Miracle-dz/UniFAR-FTUs huggingface dataset:
Central-pair microtubular complex of Chlamydomonas flagella: polypeptide composition as revealed by analysis of mutants

Four mutants of Chlamydomonas reinhardtii representing independent gene loci have been shown to lack totally (pf-18, pf-19, and pf-15) or nearly totally (pf-20) the central microtubular pair complex in isolated axonemal preparations. Analysis of 35S-labeled axonemal proteins, using two methods of electrophoresis, reveals that all four mutants lack or are markedly deficient in 18 polypeptides, ranging in molecular weight from 360,000 to 20,000, that are regularly present in wild-type axonemes. Analyses of axonemal proteins labeled by cellular growth on 32P-labeled medium indicates that a subset of 8 of the 18 polypeptides are phosphorylated. Mutant and wild-type axonemes and flagella have been analyzed for their content of tubulin subunits using a high resolution two-dimensional electrophoresis system combined with agarose gel overlays containing either anti-alpha or anti-beta tubulin sera prepared from Chlamydomonas tubulins. The immunoprecipitates identify two major alpha tubulins, a major beta tubulin, and a minor component which is also precipitated by the anti-beta serum. None of these tubulins shows a specific defect in mutant axonemes, nor do the tubulin polypeptides show altered two-dimensional map positions in the mutant flagella. The 18 polypeptides provide a useful signature for identifying other mutants affecting the central-pair microtubular complex. Such mutants could be useful in defining the structural or functional role of these polypeptides in the central microtubules. Efforts to obtain additional central-pair mutants based on the motility phenotype of the four mutants analyzed here have yielded mutants which are allelic to three of the four mutants.
Large-scale Chromosomal Movements During Interphase Progression in Drosophila

We examined the effect of cell cycle progression on various levels of chromosome organization in Drosophila. Using bromodeoxyuridine incorporation and DNA quantitation in combination with fluorescence in situ hybridization, we detected gross chromosomal movements in diploid interphase nuclei of larvae. At the onset of S-phase, an increased separation was seen between proximal and distal positions of a long chromsome arm. Progression through S-phase disrupted heterochromatic associations that have been correlated with gene silencing. Additionally, we have found that large-scale G1 nuclear architecture is continually dynamic. Nuclei display a Rabl configuration for only ∼2 h after mitosis, and with further progression of G1-phase can establish heterochromatic interactions between distal and proximal parts of the chromosome arm. We also find evidence that somatic pairing of homologous chromosomes is disrupted during S-phase more rapidly for a euchromatic than for a heterochromatic region. Such interphase chromosome movements suggest a possible mechanism that links gene regulation via nuclear positioning to the cell cycle: delayed maturation of heterochromatin during G1-phase delays establishment of a silent chromatin state.
Significance of intraplaque neovascularisation for vulnerability: optical coherence tomography study

Objectives This study aimed to investigate the role of intraplaque neovascularisation (NV) in culprit lesions and non-culprit lesions of unstable angina pectoris (UAP) and in lesions of stable angina pectoris (SAP) using optical coherence tomography (OCT). Design This study was a retrospective study. Setting The significance of NV for culprit and non-culprit plaques remains unclear. Participants A total of 356 plaques from 92 UAP patients and 25 SAP patients who underwent OCT imaging were divided into three groups: culprit lesions in UAP (92), non-culprit lesions in UAP (203) and lesions of SAP (61). Main outcome measures NV and plaque characteristics were examined by OCT and plaques with and without NV were compared. Results Among UAP culprit lesions, plaques with NV had significantly higher incidence of thin cap fibroatheroma (81% vs 47%, p=0.002) compared with those without NV. In addition, the fibrous cap was thinner (56±20 μm vs 75±30 μm, p<0.001), lipid arc was greater (254±66° vs 222±65°, p=0.024) and lipid core length was longer (13±5 mm vs 10±6 mm, p=0.007). No significant difference was observed between non-culprit lesions of UAP with and without NV, and between lesions of SAP with and without NV. Conclusion In patients with UAP, the culprit plaques with NV had vulnerable features such as thinner fibrous cap, greater lipid arc, longer lipid core length and more frequent thin cap fibroatheroma compared with those without NV. In both non-culprit lesions of UAP patients and in lesions of SAP patients NV was not associated with vulnerable plaque characteristics.
Regular Physical Activity Improves Endothelial Function in Patients With Coronary Artery Disease by Increasing Phosphorylation of Endothelial Nitric Oxide Synthase

Background—In stable coronary artery disease (CAD), exercise training has well-documented positive effects on arterial endothelial function. NO derived from endothelial NO synthase (eNOS) is regarded as a protective factor against atherosclerosis. The aim of the present study was to investigate the effects of exercise training on the endothelial function in relation to the expression of eNOS and Akt-dependent eNOS phosphorylation in the left internal mammary artery (LIMA) of patients with stable CAD. Methods and Results—In 17 training patients (T) and 18 control patients (C), endothelium-dependent vasodilation and average peak flow velocity (APV) in response to acetylcholine were measured invasively at study beginning and after 4 weeks in the LIMA. In LIMA tissue sampled during bypass surgery, eNOS expression and content of pospho-eNOS-Ser1177, Akt, and phospho-Akt were determined by Western blot and quantitative reverse transcriptase–polymerase chain reaction. After exercise training, LIMA APV in response to acetylcholine was increased by 56±8% (from +48±8% at beginning to +104±11% after 4 weeks, P <0.001). Patients in T had a 2-fold higher eNOS protein expression (T 1.0±0.7 versus C 0.5±0.3 arbitrary units, P <0.05) and 4-fold higher eNOS Ser1177-phosphorylation levels in LIMA-endothelium (1.2±0.9 versus 0.3±0.2 arbitrary units, P <0.01). A linear correlation was confirmed between Akt phosphorylation and phospho-eNOS levels (R =0.80, P <0.05) and between phospho-eNOS and &Dgr; APV (R =0.59, P <0.05). Conclusions—Exercise training in stable CAD leads to an improved agonist-mediated endothelium-dependent vasodilatory capacity. The change in acetylcholine-induced vasodilatation was closely related to a shear stress–induced/Akt-dependent phosphorylation of eNOS on Ser1177.
Considering Relativistic Symmetry as the First Principle of Quantum Mechanics

On the basis of the relativistic symmetry of Minkowski space, we derive a Lorentz invariant equation for a spread electron. This equation slightly differs from the Dirac equation and includes additional terms originating from the spread of an electron. Further, we calculate the anomalous magnetic moment based on these terms. These calculations do not include any divergence; therefore, renormalization procedures are unnecessary. In addition, the relativistic symmetry existing among coordinate systems will provide a new prospect for the foundations of quantum mechanics like the measurement process.
Fingerprints of the Visible Hand. Chandlerian Organizations and Their Inward Looking Malaise

This paper investigates the relationships between firm organization attributes, namely a structure a la Chandler, and their inward looking or “exploitation” attitude in R&D and innovation. We argue that because of sunk costs and learning processes an inward looking behavior is a consequence of increases in firm size. However, it is also produced by an organizational model based on hierarchical managerial decisions, typical of the Chandlerian firms, that is not directly related to size. We find that the US States populated by larger firms show a higher share of patent self-citations normalized by their share of world patents. Even after controlling for firm size, a proxy for the extent of firm divisionalization in the States exhibits a significant effect on patent self-citations normalized by patent shares. This supports our point that the inward looking behavior of the Chandlerian firms is not just a consequence of size, but also of the Chandlerian organizational model. Among other things, this suggests that “exploration”, which leads to the opening of new innovation trajectories, requires not only small firms, but also different organizational setups and decision processes.
Endocytosis is required for the growth of vacuolar H(+)-ATPase- defective yeast: identification of six new END genes

Yeast mutants that are defective in acidification of the lysosome-like vacuole are able to grow at pH 5.5, but not at pH 7. Here, we present evidence that endocytosis is required for this low pH-dependent growth and use this observation to develop a screen for mutants defective in endocytosis. By isolating mutants that cannot grow when they lack the 60-kD vacuolar ATPase subunit (encoded by the VAT2 gene), we isolated a number of vat2-synthetic lethal (Vsl-) mutant strains. Seven of the Vsl- mutants are defective in endocytosis. Four of these mutant strains (end8-1, end9-1, end10-1, and end11-1) show altered uptake of the endocytosed ligand, alpha-factor, and three (end12-1, end12-2, and end13-1) are probably defective in transfer of internalized material to the vacuole. Most of the mutations also confer a strong Ts- growth defect. The mutants defective in uptake of alpha-factor sort newly synthesized vacuolar proteins correctly, while those which may be defective in subsequent transport steps secrete at least a fraction of the newly synthesized soluble vacuolar proteins. The mutations that result in a defect in alpha-factor uptake are not allelic to any of the genes previously shown to encode endocytic functions.
Vlgr1 is required for proper stereocilia maturation of cochlear hair cells

Very large G‐protein coupled receptor (Vlgr1b) is the largest known G‐protein coupled receptor. Its function is unknown, although mice with deletion of Vlgr1 (Vlgr1b together with other splicing variants, Vlgr1c, Vlgr1d and Vlgr1e) are known to exhibit audiogenic seizure susceptibility and VLGR1 is reported to be the gene responsible for Usher type 2C syndrome. We demonstrated here that Vlgr1‐mutated mice suffered from a hearing defect because of inner ear dysfunction, as indicated by auditory brainstem response (ABR) and distortion product oto‐acoustic emissions (DPOAE). The expression of Vlgr1 was identified in the developing hair cells perinatally, and the translated products were seen to be localized in the base of stereocilia on hair cells using confocal microscopy. This Vlgr1 localization was limited to the base of stereocilia within approximately 200–400 nm from the apical surface of hair cells, as shown by immunoelectron microscopy. The Vlgr1‐mutated mice exhibited malformation of the stereocilia; the cochlear hair bundles were apparently normal at birth but then became disarranged at postnatal day 8. Furthermore, the stereocilia in the mutant mice became slanted and disarranged thereafter. These results indicate that loss of Vlgr1 resulted in abnormal development of stereocilia formation.
Dynamic Meta-Learning for Failure Prediction in Large-Scale Systems: A Case Study

Despite great efforts on the design of ultra-reliable components, the increase of system size and complexity has outpaced the improvement of component reliability. As a result, fault management becomes crucial in high performance computing. The advance of fault management relies on effective failure prediction. Despite years of research on failure prediction, it remains an open problem, especially in large-scale systems. In this paper, we address the problem by presenting a dynamic meta-learning prediction engine. It extends our previous work by exploring dynamic training, testing and prediction. Here, the "dynamic" part is from two perspectives: one is to continuously increase the training set during the system operation; and the other is to dynamically modify the rules of failure patterns by tracing prediction accuracy at runtime. Our case study indicates that the proposed predictor is promising by being capable of capturing more than 70% of failures, with the false alarm rate less than 10%.
Application status and evaluation method of renewable energy in green building in China

Application status of solar energy and geothermal energy in Green Building Label (GBL) projects is investigated at first. Then, characteristic features of provisions for evaluating renewable energy utilization in current Chinese national standard are analyzed. It's followed by introduction of evaluation method for renewable energy in other green building systems. At last, discussion on scientific and technical rationality of the evaluation method is proposed. The investigation and analysis could be helpful for revising related provisions in current Chinese standard.
Multimedia service configuration and reservation in heterogeneous environments

Widely deployed multimedia services are expected to accommodate clients in a highly heterogeneous environment. Clients of a multimedia service may vary greatly in processing and communication capabilities. In addition, due to workload, location, and service time differences, the availability of end-to-end resources between a client and a server may also vary. Current solutions tend to focus on either the qualitative heterogeneity (in client and resource types) or the quantitative heterogeneity (in resource availability) problem. We present a framework for dynamic end-to-end multimedia service configuration and reservation: an integrated solution to both aspects of the heterogeneity problem. Service configuration is responsible for choosing appropriate service components to compose a customized service deliver to each client; while service reservation is responsible for reserving the end-to-end resources in a coordinated manner and providing the best possible quality within the chosen configuration. We have implemented a prototype of this framework as part of the 2K operating system and tested it by building a proof-of-concept video streaming service on top of it. Our experiments show the soundness of this framework.
YKL-40—A Protein in the Field of Translational Medicine: A Role as a Biomarker in Cancer Patients?

YKL-40 is a 40 kDa glycoprotein produced by cancer cells, inflammatory cells and stem cells. It probably has a role in cell proliferation and differentiation, inflammation, protection against apoptosis, stimulation of angiogenesis, and regulation of extracellular tissue remodelling. Plasma levels of YKL-40 are often elevated in patients with localized or advanced cancer compared to age-matched healthy subjects. Several studies have demonstrated that high plasma YKL-40 is an independent prognostic biomarker of short survival in patients with different types of cancer. However, there is not yet sufficient data to support determination of plasma YKL-40 outside research projects as a biomarker for screening of gastrointestinal cancer and determination of treatment response and poor prognosis before or during treatment and follow-up. Plasma YKL-40 is also elevated in patients with other diseases than cancer, e.g., severe infections, cardiovascular disease, diabetes, chronic obstructive lung disease, asthma, liver fibrosis and rheumatoid arthritis. Co-morbidity should therefore always be considered in patients with cancer, since other sources than cancer cells can increase plasma YKL-40 levels. Future focused translational research projects combining basic and clinical research are needed in a joint effort to answer questions of the complex function and regulation of YKL-40 and the question if plasma YKL-40 is a clinical useful biomarker in patients with cancer.
Physically justifiable die-level modeling of spatial variation in view of systematic across wafer variability

Modeling spatial variation is important for statistical analysis. Most existing works model spatial variation as spatially correlated random variables. We discuss process origins of spatial variability, all of which indicate that spatial variation comes from deterministic across-wafer variation, and purely random spatial variation is not significant. We analytically study the impact of across-wafer variation and show how it gives an appearance of correlation. We have developed a new die-level variation model considering deterministic across-wafer variation and derived the range of conditions under which ignoring spatial variation altogether may be acceptable. Experimental results show that our model is within 1% error from exact simulation result while the error of the existing distance-based spatial variation model is up to 8%. Moreover, our new model is also 10× faster than the spatial variation model for Monte-Carlo analysis.
Semi-Supervised Feature Transformation for Dependency Parsing

In current dependency parsing models, conventional features (i.e. base features) defined over surface words and part-of-speech tags in a relatively high-dimensional feature space may suffer from the data sparseness problem and thus exhibit less discriminative power on unseen data. In this paper, we propose a novel semi-supervised approach to addressing the problem by transforming the base features into high-level features (i.e. meta features) with the help of a large amount of automatically parsed data. The meta features are used together with base features in our final parser. Our studies indicate that our proposed approach is very effective in processing unseen data and features. Experiments on Chinese and English data sets show that the final parser achieves the best-reported accuracy on the Chinese data and comparable accuracy with the best known parsers on the English data.
A Survey on Node Clustering in Cognitive Radio Wireless Sensor Networks

Cognitive radio wireless sensor networks (CR-WSNs) have attracted a great deal of attention recently due to the emerging spectrum scarcity issue. This work attempts to provide a detailed analysis of the role of node clustering in CR-WSNs. We outline the objectives, requirements, and advantages of node clustering in CR-WSNs. We describe how a CR-WSN with node clustering differs from conventional wireless sensor networks, and we discuss its characteristics, architecture, and topologies. We survey the existing clustering algorithms and compare their objectives and features. We suggest how clustering issues and challenges can be handled.
On the Representational Efficiency of Restricted Boltzmann Machines

This paper examines the question: What kinds of distributions can be efficiently represented by Restricted Boltzmann Machines (RBMs)? We characterize the RBM's unnormalized log-likelihood function as a type of neural network, and through a series of simulation results relate these networks to ones whose representational properties are better understood. We show the surprising result that RBMs can efficiently capture any distribution whose density depends on the number of 1's in their input. We also provide the first known example of a particular type of distribution that provably cannot be efficiently represented by an RBM, assuming a realistic exponential upper bound on the weights. By formally demonstrating that a relatively simple distribution cannot be represented efficiently by an RBM our results provide a new rigorous justification for the use of potentially more expressive generative models, such as deeper ones.
Sparse Constraint Graphs and Exceptionally Hard Problems

Many types of problem exhibit a phase transition as a problem parameter is varied, from a region where most problems are easy and soluble to a region where most problems are easy but insoluble. In the intervening phase transition region, the median problem difficulty is greatest. However, occasional exceptionally hard problems (ehps) can be found in the easy and soluble region; these problems can be much harder than any problem occurring in the phase transition. We show that, in binary constraint satisfaction problems, ehps are much more likely to occur when the constraints are sparse than when they are dense. Ehps occur when the search algorithm encounters a large insoluble subproblem at an early stage; the exceptional difficulty is due to the cost of searching the subproblem to prove insolubility. This cost can be dramatically reduced by using conflict-directed backjumping (CBJ) rather than a chronological backtracker. However, when used with forward checking and the fail-first heuristic, it is only on ehps that CBJ gives great savings over backtracking chronologically.
Prevalence of latent tuberculosis infection among gold miners in South Africa.

SETTING South African gold mines. OBJECTIVE To determine the prevalence of latent tuberculosis infection (LTBI) and risk factors for a positive tuberculin skin test (TST) among gold miners. DESIGN Cross-sectional survey. Human immunodeficiency virus (HIV) status was determined by self-report and medical records. TST positivity was defined by the mirror method to estimate the prevalence of LTBI, and by the US Centers for Disease Control and Prevention definitions to explore risk factors at the individual level. RESULTS Among 429 participants (105/130 subjects aged <30 years, 324/390 > or = 30 years), the estimated prevalence of LTBI was 89%; 45.5% of HIV-positive participants had a zero TST response compared to respectively 13% and 13.5% in the HIV-negative and status unknown participants. In participants with TST > 0, there was no significant difference between size of response by HIV status: the mean (standard deviation) widths for HIV-positive, HIV-negative and HIV status unknown were respectively 11.84 (2.75), 12.03 (2.75) and 12.52 mm (3.04) (analysis of variance P = 0.28). Factors independently associated with a TST < 10 mm were positive HIV status (aOR 0.41, 95%CI 0.17-0.96) and not working underground (aOR 0.25, 95%CI 0.09-0.71). CONCLUSIONS The prevalence of LTBI is very high in gold miners in South Africa. HIV-infected individuals are more likely to have a negative TST, but HIV infection does not affect the size of TST response.
Semantics-based Multiword Expression Extraction

This paper describes a fully unsupervised and automated method for large-scale extraction of multiword expressions (MWEs) from large corpora. The method aims at capturing the non-compositionality of mwes; the intuition is that a noun within a mwe cannot easily be replaced by a semantically similar noun. To implement this intuition, a noun clustering is automatically extracted (using distributional similarity measures), which gives us clusters of semantically related nouns. Next, a number of statistical measures -- based on selectional preferences --- is developed that formalize the intuition of non-compositionality. Our approach has been tested on Dutch, and automatically evaluated using Dutch lexical resources.