Miracle-dz/UniFAR-FTUs huggingface dataset:
Plenoptic sampling

This paper studies the problem of plenoptic sampling in image-based rendering (IBR). From a spectral analysis of light field signals and using the sampling theorem, we mathematically derive the analytical functions to determine the minimum sampling rate for light field rendering. The spectral support of a light field signal is bounded by the minimum and maximum depths only, no matter how complicated the spectral support might be because of depth variations in the scene. The minimum sampling rate for light field rendering is obtained by compacting the replicas of the spectral support of the sampled light field within the smallest interval. Given the minimum and maximum depths, a reconstruction filter with an optimal and constant depth can be designed to achieve anti-aliased light field rendering. Plenoptic sampling goes beyond the minimum number of images needed for anti-aliased light field rendering. More significantly, it utilizes the scene depth information to determine the minimum sampling curve in the joint image and geometry space. The minimum sampling curve quantitatively describes the relationship among three key elements in IBR systems: scene complexity (geometrical and textural information), the number of image samples, and the output resolution. Therefore, plenoptic sampling bridges the gap between image-based rendering and traditional geometry-based rendering. Experimental results demonstrate the effectiveness of our approach.
Can clinical algorithms deliver an accurate diagnosis of HIV infection in infancy?

The Integrated Management of Childhood Illness (IMCI) guidelines established clinical criteria to identify children with suspected HIV infection for HIV testing and specific management. In an article published in the Bulletin based on a study conducted in South Africa Horwood et al. report that they have fine-tuned these criteria into a clinical algorithm. This algorithm has been incorporated into the 2003 edition of the South African IMCI guidelines to maximize identification of HIV infected children. Horwood et al.’s study clinically assessed 690 hospital outpatients aged 2–59 months in an HIV prevalence setting of 28.7%. In the absence of screening questions the clinical algorithm was applied and yielded a sensitivity of 70% specificity of 80% and a positive predictive value (PPV) of 59%. The validity of the algorithm for the 226 infants (2–11 months) 38% of whom were infected did not differ from that for the other age categories. Validation of the clinical algorithm in different settings was invited. (excerpt)
Pulmonary Infection Is an Independent Risk Factor for Long-Term Mortality and Quality of Life for Sepsis Patients

Background. Long-term outcomes (mortality and health-related quality of life) of sepsis have risen as important indicators for health care. Pulmonary infection and abdominal infection are the leading causes of sepsis. However, few researches about long-term outcomes focused on the origin of sepsis. Here we aim to study the clinical differences between pulmonary-sepsis and abdominal-sepsis and to investigate whether different infection foci were associated with long-term outcomes. Methods. Patients who survived after hospital discharge were followed up by telephone interview. Quality of life (QoL) was assessed using the EuroQol 5-dimension (EQ5D) questionnaire. Results. Four hundred and eighty-three sepsis patients were included, 272 (56.3%) had pulmonary-sepsis, and 180 (37.3%) had abdominal-sepsis. The overall ICU and one-year mortality rates of the cohort were 17.8% and 36.1%, respectively. Compared with abdominal-sepsis, pulmonary-sepsis patients had older age, higher APACHE II, higher ICU mortality (31.7% versus 12.6%), and one-year mortality (45.4% versus 24.4%), together with worse QoL. Age, septic shock, acute renal failure, fungus infection, anion gap, and pulmonary infection were predictors for one-year mortality and pulmonary infection was a risk factor for poor QoL. Conclusions. Pulmonary-sepsis showed worse outcome than abdominal-sepsis. Pulmonary infection is a risk factor for one-year mortality and QoL after sepsis.
Constitutive expression of thrombospondin 1 in MC3T3‐E1 osteoblastic cells inhibits mineralization

Thrombospondin 1 (TSP1) is a multifunctional extracellular glycoprotein present mainly in the fetal and adult skeleton. Although an inhibitory effect of TSP1 against pathological mineralization in cultured vascular pericytes has been shown, its involvement in physiological mineralization by osteoblasts is still unknown. To determine the role of TSP1 in biomineralization, mouse osteoblastic MC3T3‐E1 cells were cultured in the presence of antisense phosphorothioate oligodeoxynucleotides complementary to the TSP1 sequence. The 18‐ and 24‐mer antisense oligonucleotides caused concentration‐dependent increases in the number of mineralized nodules, acid‐soluble calcium deposition in the cell/matrix layer, and alkaline phosphatase activity within 9 days, without affecting cell proliferation. The corresponding sense or scrambled oligonucleotides did not affect these parameters. In the antisense oligonucleotide‐treated MC3T3‐E1 cells, thickened extracellular matrix, well‐developed cell processes, increased intracellular organelles, and collagen fibril bundles were observed. On the other hand, the addition of TSP1 to the culture decreased the production of a mineralized matrix by MC3T3‐E1 cells. Furthermore, MC3T3‐E1 clones overexpressing mouse TSP1 were established and assayed for TSP1 protein and their capacity to mineralize. TSP1 dose‐dependently inhibited mineralization by these cells both in vitro and in vivo. These results indicate that TSP1 functions as an inhibitory regulator of bone mineralization and matrix production by osteoblasts to sustain bone homeostasis. J. Cell. Physiol. 209: 322–332, 2006. © 2006 Wiley‐Liss, Inc.
Solving stochastic programs with network recourse

In this paper we provide computational procedures for solving stochastic programs with network recourse. Special attention is paid to the feasibility problem, and we show how to solve the recourse or second stage problem. This problem is how to solve a large number of networks where the only differences are the amounts supplied and demanded at the nodes. For this purpose we have developed the Schur complement for networks. Computational results are given. Finally we show how preprocessing based upon facet generation can simplify the rest of the procedures.
Spatial learning impairment parallels the magnitude of dorsal hippocampal lesions, but is hardly present following ventral lesions

The hippocampus plays an essential role in spatial learning. To investigate whether the whole structure is equally important, we compared the effects of variously sized and localized hippocampal aspiration lesions on spatial learning in a Morris water maze. The volume of all hippocampal lesions was determined. Dorsal hippocampal lesions consistently impaired spatial learning more than equally large ventral lesions. The dorsal lesions had to be larger than 20% of the total hippocampal volume to prolong final escape latencies. The acquisition rate and precision on a probe test without platform were sensitive to even smaller dorsal lesions. The degree of impairment correlated with the lesion volume. In contrast, the lesions of the ventral half of the hippocampus spared both the rate and the precision of learning unless nearly all of the ventral half was removed. There was no significant effect of the location (dorsal or ventral) of damage to the overlying neocortex only. In conclusion, the dorsal half of the hippocampus appears more important for spatial learning than the ventral half. The spatial learning ability seems related to the amount of damaged dorsal hippocampal tissue, with a threshold at about 20% of the total hippocampal volume, under which normal learning can occur.
Activation of the “Splenocardiac Axis” by electronic and tobacco cigarettes in otherwise healthy young adults

The “Splenocardiac Axis” describes an inflammatory signaling network underlying acute cardiac ischemia, characterized by sympathetic nerve stimulation of hematopoietic tissues, such as the bone marrow and spleen, which then release proinflammatory monocytes that populate atherosclerotic plaques, thereby promoting ischemic heart disease. Electronic (e) cigarettes, like tobacco cigarettes trigger sympathetic nerve activation, but virtually nothing is known about their influence on hematopoietic and vascular tissues and cardiovascular risks. The objective of this study was to determine if the Splenocardiac Axis is activated in young adults who habitually use either tobacco or e‐cigarettes. In otherwise healthy humans who habitually use tobacco cigarettes or e‐cigarettes (not both), we used 18F‐flurorodeoxyglucose positron emission tomography/computer tomography (FDG‐PET/CT) to test the hypothesis that tobacco or e‐cigarettes increased metabolic activity of the hematopoietic and vascular tissues. FDG uptake in the spleen increased from nonuser controls (1.62 ± 0.07), to the e‐cigarette users (1.73 ± 0.04), and was highest in tobacco cigarette smokers (1.82 ± 0.09; monotone P = 0.05). Similarly, FDG uptake in the aorta increased from the nonuser controls (1.87 ± 0.07) to the e‐cigarette users (1.98 ± 0.07), and was highest in tobacco cigarette smokers (2.10 ± 0.07; monotone P = 0.04). FDG uptake in the skeletal muscle, which served as a control tissue, was not different between the groups. In conclusion, these findings are consistent with activation of the Splenocardiac Axis by emissions from tobacco cigarettes and e‐cigarettes. This activation suggests a mechanism by which tobacco cigarettes, and potentially e‐cigarettes, may lead to increased risk of future cardiovascular events.
2012 TAU power grid simulation contest: Benchmark suite and results

Although power grid analysis has been an active research area for a number of years, increasing chip size has exposed new challenges in this traditional topic. The simulation of these large scale networks is becoming a dominant step in the design verification flow and it often requires the very largest computer available to the design team. To spur academic research in this vital verification step, the IBM Austin Research Laboratory, with support from the ACM TAU Workshop, has successfully organized two annual TAU Power Grid Simulation Contests, and over twenty university teams across the world have participated. For 2012, the contest is focused on dynamic analysis and parallel implementation. In this paper, the organizers review the TAU 2012 Power Grid Simulation Contest. This contest was held to seek new efficient methods with parallel implementation for performing dynamic (i.e. time domain) analysis for large power grid networks. Accuracy, run-time and memory consumption were used as metrics to evaluate the various contestants, and prizes were accordingly awarded to the top three teams. The benchmarks in [1] were expanded to be suitable for dynamic analysis. These are made public, along with the scores from various teams that participated in the contest, in order to further encourage their use in future research on this important topic.
PALM: A Paralleled and Integrated Framework for Phylogenetic Inference with Automatic Likelihood Model Selectors

Background Selecting an appropriate substitution model and deriving a tree topology for a given sequence set are essential in phylogenetic analysis. However, such time consuming, computationally intensive tasks rely on knowledge of substitution model theories and related expertise to run through all possible combinations of several separate programs. To ensure a thorough and efficient analysis and avert tedious manipulations of various programs, this work presents an intuitive framework, the phylogenetic reconstruction with automatic likelihood model selectors (PALM), with convincing, updated algorithms and a best-fit model selection mechanism for seamless phylogenetic analysis. Methodology As an integrated framework of ClustalW, PhyML, MODELTEST, ProtTest, and several in-house programs, PALM evaluates the fitness of 56 substitution models for nucleotide sequences and 112 substitution models for protein sequences with scores in various criteria. The input for PALM can be either sequences in FASTA format or a sequence alignment file in PHYLIP format. To accelerate the computing of maximum likelihood and bootstrapping, this work integrates MPICH2/PhyML, PalmMonitor and Palm job controller across several machines with multiple processors and adopts the task parallelism approach. Moreover, an intuitive and interactive web component, PalmTree, is developed for displaying and operating the output tree with options of tree rooting, branches swapping, viewing the branch length values, and viewing bootstrapping score, as well as removing nodes to restart analysis iteratively. Significance The workflow of PALM is straightforward and coherent. Via a succinct, user-friendly interface, researchers unfamiliar with phylogenetic analysis can easily use this server to submit sequences, retrieve the output, and re-submit a job based on a previous result if some sequences are to be deleted or added for phylogenetic reconstruction. PALM results in an inference of phylogenetic relationship not only by vanquishing the computation difficulty of ML methods but also providing statistic methods for model selection and bootstrapping. The proposed approach can reduce calculation time, which is particularly relevant when querying a large data set. PALM can be accessed online at http://palm.iis. sinica.edu. tw.
Synoptic Climatology of Precipitation in Iran

The uplift mechanisms associated with 24-hour precipitation receipts of 0.1 mm or greater in Iran were investigated. Based on a subjective analysis of daily surface and 500 mb weather charts, we systematically attributed all precipitation at 40 stations for the period 1965–69 to upper tropospheric mechanisms, surface disturbances, marine influence, or instability due primarily to surface heating. These mechanisms together explained 84 percent of all precipitation days. Upper-level disturbances alone explained over 50 percent; when combined with recognizable surface disturbances, this uplift mechanism collectively accounted for over 70 percent of all precipitation days. Surface disturbances were more frequent in the north, but upper-level disturbances alone attained greater relative importance in the south where precipitation was lower. Marine influence was important only near the Caspian Sea and surface heating was a minor trigger in summer only.
A Novel Human Lipid Binding Protein Coding Gene: PERF15, Sequence and Cloning

Introduction PERF15 is a testicular germ-cell specific fatty-acid binding protein (FABP) isolated from mammals, originally from rats. It encodes one of the most abundant proteins of rat spermatozoa localized in the perinuclear theca. Northern blot analysis has demonstrated that rat PERF15 mRNA is exclusively transcribed during meiosis and post-meiosis. In this study, we cloned and sequenced human PERF15 gene. Materials and Methods According to the open reading frame of automated computational analysis of Homo sapiens similar to testis fatty acid binding protein nine, two specific Primers were designed to amplify human PERF15 gene. To confirm the identity of the amplified gene, PCR products of PERF15 were cloned into appropriate plasmid vectors followed by sequencing of the inserts. Results A unique band of ∼3kb was obtained after PCR amplification. Restriction enzyme digestion using PvuII confirmed that the fragment was related to PERF15. Gene alignment, direct sequencing and application of specific primers to the gene showed 100% similarity between this gene and the computational data by gel extraction of the ∼3 kb band. The human PERF15 gene contained four exons and three introns. Exons one, two, three and four, respectively, coded for 24, 57, 34 and 17 amino acids. The existing three introns were composed of 2113, 461, and 168 nucleotides. Conclusion In spite of the homology between exonic regions and exon-intron boundaries of human PERF15 gene and that of animals, human PERF15 gene is different in size and sequence from corresponding introns in rat and murine PERF15.
ABC: a hypermedia system for artifact-based collaboration

Abstract : Our project is studying the process by which groups of individuals work together to build large, complex structures of ideas, and we are developing a distributed hypermedia system to support the process. This description includes a brief overview of the system, but emphasizes three components: a hypermedia data management system or graph server, a set of browsers for working with graph objects, and a set of applications for working with data contents of graph nodes. A number of research issues are raised and discussed in context, including: composite objects; anchored links; scaling up for large applications; partitioning the hypermedia graph; consistency and completeness across subgraphs; and an open, extensible architecture for applications.
A clinical-biological risk stratification model for resected gastric cancer: prognostic impact of Her2, Fhit, and APC expression status.

BACKGROUND To obtain a prognostic stratification model for resected gastric cancer patients. PATIENTS AND METHODS Clinicopathological and molecular data (expression of Cdx2, Apc, β-catenin, E-cadherin, Fhit, p53, and human epidermal growth factor receptor-2 (Her2); HER2 and TOPO2A gene copy number; PIK3CA mutations; microsatellite instability) were correlated to cancer-specific/overall survival (CSS/OS) using a Cox model. Individual patient probability (IPP) was estimated by logistic equation. A continuous score to identify risk-classes was derived according to the model ratios. RESULTS Two-hundred eight patients were studied (median follow-up 20 months). At multivariate analysis, sex, stage, margins, location, nodes, Apc, and Fhit were independent predictors for CSS; the same factors (and age and Her2, except Fhit) predicted OS. Multivariate model predicted IPP with high prognostic accuracy (0.90 for CSS; 0.91 for OS). A two-class model significantly separated low- and high-risk patients for CSS (23.4% and 85.6%, P < 0.0001) and OS (21.4% and 82.0%, P < 0.0001). A three-class model differentiated low-, intermediate-, and high-risk patients for CSS (6.3%, 35.3%, and 88.0%, P < 0.0001) and OS (6.1%, 34.6%, and 86.5%, P < 0.0001). CONCLUSIONS A risk classification system comprising the immunohistochemical expression of three proteins (Apc, Fhit, and Her2) and five clinicopathological parameters (stage, resected nodes, margins, location, and sex) accurately separates the resected gastric cancer patients into three classes of risk.
Evaluation of Cynomolgus Macaque (Macaca fascicularis) Endogenous Retrovirus Expression Following Simian Immunodeficiency Virus Infection

Human endogenous retrovirus type K (HERV-K) transcripts are upregulated in the plasma of HIV-infected individuals and have been considered as targets for an HIV vaccine. We evaluated cynomolgus macaque endogenous retrovirus (CyERV) mRNA expression by RT-qPCR in PBMCs isolated from a cohort of animals previously utilized in a live attenuated SIV vaccine trial. CyERV env transcript levels decreased following vaccination (control and vaccine groups) and CyERV env and gag mRNA expression was decreased following acute SIV-infection, whereas during chronic SIV infection, CyERV transcript levels were indistinguishable from baseline. Reduced susceptibility to initial SIV infection, as measured by the number of SIV challenges required for infection, was associated with increased CyERV transcript levels in PBMCs. In vitro analysis revealed that SIV infection of purified CD4+ T-cells did not alter CyERV gene expression. This study represents the first evaluation of ERV expression in cynomolgus macaques following SIV infection, in an effort to assess the utility of cynomolgus macaques as an animal model to evaluate ERVs as a target for an HIV/SIV vaccine. This non-human primate model system does not recapitulate what has been observed to date in the plasma of HIV-infected humans suggesting that further investigation at the cellular level is required to elucidate the impact of HIV/SIV infection on endogenous retrovirus expression.
Developmental Exposure to Concentrated Ambient Particles and Preference for Immediate Reward in Mice

Background: Recent epidemiological studies indicate negative associations between a diverse group of air pollutants and cognitive functioning in children and adults, and aspects of attention deficit in children. Neuroinflammation and oxidative stress are two putative biological mechanisms by which air pollutants may adversely affect the brain. Objectives: We sought to determine whether exposure to concentrated ambient particulate matter (CAPS) during the first 2 weeks of life, alone or again in adulthood, could alter responding for delayed reward, a critical component of human decision making. Greater preference for immediate reward has been implicated as a component of several psychiatric disorders, addiction, obesity, and attention deficit. Methods: C57BL/6J mice were exposed to ultrafine particles (< 100 nm in aerodynamic diameter; CAPS) using the Harvard University Concentrated Ambient Particle System (HUCAPS) or filtered air in the postnatal period (days 4–7 and 10–13) with and without adult exposure over days 56–60. In adulthood, delay behavior was assessed using a fixed-ratio waiting-for-reward (FR wait) paradigm in which 25 responses (FR25) were required to initiate the waiting-for-reward component during which mice obtained “free” sucrose pellets with the stipulation that these “free” pellets were delivered at increasing delay intervals. Results: Coupled with increased FR response rates, mice exposed to postnatal CAPS displayed increased FR resets that reinstated short delays, indicating a preference for shorter delays, despite the added response cost of the FR25. No associated changes in locomotor activity were observed. Conclusions: Postnatal CAPS exposure produces an enhanced bias towards immediate rewards, a risk factor for several central nervous system (CNS) disorders. This enhancement does not appear to be the result of hyperactivity. The findings underscore the need for further evaluation of air pollution effects on the CNS and its potential contribution to CNS diseases and disorders.
“Unraveling the Paradoxes of China’s Trade Imbalances Following the Global Financial Crises”

* Professor of Economics, Aix-Marseille School of Economics (AMSE), CNRS and EHESS, 2 rue de la Charité13002 Marseille cedex, Fr ance, Telephone: 33-42914836. Fax: 33-42914873. E-Mail: eric.girardin@univmed.fr . ** Professor of Economics, University of Nantes, Fr ance; Professional address: LEMNA Research Center, Nantes School of Economics a nd Management I.A. E. , University of Nantes, Chemin de la Censive du Tertr e, B. P. 52231, 44322 Nantes Cedex 3, Telephone and Fax Numbers: 33-2-40141717 (office ), 33-676878853 (cell) and 33-240141700 (fax). E-mail address: robertfowen@gmail . com Cellular phone number: 33676878853. (Corresponding submitter) *** Doctoral Student, Aix-Marseille School of Eco n mics (AMSE), CNRS and EHESS Château Lafarge Route des Milles 13290 Les Milles Aix-en-Provence, France, Telephone: 33-684917887. E-Mail: emkafall@yahoo.fr
A new average case analysis for completion time scheduling

We present a new average case analysis for the problem of scheduling n jobs on m machines so that the sum of job completion times is minimized. Our goal is to use the concept of competitive ratio---which is a typical worst case notion---also within an average case analysis. We show that the classic SEPT scheduling strategy with Ω(n) worst-case competitive ratio achieves an average of O(1) under several natural distributions, among them the exponential distribution. Our analysis technique allows to also roughly estimate the probability distribution of the competitive ratio. Thus, our result bridges the gap between worst case and average case performance guarantee.