Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K‐12

Mining the emerging abundance of microbial genome sequences for hypotheses is an exciting prospect of “functional genomics”. At the forefront of this effort, we compared the predictions of the complete Escherichia coli genomic sequence with the observed gene products by assessing 381 proteins for their mature N‐termini, in vivo abundances, isoelectric points, molecular masses, and cellular locations. Two‐dimensional gel electrophoresis (2‐DE) and Edman sequencing were combined to sequence Coomassie‐stained 2‐DE spots representing the abundant proteins of wild‐type E. coli K‐12 strains. Greater than 90% of the abundant proteins in the E. coli proteome lie in a small isoelectric point and molecular mass window of 4–7 and 10–100 kDa, respectively. We identified several highly abundant proteins, YjbJ, YjbP, YggX, HdeA, and AhpC, which would not have been predicted from the genomic sequence alone. Of the 223 uniquely identified loci, 60% of the encoded proteins are proteolytically processed. As previously reported, the initiator methionine was efficiently cleaved when the penultimate amino acid was serine or alanine. In contrast, when the penultimate amino acid was threonine, glycine, or proline, cleavage was variable, and valine did not signal cleavage. Although signal peptide cleavage sites tended to follow predicted rules, the length of the putative signal sequence was occassionally greater than the consensus. For proteins predicted to be in the cytoplasm or inner membrane, the N‐terminal amino acids were highly constrained compared to proteins localized to the periplasm or outer membrane. Although cytoplasmic proteins follow the N‐end rule for protein stability, proteins in the periplasm or outer membrane do not follow this rule; several have N‐terminal amino acids predicted to destabilize the proteins. Surprisingly, 18% of the identified 2‐DE spots represent isoforms in which protein products of the same gene have different observed pI and Mr, suggesting they are post‐translationally processed. Although most of the predicted and observed values for isoelectric point and molecular mass show reasonable concordance, for several proteins the observed values significantly deviate from the expected values. Such discrepancies may represent either highly processed proteins or misinterpretations of the genomic sequence. Our data suggest that AhpC, CspC, and HdeA exist as covalent homomultimers, and that IcdA exists as at least three isoforms even under conditions in which covalent modification is not predicted. We enriched for proteins based on subcellular location and found several proteins in unexpected subcellular locations.
A Novel Protocol for Accuracy Assessment in Classification of Very High Resolution Multispectral and SAR Images

This paper presents a novel protocol for the accuracy assessment of thematic maps obtained by the classification of very high resolution images. As the thematic accuracy alone is not sufficient to adequately characterize the geometrical properties of classification maps, we propose a novel protocol that is based on the analysis of two families of indexes: (i) the traditional thematic accuracy indexes, and (ii) a set of geometric indexes that characterize different geometric properties of the objects recognized in the map. These indexes can be used in the training phase of a classifier for identifying the parameters values that optimize classification results on the basis of a multi-objective criterion. Experimental results obtained on Quickbird images show the effectiveness of the proposed protocol in selecting classification maps characterized by better tradeoff between thematic and geometric accuracy with respect to standard accuracy measures.
An Online Algorithm for Learning Selectivity to Mixture Means

We develop a biologically-plausible learning rule called Triplet BCM that provably converges to the class means of general mixture models. This rule generalizes the classical BCM neural rule, and provides a novel interpretation of classical BCM as performing a kind of tensor decomposition. It achieves a substantial generalization over classical BCM by incorporating triplets of samples from the mixtures, which provides a novel information processing interpretation to spike-timing-dependent plasticity. We provide complete proofs of convergence of this learning rule, and an extended discussion of the connection between BCM and tensor learning.
Trust Key Management Scheme for Wireless Body Area Networks

With recent advances in wireless sensor networks and embedded computing technologies, miniaturized pervasive health monitoring devices have become practically feasible. In addition to providing continuous monitoring and analysis of physiological parameters, the recently pro- posed Wireless Body Area Networks (WBAN) incorporates context aware sensing for increased sensitivity and specificity. A number of tiny wireless sensors, strategically placed on the human body, create a WBAN that can monitor various vital signs, providing real-time feed-back to the user and medical personnel. The wireless body area networks promise to revolutionize health monitoring. Since the sensors collect personal medical data, security and privacy are important components in this kind of networks. It is a challenge to implement traditional security infrastructures in these types of lightweight networks, since they are by design limited in both computational and communication resources. A key enabling technology for secure communications in WBANs has emerged to be biometrics. In this paper, we present an approach that exploits physiological signals (electrocardiogram (ECG)) to address security issues in WBAN: a Trust Key Management Scheme for Wireless Body Area Network. This approach manages the generation and distribution of symmetric cryptographic keys to constituent sensors in a WBAN (using ECG signal) and protects the privacy.
Integrin αvβ5 Regulates Lung Vascular Permeability and Pulmonary Endothelial Barrier Function

Increased lung vascular permeability is an important contributor to respiratory failure in acute lung injury (ALI). We found that a function-blocking antibody against the integrin αvβ5 prevented development of lung vascular permeability in two different models of ALI: ischemia-reperfusion in rats (mediated by vascular endothelial growth factor [VEGF]) and ventilation-induced lung injury (VILI) in mice (mediated, at least in part, by transforming growth factor-β [TGF-β]). Knockout mice homozygous for a null mutation of the integrin β5 subunit were also protected from lung vascular permeability in VILI. In pulmonary endothelial cells, both the genetic absence and blocking of αvβ5 prevented increases in monolayer permeability induced by VEGF, TGF-β, and thrombin. Furthermore, actin stress fiber formation induced by each of these agonists was attenuated by blocking αvβ5, suggesting that αvβ5 regulates induced pulmonary endothelial permeability by facilitating interactions with the actin cytoskeleton. These results identify integrin αvβ5 as a central regulator of increased pulmonary vascular permeability and a potentially attractive therapeutic target in ALI.
A Java Applet for Exploring the New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

ABSTRACT. We have converted the hierarchically organized new higher level classification of eukaryotes with emphasis on the taxonomy of protists proposed by Adl et al. into an interactive and dynamic Java applet. The current version of the applet can be accessed via http://phylogenetics.bioapps. biozentrum.uni‐wuerzburg.de/etv. We use the layout from a Degree‐of‐Interest tree (DOITree) that effectively displays all the taxonomic information as well as the phylogenetic relationships described in the original article by Adl et al. The tree was made using the Prefuse Toolkit for interactive information visualization. All browsers capable of using Java applets will be able to view the tree. The applet is freely available for scientists, teachers, and students.
The HOX Homeodomain Proteins Block CBP Histone Acetyltransferase Activity

ABSTRACT Despite the identification of PBC proteins as cofactors that provide DNA affinity and binding specificity for the HOX homeodomain proteins, HOX proteins do not demonstrate robust activity in transient-transcription assays and few authentic downstream targets have been identified for these putative transcription factors. During a search for additional cofactors, we established that each of the 14 HOX proteins tested, from 11 separate paralog groups, binds to CBP or p300. All six isolated homeodomain fragments tested bind to CBP, suggesting that the homeodomain is a common site of interaction. Surprisingly, CBP-p300 does not form DNA binding complexes with the HOX proteins but instead prevents their binding to DNA. The HOX proteins are not substrates for CBP histone acetyltransferase (HAT) but instead inhibit the activity of CBP in both in vitro and in vivo systems. These mutually inhibitory interactions are reflected by the inability of CBP to potentiate the low levels of gene activation induced by HOX proteins in a range of reporter assays. We propose two models for HOX protein function: (i) HOX proteins may function without CBP HAT to regulate transcription as cooperative DNA binding molecules with PBX, MEIS, or other cofactors, and (ii) the HOX proteins may inhibit CBP HAT activity and thus function as repressors of gene transcription.
Bridging the Gap between Geometric and Task Level Manipulation Planning

In manipulation planning works like [Siméon et al., 2000], although two levels have been distinguished, calling “task level” to the higher one, actually everything has been formulated in geometric terms. However, when properly talking about task planning, an abstract symbolic formulation is generally meant. And complex manipulation tasks may require some kind of symbolic structuring in order to bound the huge search space at geometric level.
Solving and creating difficult instances of Post's correspondence problem

Post’s correspondence problem (PCP) was invented by Emil L. Post in 1946. It is an undecidable problem, which means that it is impossible to find an algorithm to solve the whole problem. This problem has been extensively discussed in the theoretical computer science literature, but only recently did some researchers begin to look into the empirical properties of this problem. Although this problem cannot be completely solved, some of its instances can be solved and may have very long solutions. It is instructive and important to find instances that have very long shortest solutions to reveal new properties and understand the complexity of this problem. In this thesis, several problem-specific search enhancements have been employed to find the shortest solutions of instances efficiently and effectively. New disproof methods were invented to identify instances that have no solution. All of these methods made it possible to completely solve 7 PCP subclasses and to fully scan 3 other PCP subclasses. Our effort culminated in the discovery of 199 hard instances with very long shortest solutions and in setting new records for the hardest instances known in 4 PCP subclasses. In addition, we present experimental results on several important properties of PCP and on the search and disproof methods used. These results will lead to a better understanding of the theoretical and empirical properties of this problem.
Multispectral Remote Sensing from Unmanned Aircraft: Image Processing Workflows and Applications for Rangeland Environments

Using unmanned aircraft systems (UAS) as remote sensing platforms offers the unique ability for repeated deployment for acquisition of high temporal resolution data at very high spatial resolution. Multispectral remote sensing applications from UAS are reported in the literature less commonly than applications using visible bands, although light-weight multispectral sensors for UAS are being used increasingly. In this paper, we describe challenges and solutions associated with efficient processing of multispectral imagery to obtain orthorectified, radiometrically calibrated image mosaics for the purpose of rangeland vegetation classification. We developed automated batch processing methods for file conversion, band-to-band registration, radiometric correction, and orthorectification. An object-based image analysis approach was used to derive a species-level vegetation classification for the image mosaic with an overall accuracy of 87%. We obtained good correlations between: (1) ground and airborne spectral reflectance (R 2 = 0.92); and (2) spectral reflectance derived from airborne and WorldView-2 satellite data for selected vegetation and soil targets. UAS-acquired multispectral imagery provides quality high resolution information for rangeland applications with the potential for upscaling the data to larger areas using high resolution satellite imagery.
Quantification of Abdominal Fat in Obese and Healthy Adolescents Using 3 Tesla Magnetic Resonance Imaging and Free Software for Image Analysis

Background and Aims Computed tomography, which uses ionizing radiation and expensive software packages for analysis of scans, can be used to quantify abdominal fat. The objective of this study is to measure abdominal fat with 3T MRI using free software for image analysis and to correlate these findings with anthropometric and laboratory parameters in adolescents. Methods This prospective observational study included 24 overweight/obese and 33 healthy adolescents (mean age 16.55 years). All participants underwent abdominal MRI exams. Visceral and subcutaneous fat area and percentage were correlated with anthropometric parameters, lipid profile, glucose metabolism, and insulin resistance. Student’s t test and Mann-Whitney’s test was applied. Pearson’s chi-square test was used to compare proportions. To determine associations Pearson’s linear correlation or Spearman’s correlation were used. Results In both groups, waist circumference (WC) was associated with visceral fat area (P = 0.001 and P = 0.01 respectively), and triglycerides were associated with fat percentage (P = 0.046 and P = 0.071 respectively). In obese individuals, total cholesterol/HDL ratio was associated with visceral fat area (P = 0.03) and percentage (P = 0.09), and insulin and HOMA-IR were associated with visceral fat area (P = 0.001) and percentage (P = 0.005). Conclusions 3T MRI can provide reliable and good quality images for quantification of visceral and subcutaneous fat by using a free software package. The results demonstrate that WC is a good predictor of visceral fat in obese adolescents and visceral fat area is associated with total cholesterol/HDL ratio, insulin and HOMA-IR.
A Differentiated Services Code Point (DSCP) for Capacity-Admitted Traffic

This document requests one DSCP from the IANA for real-time traffic classes similar to voice conforming to the Expedited Forwarding Per Hop Behavior, and admitted using a CAC procedure involving authentication, authorization, and capacity admission, as compared to a class of real-time traffic conforming to the Expedited Forwarding Per Hop Behavior but not subject to capacity admission or subject to very coarse capacity admission. It also recommends that certain classes of video traffic described in RFC 4594 and which have similar requirements be require admission using a CAC procedure involving authentication, authorization, and capacity admission. One of the reasons behind this is the need for classes of traffic that are handled under special policies, such as the non-preemptive Emergency Telecommunication Service, the US DoD's Assured Service (which is similar to MLPP), or e-911. Capacity-admitted traffic classes need separation from traffic not subject to admission control, from which they can deterministically obtain their service requirements, including SLA matters.
T-wave alternans predicts mortality in a population undergoing a clinically indicated exercise test.

AIMS As a part of the Finnish Cardiovascular Study, we tested the hypothesis that T-wave alternans (TWA) predicts mortality in a general population of patients referred for a clinical exercise test. METHODS AND RESULTS A total of 1037 consecutive patients (mean age+/-SD of 58+/-13 years, 673 men and 364 women) with a clinically indicated exercise test and with technically successful electrocardiographic (ECG) data during a bicycle ergometer test were included in the study. Digital ECGs were recorded and TWA was analysed continuously with the time-domain modified moving average method. The maximum TWA value at heart rate (HR)<125 b.p.m. was derived and its capacity to stratify risk for all-cause death, cardiovascular death, and sudden cardiac death (SCD) was tested. During a follow-up of 44+/-7 months (mean+/-SD), 59 patients died; 34 were due to cardiovascular causes and 20 were due to SCD. In multivariate analysis after adjustment for age, sex, use of beta-blockers, functional class, maximal HR during exercise, previous myocardial infarction, and other common coronary risk factors, the relative risk of TWA>or=65 microV for SCD was 7.4 (95% CI, 2.8-19.4; P<0.001), for cardiovascular mortality 6.0 (95% CI, 2.8-12.8; P<0.001), and for all-cause mortality 3.3 (95% CI, 1.8-6.3; P=0.001). CONCLUSION Time-domain TWA analysis powerfully predicts mortality in a general population undergoing a clinical exercise test.
Predictive coding in a homomorphic vocoder

Application of a type of predictive coding to the channel signals of a homomorphic vocoder has produced sizable bit rate reductions. With only slight degradation in speech quality, reduction (for the spectral envelope information) from 7800 to 4000 bits/s was achieved. A technique for obtaining the formant frequencies from the predictive coding parameters is described; this approach promises further bit rate reductions. As a by-product of this study of predictive coding, direct and cascade form speech synthesizers are compared on the basis of differing quantization effects.
A novel design of flexible foot system for humanoid robot

The Large-scale uneven ground is mostly unsmooth and in the irregular state in which the irregularity is usually unknown (such as footway, carriageway, unexplored desert, mountainous area, surface of the Mars). In order to walk steadily and rapidly on such ground, a chief problem to overcome is that the humanoid robot¿s foot is not matching with the unknown model of the ground. Therefore, the humanoid robot¿s foot should have the flexibility mimic the human¿s foot, and can adapt to and steadily interacted with any unsmooth ground. Also interferences and disjoints between soles and irregular unsmooth ground should be avoided. Aiming at solving the key problem for humanoid robot to steadily and rapidly walk on the large-scale and three- dimension uneven ground, we¿ve set up a new multidegree- of-freedom flexible foot mechanism which can make the humanoid robot¿s walking gesture and gait automatically adapt to the terrain, and then carry out the research of the globally stable control of the gait. The flexibility can obviously improve the humanoid robot¿s walking stability and speediness on the large-scale uneven ground.
Antiangiogenic Effect of Interleukin-10 in Ischemia-Induced Angiogenesis in Mice Hindlimb

Ischemia induces both hypoxia and inflammation that trigger angiogenesis. The inflammatory reaction is modulated by production of anti-inflammatory cytokines. This study examined the potential role of a major anti-inflammatory cytokine, interleukin (IL)–10, on angiogenesis in a model of surgically induced hindlimb ischemia. Ischemia was produced by artery femoral occlusion in both C57BL/6J IL-10+/+ and IL-10–/– mice. After 28 days, angiogenesis was quantified by microangiography, capillary, and arteriole density measurement and laser Doppler perfusion imaging. The protein levels of IL-10 and vascular endothelial growth factor (VEGF) were determined by Western blot analysis in hindlimbs. IL-10 was markedly expressed in the ischemic hindlimb of IL-10+/+ mice. Angiogenesis in the ischemic hindlimb was significantly increased in IL-10–/– compared with IL-10+/+ mice. Indeed, angiographic data showed that vessel density in the ischemic leg was 10.2±0.1% and 5.7±0.4% in IL-10–/– and IL-10+/+ mice, respectively (P <0.01). This corresponded to improved ischemic/nonischemic leg perfusion ratio by 1.4-fold in IL-10–/– mice compared with IL-10+/+ mice (0.87±0.05 versus 0.63±0.01, respectively;P <0.01). Revascularization was associated with a 1.8-fold increase in tissue VEGF protein level in IL-10–/– mice compared with IL-10+/+ mice (P <0.01). In vivo electrotransfer of murine IL-10 cDNA in IL-10–/– mice significantly inhibited both the angiogenic process and the rise in VEGF protein level observed in IL-10–/– mice. No changes in vessel density or VEGF content were observed in the nonischemic hindlimb. These findings underscore the antiangiogenic effect of IL-10 associated with the downregulation of VEGF expression and suggest a role for the inflammatory balance in the modulation of ischemia-induced angiogenesis.
A Smart-Dumb/Dumb-Smart Algorithm for Efficient Split-Merge MCMC

Split-merge moves are a standard component of MCMC algorithms for tasks such as multi-target tracking and fitting mixture models with unknown numbers of components. Achieving rapid mixing for split-merge MCMC has been notoriously difficult, and state-of-the-art methods do not scale well. We explore the reasons for this and propose a new split-merge kernel consisting of two sub-kernels: one combines a "smart" split move that proposes plausible splits of heterogeneous clusters with a "dumb" merge move that proposes merging random pairs of clusters; the other combines a dumb split move with a smart merge move. We show that the resulting smart-dumb/dumb-smart (SDDS) algorithm outperforms previous methods. Experiments with entity-mention models and Dirichlet process mixture models demonstrate much faster convergence and better scaling to large data sets.
Enhancing Green Absorptive Capacity, Green Dynamic Capacities and Green Service Innovation to Improve Firm Performance: An Analysis of Structural Equation Modeling (SEM)

This study discusses the influences of green absorptive capacity, green dynamic capacities, and green service innovation on firm performance. In order to fill the research gap, this study proposes the concept of green service innovation. The results are as follows: First, this study finds that green absorptive capacity has positive effects on green dynamic capacities, green service innovation, and firm performance. Second, this study points out that green dynamic capacities have positive effects on green service innovation and firm performance. Third, this study observes that green dynamic capacities and green service innovation intercede the positive connection between green absorptive capacity and firm performance.
Differential Impacts of Solar UV Radiation on Photosynthetic Carbon Fixation from the Coastal to Offshore Surface Waters in the South China Sea

We carried out experiments during an expedition (14 August to 14 September, 2007) that covered up to 250 000 km2 to investigate the effects of solar UV radiation (UVR, 280–400 nm) on the photosynthetic carbon fixation of tropical phytoplankton assemblages in surface seawater of the South China Sea. From coastal to pelagic surface seawaters, UV‐B (280–315 nm) caused similar inhibition, while UV‐A (315–400 nm) induced photosynthetic inhibition increased from coastal to offshore waters. UV‐B resulted in an inhibition by up to 27% and UV‐A by up to 29%. Under reduced levels of solar radiation with heavy overcast, UV‐A resulted in enhanced photosynthetic carbon fixation by up to 25% in coastal waters where microplankton was abundant. However, such a positive impact was not observed in the offshore waters where piconanoplankton was more abundant. The daily integrated inhibition of UV‐A reached 4.3% and 13.2%, and that of UV‐B reached 16.5% and 13.5%, in the coastal and offshore waters, respectively.