Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profiling of Fixed Tissues Identified Hypoxia-Inducible Factor-1α, VEGF, and Matrix Metalloproteinase-2 as Biomarkers of Lymph Node Metastasis in Hepatocellular Carcinoma

Purpose: Hepatocellular carcinoma (HCC) most often develops in patients infected with hepatitis B or hepatitis C virus. Differential gene expression profiling is useful for investigating genes associated with lymph node metastasis (LNM). We screened genes to identify potential biomarkers for LNM in HCC. Experimental Design: RNA was extracted from formalin-fixed specimens of paired intratumoral and peritumoral tissues of patients with lymph node–positive (n = 36) or negative (n = 36) HCC. A cDNA-mediated annealing, selection, extension, and ligation assay was done with an array of 502 known cancer-related genes to identify differentially expressed genes in 20 pairs of patients with or without LNM. Candidate biomarkers were evaluated by using immunohistochemistry and tissue microarrays in an independent cohort of 309 HCC patients who had undergone hepatectomy. Of the 309 patients, 235 (76.1%) patients were infected with hepatitis B. Results: Compared with lymph node–negative patients, lymph node–positive patients had 17 overexpressed genes and 19 underexpressed genes in intratumoral tissues, and 25 overexpressed genes and 22 underexpressed genes in peritumoral tissues. Hypoxia-inducible factor (HIF)-1α, VEGF, and matrix metalloproteinase (MMP)-2 were selected for analysis in the cohort of 309 HCC patients. We found that intratumoral protein levels of HIF-1α, VEGF, and MMP-2 were independent risk factors for developing LNM. Conclusion: We identified 83 cancer genes that were differentially expressed in lymph node–positive and lymph node–negative HCC. Our findings show that the combination of intratumoral HIF-1α, VEGF, and MMP-2 may be useful as a molecular prediction model for LNM. Clin Cancer Res; 17(16); 5463–72. ©2011 AACR.
Implications of large scale shifts in tropospheric NO x levels in the remote tropical Pacific

A major observation recorded during NASA's western Pacific Exploratory Mission (PEM-West B) was the large shift in tropical NO levels as a function of geographical location. High-altitude NO levels exceeding 100 pptv were observed during portions of tropical flights 5–8, while values almost never exceeded 20 pptv during tropical flights 9 and 10. The geographical regions encompassing these two flight groupings are here labeled “high” and “low” NOx regimes. A comparison of these two regimes, based on back trajectories and chemical tracers, suggests that air parcels in both were strongly influenced by deep convection. The low NOx regime appears to have been predominantly impacted by marine convection, whereas the high NOx regime shows evidence of having been more influenced by deep convection over a continental land mass. DMSP satellite observations point strongly toward lightning as the major source of NOx in the latter regime. Photochemical ozone formation in the high NOx regime exceeded that for low NOx by factors of 2 to 6, whereas O3 destruction in the low NOx regime exceeded that for high NOx by factors of up to 3. Taking the tropopause height to be 17 km, estimates of the net photochemical effect on the O3 column revealed that the high NOx regime led to a small net production. By contrast, the low NOx regime was shown to destroy O3 at the rate of 3.4% per day. One proposed mechanism for off-setting this projected large deficit would involve the transport of O3 rich midlatitude air into the tropics. Alternatively, it is suggested that O3 within the tropics may be overall near self-sustaining with respect to photochemical activity. This scenario would require that some tropical regions, unsampled at the time of PEM-B, display significant net column O3 production, leading to an overall balanced budget for the “greater” tropical Pacific basin. Details concerning the chemical nature of such regimes are discussed.
Survey on Resource Allocation Policy and Job Scheduling Algorithms of Cloud Computing1

Cloud computing is the product of the evolution of calculation. It is a new distributed computing model. As more and more people put into the research and applications on cloud computing, the technology of computing becomes more and more widely used. Cloud computing has a huge user group. It has to deal with a large number of tasks. How to make appropriate decisions when allocating hardware resources to the tasks and dispatching the computing tasks to resource pool has become the main issue in cloud computing. This paper is based on the current situation of resource allocation policy and job scheduling algorithms under cloud circumstance. It summarizes some methods to improve the performance, including dynamic resource allocation strategy based on the law of failure, dynamic resource assignment on the basis of credibility, ant colony optimization algorithm for resource allocation, dynamic scheduling algorithm based on threshold, optimized genetic algorithm with dual fitness and improved ant colony algorithm for job scheduling.
Retroversion of the Humerus in the Throwing Shoulder of College Baseball Pitchers

Background Increased external rotation and decreased internal rotation have been noted to occur progressively in the throwing shoulder of baseball pitchers. Hypothesis Proximal remodeling of the humerus contributes to the rotational asymmetry between shoulders in pitchers. Study Design Descriptive anatomic study. Methods Both shoulders of 19 male college baseball pitchers were evaluated and retroversion of the humerus calculated by using the technique of Söderlund et al. Measurements were taken of passive glenohumeral external rotation at 0° and 90° of abduction and internal rotation at 90° of abduction under a 3.5-kg load. Subjects completed a questionnaire on the amount and duration of overhead throwing performed during the ages 8 through 16 years. Results All of the subjects had greater external rotation at 0° and 90° of abduction, decreased internal rotation at 90° of abduction, and greater retroversion of the humerus in their dominant compared with nondominant shoulders. A significant difference was found between dominant and nondominant external rotation at 0° and 90° of abduction, internal rotation at 90° of abduction, and retroversion of the humerus. In the dominant arm, there was a significant correlation between retroversion of the humerus and external rotation at 0° and 90° of abduction. There was also a significant correlation between the side-to-side difference in retroversion of the humerus compared with the side-to-side difference in external rotation at 90° of abduction. Conclusions Rotational changes in the throwing shoulder are due to bony as well as soft tissue adaptations.
Monte Carlo Test Assembly for Item Pool Analysis and Extension

A new test assembly algorithm based on a Monte Carlo random search is presented in this article. A major advantage of the Monte Carlo test assembly over other approaches (integer programming or enumerative heuristics) is that it performs a uniform sampling from the item pool, which provides every feasible item combination (test) with an equal chance of being built during an assembly. This allows the authors to address the following issues of pool analysis and extension: compare the strengths and weaknesses of different pools, identify the most restrictive constraint(s) for test assembly, and identify properties of the items that should be added to a pool to achieve greater usability of the pool. Computer experiments with operational pools are given.
Mg+ morphology from visual airglow experiment observations

Observations of low-latitude Mg+ by the Visual Airglow Experiment on Atmosphere Explorer E were analyzed by a two-dimensional inversion technique. Number density profiles as functions of geographic position were obtained in the F2 region. The profiles represent daytime northern winter, solar maximum conditions and reveal frequent occurrences of large number densities (50–100 cm−3) at altitudes up to 475 km. Maximum densities are usually found near the equator at 1200–1400 LT. The equatorial density then decreases as the peak concentrations shift to higher latitudes. Longitudinal differences in the time development of the metal ion density appear in the afternoon. These seem to be due to the increasing importance of zonal winds and/or to longitudinal differences in the vertical ion drift velocity.
Stress/strain changes and triggered seismicity following the Mw 7.3 Landers, California earthquake

Calculations of dynamic stresses and strains, constrained by broadband seismograms, are used to investigate their role in generating the remotely triggered seismicity that followed the June 28, 1992 Mw7.3 Landers, California earthquake. I compare straingrams and dynamic Coulomb failure functions calculated for the Landers earthquake at sites that did experience triggered seismicity with those at sites that did not. Bounds on triggering thresholds are obtained from analysis of dynamic strain spectra calculated for the Landers and Mw6.1 Joshua Tree, California earthquakes at various sites, combined with results of static strain investigations by others. I interpret three principal results of this study with those of a companion study by Gomberg and Davis [this issue]. First, the dynamic elastic stress changes themselves cannot explain the spatial distribution of triggered seismicity, particularly the lack of triggered activity along the San Andreas fault system. In addition to the requirement to exceed a Coulomb failure stress level, this result implies the need to invoke and satisfy the requirements of appropriate slip instability theory. Second, results of this study are consistent with the existence of frequency- or rate-dependent stress/strain triggering thresholds, inferred from the companion study and interpreted in terms of earthquake initiation involving a competition of processes, one promoting failure and the other inhibiting it. Such competition is also part of relevant instability theories. Third, the triggering threshold must vary from site to site, suggesting that the potential for triggering strongly depends on site characteristics and response. The lack of triggering along the San Andreas fault system may be correlated with the advanced maturity of its fault gouge zone; the strains from the Landers earthquake were either insufficient to exceed its larger critical slip distance or some other critical failure parameter; or the faults failed stably as aseismic creep events. Variations in the triggering threshold at sites of triggered seismicity may be attributed to variations in gouge zone development and properties. Finally, these interpretations provide ready explanations for the time delays between the Landers earthquake and the triggered events.
The reliability of isoinertial force–velocity–power profiling and maximal strength assessment in youth

The purpose of this study was to quantify the inter-session reliability of force–velocity–power profiling and estimated maximal strength in youth. Thirty-six males (11–15 years old) performed a ballistic supine leg press test at five randomized loads (80%, 100%, 120%, 140%, and 160% body mass) on three separate occasions. Peak and mean force, power, velocity, and peak displacement were collected with a linear position transducer attached to the weight stack. Mean values at each load were used to calculate different regression lines and estimate maximal strength, force, velocity, and power. All variables were found reliable (change in the mean [CIM] = − 1 to 14%; coefficient of variation [CV] = 3–18%; intraclass correlation coefficient [ICC] = 0.74–0.99), but were likely to benefit from a familiarization, apart from the unreliable maximal force/velocity ratio (CIM = 0–3%; CV = 23–25%; ICC = 0.35–0.54) and load at maximal power (CIM = − 1 to 2%; CV = 10–13%; ICC = 0.26–0.61). Isoinertial force–velocity–power profiling and maximal strength in youth can be assessed after a familiarization session. Such profiling may provide valuable insight into neuromuscular capabilities during growth and maturation and may be used to monitor specific training adaptations.
A Tutorial on Graph-Based SLAM

Being able to build a map of the environment and to simultaneously localize within this map is an essential skill for mobile robots navigating in unknown environments in absence of external referencing systems such as GPS. This so-called simultaneous localization and mapping (SLAM) problem has been one of the most popular research topics in mobile robotics for the last two decades and efficient approaches for solving this task have been proposed. One intuitive way of formulating SLAM is to use a graph whose nodes correspond to the poses of the robot at different points in time and whose edges represent constraints between the poses. The latter are obtained from observations of the environment or from movement actions carried out by the robot. Once such a graph is constructed, the map can be computed by finding the spatial configuration of the nodes that is mostly consistent with the measurements modeled by the edges. In this paper, we provide an introductory description to the graph-based SLAM problem. Furthermore, we discuss a state-of-the-art solution that is based on least-squares error minimization and exploits the structure of the SLAM problems during optimization. The goal of this tutorial is to enable the reader to implement the proposed methods from scratch.
Plasma Membrane Lipids Associated with Genetic Variability in Freezing Tolerance and Cold Acclimation of Solanum Species

Simultaneous comparisons were made between a freezing-tolerant, cold-acclimating (CA) wild potato species (Solanum commersonii) and a freezing-sensitive, nonacclimating (NA) cultivated species (Solanum tuberosum). Comparative studies allowed differentiation of plasma membrane lipid changes associated with increased freezing tolerance following CA from lipid changes that can result from metabolic adjustment to reduced temperature during CA. Following CA treatment lipid changes found in both the NA and CA species included a decrease in palmitic acid, an increase in unsaturated to saturated fatty acid ratio, an increase in free sterols, an increase in sitosterol, and a slight decrease in cerebrosides. Lipid changes detected only in the acclimating species included an increase in phosphatidylethanolamine, a decrease in sterol to phospholipid ratio, an increase in linoleic acid, a decrease in linolenic acid, and an increase in acylated steryl glycoside to steryl glycoside ratio. These changes were either absent or opposite in the NA species, suggesting an association of these lipid changes with CA. Furthermore, the lipid changes associated with increased freezing tolerance during CA were distinct from lipid differences between the two species in the NA state.
Analysis of the processing of Nashville urban emissions on July 3 and July 18, 1995

This paper analyzes data obtained on July 3 and 18, 1995, during the summer 1995 Southern Oxidant Study (SOS) field campaign. In a previous paper (Nunnermacker et al., 1998) we analyzed measurements of key species that contribute to formation of O3 in the Nashville urban plume and presented a semiquantitative picture of O3 production in the plume from the point of emission to locations where no net O3 was being formed. In this paper we use a box model constrained by observed concentrations of stable species to obtain a detailed mechanistic description of the instantaneous processing of urban emissions at various times in the chemical evolution of the urban plume. Instantaneous ozone production rates and efficiencies with respect to NOx and to primary radical production are examined. At high NOx concentrations in the fresh urban plume the O3 production rate was found to be directly proportional to the hydrocarbon to NOx reactivity ratio. At lower NOx concentrations, corresponding to the mature urban plume and the background atmosphere, the O3 production rate was found to be directly proportional to the NOx concentration and independent of the hydrocarbon reactivity. NOx was found to be most efficiently used for ozone production at low NOx concentrations. In contrast, the efficiency with which the system uses primary radicals was found to be very low at low NOx concentrations and to peak at a NOx concentration of approximately 4 ppbv. A sensitivity study of the instantaneous O3 production rates to changes in NOx or hydrocarbon concentrations showed that the instantaneous 03 production rate at the center of the urban plume, when half of the urban NOx emissions had been processed, is hydrocarbon sensitive. However, 03 production becomes NOx sensitive as the plume matures.
Palaeomagnetic implications for the timing of hematite precipitation and remagnetization in the Carboniferous Barren Red Measures, UK southern North Sea

Abstract Although rocks of the Carboniferous Barren Red Measures in the UK southern North Sea are often primarily reddened, they also show secondary reddening by fine-grained hematite precipitated as a result of deep weathering below the Permian unconformity. However, palaeomagnetic and petrographic analyses of samples from wells 49/1–3 and 49/2–3 have shown that a third phase of hematite was precipitated in the Triassic. The specularite grains associated with this magnetization are larger than those precipitated in the Permian and also contain a more dominant magnetic signature. Although Permian hematite precipitation was largely produced as a result of oxidation through vertical percolation, the occurrence of Triassic hematite grains appears to be related to distinct fluvial channels. It is suggested that lateral fluid flow is responsible for the precipitation of hematite in the Triassic and that this is associated with fluvial channel sandstones which have the best permeabilities and interconnectivities. The palaeomagnetic technique is therefore useful for assessing the degree of lateral communication in reservoir sandstones.
Polymorphisms in the hANP (Human Atrial Natriuretic Peptide) Gene, Albuminuria, and Hypertension

Atrial natriuretic peptide (ANP) jointly affects kidney function and blood pressure homeostasis and is a candidate susceptibility gene for both essential hypertension and kidney disease. We evaluated the relation between the ScaI and BstXI polymorphisms of the human ANP (hANP) gene, hypertension, and albuminuria in a clinical cohort of 1033 subjects, including type 1 and type 2 diabetic patients, nondiabetic subjects with essential hypertension, and nondiabetic normotensive control subjects. Microalbuminuria was present in 15%, 29%, and 2%, respectively, of type 1 diabetic, type 2 diabetic, and nondiabetic patients. Macroalbuminuria was present in 9% of type 1 diabetics, 21% of type 2 diabetics, and 31% of nondiabetics. Prevalence of hypertension was 31%, 58%, and 61% in normoalbuminuric, microalbuminuric, and macroalbuminuric subjects, respectively (P <0.0001). Genotype distributions were in Hardy-Weinberg equilibrium in all 4 patient subgroups. The frequency of the ScaI mutated allele (A1) was significantly lower in hypertensive than in control subjects (11% versus 19%, P =0.018) and in patients with macroalbuminuria (5%) as compared with normoalbuminuric subjects (16%;P <0.0001). In a nominal logistic model adjusting for gender, age, obesity, diabetes, micro/macroalbuminuria, and hypertension, the A1 allele was independently associated with macroalbuminuria (odds ratio, 0.57; confidence interval, 1.39 to 3.59;P =0.003) but not with hypertension. In the same model, the frequency of the BstXI mutated allele (T708) was increased in the presence of microalbuminuria (odds ratio, 2.25; confidence interval, 1.39 to 3.59;P <0.001). We conclude that the mutated genotypes of the ScaI polymorphism are negatively associated with overt nephropathy, whereas the mutated genotypes of BstXI polymorphism are positively associated with microalbuminuria. hANP gene variants may exert a protective effect against the development and progression of kidney damage in diabetes.
Behavior Modulates Effective Connectivity between Cortex and Striatum

It has been notoriously difficult to understand interactions in the basal ganglia because of multiple recurrent loops. Another complication is that activity there is strongly dependent on behavior, suggesting that directional interactions, or effective connections, can dynamically change. A simplifying approach would be to examine just the direct, monosynaptic projections from cortex to striatum and contrast this with the polysynaptic feedback connections from striatum to cortex. Previous work by others on effective connectivity in this pathway indicated that activity in cortex could be used to predict activity in striatum, but that striatal activity could not predict cortical activity. However, this work was conducted in anesthetized or seizing animals, making it impossible to know how free behavior might influence effective connectivity. To address this issue, we applied Granger causality to local field potential signals from cortex and striatum in freely behaving rats. Consistent with previous results, we found that effective connectivity was largely unidirectional, from cortex to striatum, during anesthetized and resting states. Interestingly, we found that effective connectivity became bidirectional during free behaviors. These results are the first to our knowledge to show that striatal influence on cortex can be as strong as cortical influence on striatum. In addition, these findings highlight how behavioral states can affect basal ganglia interactions. Finally, we suggest that this approach may be useful for studies of Parkinson's or Huntington's diseases, in which effective connectivity may change during movement.
DNA methylation of the oxytocin receptor gene predicts neural response to ambiguous social stimuli

Oxytocin and its receptor (OXTR) play an important role in a variety of social perceptual and affiliative processes. Individual variability in social information processing likely has a strong heritable component, and as such, many investigations have established an association between common genetic variants of OXTR and variability in the social phenotype. However, to date, these investigations have primarily focused only on changes in the sequence of DNA without considering the role of epigenetic factors. DNA methylation is an epigenetic mechanism by which cells control transcription through modification of chromatin structure. DNA methylation of OXTR decreases expression of the gene and high levels of methylation have been associated with autism spectrum disorders (ASD). This link between epigenetic variability and social phenotype allows for the possibility that social processes are under epigenetic control. We hypothesized that the level of DNA methylation of OXTR would predict individual variability in social perception. Using the brain's sensitivity to displays of animacy as a neural endophenotype of social perception, we found significant associations between the degree of OXTR methylation and brain activity evoked by the perception of animacy. Our results suggest that consideration of DNA methylation may substantially improve our ability to explain individual differences in imaging genetic association studies.