Miracle-dz/UniFAR-FTUs huggingface dataset:
Dapper, a Large-Scale Distributed Systems Tracing Infrastructure

Modern Internet services are often implemented as complex, large-scale distributed systems. These applications are constructed from collections of software modules that may be developed by different teams, perhaps in different programming languages, and could span many thousands of machines across multiple physical facilities. Tools that aid in understanding system behavior and reasoning about performance issues are invaluable in such an environment. Here we introduce the design of Dapper, Google’s production distributed systems tracing infrastructure, and describe how our design goals of low overhead, application-level transparency, and ubiquitous deployment on a very large scale system were met. Dapper shares conceptual similarities with other tracing systems, particularly Magpie [3] and X-Trace [12], but certain design choices were made that have been key to its success in our environment, such as the use of sampling and restricting the instrumentation to a rather small number of common libraries. The main goal of this paper is to report on our experience building, deploying and using the system for over two years, since Dapper’s foremost measure of success has been its usefulness to developer and operations teams. Dapper began as a self-contained tracing tool but evolved into a monitoring platform which has enabled the creation of many different tools, some of which were not anticipated by its designers. We describe a few of the analysis tools that have been built using Dapper, share statistics about its usage within Google, present some example use cases, and discuss lessons learned so far.
Role of Insulin Resistance in Familial Combined Hyperlipidemia

Objective—Insulin resistance is associated with increased triglyceride levels, low high-density lipoprotein cholesterol, small dense low-density lipoprotein (LDL), and increased apolipoprotein B (apoB) levels, all characteristics of familial combined hyperlipidemia (FCH). Therefore, we explored the role of insulin resistance in FCH lipid phenotype expression. Methods and Results—FCH was defined by traditional diagnostic criteria including plasma total cholesterol or triglyceride levels >90th percentile. Insulin resistance was assessed by the Homeostasis Model Assessment (HOMA) index. In total, 132 subjects with FCH, 350 normolipidemic relatives, and 81 spouses who referenced as controls were studied. FCH subjects were significantly more insulin resistant compared with controls and normolipidemic relatives (HOMA index 2.9 [95% CI, 2.6 to 3.2], 2.2 [95% CI, 2.0 to 2.5], and 2.0 [95% CI, 1.9 to 2.2], respectively), even after correction for sex, age, and body mass index (BMI). The degree of insulin resistance was associated with the lipid phenotype expression, and a change in insulin-resistant state was associated with a change in lipid phenotype expression over 5 years. For any level of insulin resistance and degree of obesity, FCH subjects had increased levels of apoB and more small dense LDL compared with controls. Conclusion—Insulin resistance is a characteristic feature of FCH, which is not fully explained by their increased BMI and is associated with (change in) lipid phenotype expression. Furthermore, our results support the concept of genetic origin of high apoB and small dense LDL in FCH, which is modulated by insulin resistance and obesity.
Development of an intelligent pneumatic cylinder and its application to pneumatic servo mechanism

A new compact pneumatic cylinder with a micro position sensor, named intelligent pneumatic cylinder was developed. It consists of a piston rod with stripe codes and a micro optical MEMS encoder. The stripe codes were fabricated through a selective oxidization process by irradiating with a YAG laser. The cylinder realizes a compact pneumatic position servo system. The servo experimental results were very promising. The piston rod position is easily controlled at any desired position between both ends of the rod stroke. This paper reports also an adaptive servo algorithm which was newly developed for stepping positioning of the intelligent pneumatic cylinder, realizing about 0.1 to 1 mm positioning accuracy without overshooting
Malaria Vaccine-Related Benefits of a Single Protein Comprising Plasmodium falciparum Apical Membrane Antigen 1 Domains I and II Fused to a Modified Form of the 19-Kilodalton C-Terminal Fragment of Merozoite Surface Protein 1

ABSTRACT We show that the smallest module of Plasmodium falciparum AMA1 (PfAMA1) that can be expressed in the yeast Pichia pastoris while retaining the capacity to induce high levels of parasite-inhibitory antibodies comprises domains I and II. Based on this, two fusion proteins, differing in the order of the modules, were developed. Each comprised one module of PfAMA1 (FVO strain, amino acids [aa] 97 to 442) (module A) and one module of PfMSP119 (Wellcome strain, aa 1526 to 1621) (module Mm) in which a cystine had been removed to improve immune responses. Both fusion proteins retained the antigenicity of each component and yielded over 30 mg/liter purified protein under fed-batch fermentation. Rabbits immunized with purified fusion proteins MmA and AMm had up to eightfold-higher immune responses to MSP119 than those of rabbits immunized with module Mm alone or Mm mixed with module A. In terms of parasite growth inhibition, fusion did not diminish the induction of inhibitory antibodies compared with immunization with module A alone or module A mixed with module Mm, and fusion outperformed antibodies induced by immunization with module M or Mm alone. When tested against parasites expressing AMA1 heterologous to the immunogen, antibodies to the fusion proteins inhibited parasite growth to a greater extent than did antibodies either to the individual antigens or to the mixture. These results suggest that compared with the individual modules delivered separately or as a mixture, fusion proteins containing these two modules offer the potential for significant vaccine-related advantages in terms of ease of production, immunogenicity, and functionality.
Study on large-scale rotating machinery fault intelligent diagnosis multi-agent system

In order to adapt the complex equipment intelligent diagnosis task, based on advantages of multi-agent system, study on large-scale rotating machinery fault intelligent diagnosis multi-agent system is proposed. In the study, the system has broken through traditional unalterable multi algorithm fusion model and shows the social intelligence of multiple agents through the ability which is organizational, self-study and able to resolve diagnosis problems through dynamically negotiating among multiple agents according to the actual characteristics of device signal. The main contributions are as follows: Firstly, how to decompose the diagnosis task rationally is proposed. From this part, a distinctive diagnosis task decomposition method is proposed and which intelligent diagnosis methods adapted to achieving diagnosis successfully can be known; Secondly, how to design the large-scale rotating machinery intelligent diagnosis multi-agent system is introduced, From this part, how to design the system structure and how the system complete the dynamically negotiating and self-study process efficiently can be known. Thirdly, an example of the system is proposed and proves the system can complete the function efficiently.
Structure and function of ant (Hymenoptera: Formicidae) brains: Strength in numbers

This article reviews the brain of ants in the context of their behavior. Division of labor underlies the social lifestyle of ants; it results not only in behavioral specialization, but also in some adaptations of ant brains. The structure and function of major brain neuropils is described (visual and olfactory centers and central multi-sensory integrative brain compartments) together with some of their neurons. Unlike social vertebrates, which have larger brains and cerebral cortices than solitary species, ant brains are not bigger than those of solitary insects, but they are more specialized. The biological success of ants is probably not so much the result of an individual's brain as of the concerted action of a colony's hundreds or thousands of brains.
Maximum phytoplankton concentrations in the sea

A simplification of plankton dynamics using coagulation theory provides predictions of the maximum algal concentration sustainable in aquatic systems. These predictions have previously been tested successfully against results from iron fertilization experiments. We extend the test to data collected in the North Atlantic as part of the Bermuda Atlantic Time Series program as well as data collected off Southern California as part of the Southern California Bight Study program. The observed maximum particulate organic carbon and volumetric particle concentrations are consistent with the predictions. The results imply that physical processes control maximum particle concentrations in planktonic systems.
Personalized Prediction of Proliferation Rates and Metabolic Liabilities in Cancer Biopsies

Cancer is a heterogeneous disease and its genetic and metabolic mechanism may manifest differently in each patient. This creates a demand for studies that can characterize phenotypic traits of cancer on a per-sample basis. Combining two large data sets, the NCI60 cancer cell line panel, and The Cancer Genome Atlas, we used a linear interaction model to predict proliferation rates for more than 12,000 cancer samples across 33 different cancers from The Cancer Genome Atlas. The predicted proliferation rates are associated with patient survival and cancer stage and show a strong heterogeneity in proliferative capacity within and across different cancer panels. We also show how the obtained proliferation rates can be incorporated into genome-scale metabolic reconstructions to obtain the metabolic fluxes for more than 3000 cancer samples that identified specific metabolic liabilities for nine cancer panels. Here we found that affected pathways coincided with the literature, with pentose phosphate pathway, retinol, and branched-chain amino acid metabolism being the most panel-specific alterations and fatty acid metabolism and ROS detoxification showing homogeneous metabolic activities across all cancer panels. The presented strategy has potential applications in personalized medicine since it can leverage gene expression signatures for cell line based prediction of additional metabolic properties which might help in constraining personalized metabolic models and improve the identification of metabolic alterations in cancer for individual patients.
Comparison of Transcriptome Between Type 2 Diabetes Mellitus and Impaired Fasting Glucose

Background The aim of this study was to compare the transcriptome between impaired fasting glucose (IFG) and type 2 diabetes mellitus (T2DM), and further research their molecular mechanisms. Material/Methods The original microarray GSE21321, including miRNA and mRNA expression profiles, was downloaded from the GEO database. Data preprocessing was processed by limma package, and differentially expressed genes (DGs) and miRNA (DMs) were screened. Then, the regulatory relationships among miRNA, TF, and genes were screened and the regulatory network was constructed. Finally, DAVID was used for KEGG enrichment analysis. Results There were 11 upregulated IFG-related DMs and five upregulated T2DM-related DMs. Three of the DMs overlapped. In addition, there were eight downregulated IFG-related DMs and two downregulated T2DM-related DMs. Only one downregulated DM overlapped. Similarly, there were 264 upregulated IFG-related DGs and 331 upregulated T2DM-related DGs; and 196 overlapping genes were obtained. In addition, there were 400 downregulated IFG-related DMs and 568 downregulated T2DM-related DMs. A total of 326 downregulated DMs were overlapped. The overlapped DGs were enriched in various pathways, including hematopoietic cell lineage, Fc gamma R-mediated phagocytosis, and MAPK signaling pathway. TAF1 (upregulated gene) and MAFK (downregulated gene) were hub nodes both in IFG- and T2DM-related miRNA-TF-gene regulatory network. In addition, miRNAs, including hsa-miR-29a, hsa-miR-192, and hsa-miR-144, were upregulated hub nodes in the two regulatory networks. Conclusions Genes including TAF1 and MAFK, and miRNAs including hsa-miR-29a, hsa-miR-192, and hsa-miR-144 might be potential target genes and important miRNAs for IFG and T2DM.
Stochastic structural analysis for context-aware design and fabrication

In this paper we propose failure probabilities as a semantically and mechanically meaningful measure of object fragility. We present a stochastic finite element method which exploits fast rigid body simulation and reduced-space approaches to compute spatially varying failure probabilities. We use an explicit rigid body simulation to emulate the real-world loading conditions an object might experience, including persistent and transient frictional contact, while allowing us to combine several such scenarios together. Thus, our estimates better reflect real-world failure modes than previous methods. We validate our results using a series of real-world tests. Finally, we show how to embed failure probabilities into a stress constrained topology optimization which we use to design objects such as weight bearing brackets and robust 3D printable objects.
A review of parallel processing approaches to motion planning

One of the many features needed to support the activities of autonomous systems is the ability of motion planning. It enables robots to move in their environment securely and to accomplish given tasks. Unfortunately, the control loop comprising sensing, planning, and acting has not yet been closed for robots in dynamic environments. One reason involves the long execution times of the motion planning component. A solution for this problem is offered by the use of highly computational parallelism. Thus, an important task is the parallelization of existing motion planning algorithms for robots so that they are suitable for highly computational parallelism. In several cases, completely new algorithms have to be designed, so that a parallelization is feasible. We review approaches to motion planning using parallel computation.
Visual perception and visuospatial cognition

One of the core cognitive characteristics of Williams syndrome (WS) is the marked contrast between poor levels of visuospatial ability relative to stronger verbal abilities. Visuospatial cognition enables us to perceive and interact with our visual world. It includes everyday skills such as the ability to reach for and grasp our knife and fork and to recognise the food on the plate; the visual search skills required to locate our favourite cereal on a supermarket shelf or our coat on a coat rack; the processes that enable us to individuate objects in order to count them, to draw pictures, to write and recognise words, and to complete puzzles; and even the ability to know which bus stop to get off at when travelling. In WS, many of these visuospatial skills do not develop beyond the level of a typically developing six-year-old. However, there is considerable variation across levels of ability within this domain. This chapter outlines the characteristic profile of visuospatial abilities in WS within the context of developmental interactions between genes, brain, the environment, and behaviour.
Trends of under- and overweight among rural and urban poor women indicate the double burden of malnutrition in Bangladesh.

BACKGROUND Although undernutrition and communicable diseases dominate the current disease burden in resource-poor countries, the prevalence of diet related chronic diseases is increasing. This paper explores current trends of under- and overweight in Bangladeshi women. METHOD Nationally representative data on reproductive age women from rural Bangladesh (n = 242,433) and selected urban poor areas (n = 39,749) collected by the Nutritional Surveillance Project during 2000-2004 were analyzed. RESULTS While the prevalence of chronic energy deficiency [CED, body mass index (BMI) < 18.5 kg/m(2)] continues to be major nutritional problem among Bangladeshi women (38.8% rural, 29.7% urban poor; P < 0.001), between 2000-2004, 9.1% of urban poor and 4.1% of rural women were overweight (BMI > or = 25 kg/m(2), P < 0.001). In addition, 9.8% of urban poor and 5.5% of rural women were found to be 'at risk of overweight' (BMI 23.0-<25 kg/m(2)). From 2000 to 2004, prevalence of CED decreased (urban poor: 33.8-29.3%; rural: 42.6-36.6%), while prevalence of overweight increased (urban poor: 6.8-9.1%; rural: 2.8-5.5%). The risk of being overweight was higher among women who were older and of higher socioeconomic status. Rural women with at least 14 years of education had a 8.1-fold increased risk of being overweight compared with non-educated women [95% confidence intervals (CI): 6.6-8.7]. Women living in houses of at least 1000 sq ft (93 m(2)) were 3.7 times more likely to be overweight compared with women living in <250 sq ft (23 m(2)) houses (95% CI: 3.2-4.3). CONCLUSION The recent increase in overweight prevalence among both urban poor and rural women, along with high prevalence of CED, indicates the emergence of a double burden of malnutrition in Bangladesh.
Functional Validation of a Constitutive Autonomous Silencer Element

Sequences of the genome that are capable of silencing gene expression are thought to play a key role in gene regulation. However, very few silencer elements capable of functioning in mammalian cells have been described, and only a fraction of these have been tested for the ability to function in an autonomous fashion. We report here the characterization and functional validation of a constitutive autonomous silencer element from the human genome called T39, and the comparison of T39 to three other putative silencer elements previously described by others. Functional analysis included one assay for enhancer-blocking insulator activity and two independent assays for silencer activity, all based on stable transfection and comparison to a neutral spacer control. In erythroid K562 cells, T39 exhibited potent silencer activity, the previously described element PRE2-S5 exhibited modest silencer activity, and the two other previously described elements exhibited no silencer activity. T39 was further found to be capable of silencing three disparate promoters, of silencing gene expression in three disparate cell lines, and of functioning as a single copy in a topology-independent manner. Of the four elements analyzed, only T39 exhibits a constitutive pattern of DNase hypersensitivity and binding by CTCF. In its native location the T39 element also exhibits a unique interaction profile with a subset of distal putative regulatory elements. Taken together, these studies validate T39 as a constitutive autonomous silencer, identify T39 as a defined control for future studies of other regulatory elements such as insulators, and provide a basic chromatin profile for one highly potent silencer element.
Habituation of the C-Start Response in Larval Zebrafish Exhibits Several Distinct Phases and Sensitivity to NMDA Receptor Blockade

The zebrafish larva has been a valuable model system for genetic and molecular studies of development. More recently, biologists have begun to exploit the surprisingly rich behavioral repertoire of zebrafish larvae to investigate behavior. One prominent behavior exhibited by zebrafish early in development is a rapid escape reflex (the C-start). This reflex is mediated by a relatively simple neural circuit, and is therefore an attractive model behavior for neurobiological investigations of simple forms of learning and memory. Here, we describe two forms of short-lived habituation of the C-start in response to brief pulses of auditory stimuli. A rapid form, persisting for ≥1 min but <15 min, was induced by 120 pulses delivered at 0.5–2.0 Hz. A more extended form (termed “short-term habituation” here), which persisted for ≥25 min but <1 h, was induced by spaced training. The spaced training consisted of 10 blocks of auditory pulses delivered at 1 Hz (5 min interblock interval, 900 pulses per block). We found that these two temporally distinguishable forms of habituation are mediated by different cellular mechanisms. The short-term form depends on activation of N-methyl-d-aspartate receptors (NMDARs), whereas the rapid form does not.
Use of deep autochthonous resources by zooplankton: Results of a metalimnetic addition of 13C to a small lake

Resources in lakes are vertically partitioned due to stratification and trophic interactions. Metalimnetic phytoplankton could be an important resource for zooplankton that either reside in the metalimnion or migrate through this layer. However, it is difficult to estimate metalimnetic resource use, especially using isotope approaches, because surface and deep phytoplankton often have similar isotopic compositions. To overcome this limitation, we experimentally enriched the metalimnetic dissolved inorganic carbon (DIC) 13C pool in Peter Lake to enhance the isotopic separation between metalimnetic phytoplankton and other resources. Metalimnetic δ13C‐DIC peaked at 73.2‰ after the isotope addition and maintained an average enrichment of 34.5‰ above epilimnetic δ13C‐DIC for 62 d. Combining hydrogen and carbon stable isotope values, we estimated the epilimnetic, metalimnetic, and terrestrial resource use by zooplankton, using a Bayesian mixing model that accounted for uncertainties in both consumers and sources. We also measured diel vertical migration and net ecosystem production with in situ bottle incubations over the course of the experiment. Metalimnetic resource use was minor (0–8%) for zooplankton that either resided in the epilimnion of the lake during the day or migrated there at night. For consumers that resided in the metalimnion, metalimnetic phytoplankton accounted for 18–21% of zooplankton isotope composition. The most important resource for all zooplankton was terrestrial organic matter (56–73% of consumer mass), regardless of habitat. This experiment indicates that, in lakes like Peter Lake, metalimnetic autochthonous resources are of minor importance to zooplankton relative to epilimnetic autochthonous and allochthonous resources.
Actin polymerization kinetics, cap structure, and fluctuations.

Polymerization of actin proteins into dynamic structures is essential to eukaryotic cell life, motivating many in vitro experiments measuring polymerization kinetics of individual filaments. Here, we model these kinetics, accounting for all relevant steps revealed by experiment: polymerization, depolymerization, random ATP hydrolysis, and release of phosphate (P(i)). We relate filament growth rates to the dynamics of ATP-actin and ADP-P(i)-actin caps that develop at filament ends. At the critical concentration of the barbed end, c(crit), we find a short ATP cap and a long fluctuation-stabilized ADP-P(i) cap. We show that growth rates and the critical concentration at the barbed end are intimately related to cap structure and dynamics. Fluctuations in filament lengths are described by the length diffusion coefficient, D. Recently Fujiwara et al. [Fujiwara, I. , Takahashi, S. , Takaduma, H. , Funatsu, T. & Ishiwata, S. (2002) Nat. Cell Biol. 4, 666-673] and Kuhn and Pollard [Kuhn, J. & Pollard, T. D. (2005) Biophys. J. 88, 1387-1402] observed large length fluctuations slightly above c(crit), provoking speculation that growth may proceed by oligomeric rather than monomeric on-off events. For the single-monomer growth process, we find that D exhibits a pronounced peak below c(crit), due to filaments alternating between capped and uncapped states, a mild version of the dynamic instability of microtubules. Fluctuations just above c(crit) are enhanced but much smaller than those reported experimentally. Future measurements of D as a function of concentration can help identify the origin of the observed fluctuations.