G)$, as G ranges over all graphs on m edges that contain no copy of H. In this paper we study this function for various graphs H. In particular we show that for any graph H obtained by connecting a single vertex to all vertices of a fixed nontrivial forest, there is a $c(H) >0$ such that $f(m,H) \geq \frac{m}{2} + c(H) m^{4/5}$, and that this is tight up to the value of $c(H)$. We also prove that for any even cycle $C_{2k}$ there is a $c(k)>0$ such that $f(m,C_{2k}) \geq \frac{m}{2} + c(k) m^{(2k+1)/(2k+2)}$, and that this is tight, up to the value of $c(k)$, for $2k\in \{4,6,10\}$. The proofs combine combinatorial, probabilistic and spectral techniques.