Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Analyses of Mouse Aortic Endothelium in Response to Atherogenic Stimuli

Objective—Endothelial cells are central to the initiation of atherosclerosis, yet there has been limited success in studying their gene expression in the mouse aorta. To address this, we developed a method for determining the global transcriptional changes that occur in the mouse endothelium in response to atherogenic conditions and applied it to investigate inflammatory stimuli. Approach and Results—We characterized a method for the isolation of endothelial cell RNA with high purity directly from mouse aortas and adapted this method to allow for the treatment of aortas ex vivo before RNA collection. Expression array analysis was performed on endothelial cell RNA isolated from control and hyperlipidemic prelesion mouse aortas, and 797 differentially expressed genes were identified. We also examined the effect of additional atherogenic conditions on endothelial gene expression, including ex vivo treatment with inflammatory stimuli, acute hyperlipidemia, and age. Of the 14 most highly differentially expressed genes in endothelium from prelesion aortas, 8 were also perturbed significantly by ≥1 atherogenic conditions: 2610019E17Rik, Abca1, H2-Ab1, H2-D1, Pf4, Ppbp, Pvrl2, and Tnnt2. Conclusions—We demonstrated that RNA can be isolated from mouse aortic endothelial cells after in vivo and ex vivo treatments of the murine vessel wall. We applied these methods to identify a group of genes, many of which have not been described previously as having a direct role in atherosclerosis, that were highly regulated by atherogenic stimuli and may play a role in early atherogenesis.
Image perception : Relative influence of bottom-up and top-down attention

Attention and memory are very closely related and their aim is to simplify the acquired data into an intelligent structured data set. Two main points are discussed in this paper. The first one is the presentation of a novel visual attention model for still images which includes both a bottom-up and a top-down approach. The bottom-up model is based on structures rarity within the image during the forgetting process. The top-down information uses mousetracking experiments to build models of a global behavior for a given kind of image. The second interesting point is that the relative importance of bottom-up and top-down information depends on the specificity of each image. For the three different sets of images within the database the importance of the topdown information is different. The proposed models assessment is achieved on a 91-image database.
A snapshot of data quality issues in Indonesian community health

Healthcare services in Indonesia remain 'poor' by international standards. At the heart of the problem are systemic data quality issues. Little work has been done on health data quality in rural settings in this region. In this work, an exploratory study of data quality within a health centre (HC) in rural Indonesia is carried out with reference to two well-known sets of qualitative data quality measures AIMQ and PRISM. The research aims first to uncover data quality issues within a typical health facility in rural Indonesia, and second to discover whether these problems relate to operational issues. The research uses an inductive, qualitative case study approach using the following methodology. Key data quality issues are identified in the literature; these are used as a framework from which to develop seed questions for data collection via semi structured interviews. The full interview transcripts are analysed manually and using the text mining software Leximancer. Issues relating to data validation and integration are identified. Suggestions are put forward for development action both locally and nationally. This work provides a snapshot of the state of play in a typical rural health facility in Indonesia.
Early Phase of Plasticity-Related Gene Regulation and SRF Dependent Transcription in the Hippocampus

Hippocampal organotypic cultures are a highly reliable in vitro model for studying neuroplasticity: in this paper, we analyze the early phase of the transcriptional response induced by a 20 µM gabazine treatment (GabT), a GABA-Ar antagonist, by using Affymetrix oligonucleotide microarray, RT-PCR based time-course and chromatin-immuno-precipitation. The transcriptome profiling revealed that the pool of genes up-regulated by GabT, besides being strongly related to the regulation of growth and synaptic transmission, is also endowed with neuro-protective and pro-survival properties. By using RT-PCR, we quantified a time-course of the transient expression for 33 of the highest up-regulated genes, with an average sampling rate of 10 minutes and covering the time interval [10∶90] minutes. The cluster analysis of the time-course disclosed the existence of three different dynamical patterns, one of which proved, in a statistical analysis based on results from previous works, to be significantly related with SRF-dependent regulation (p-value<0.05). The chromatin immunoprecipitation (chip) assay confirmed the rich presence of working CArG boxes in the genes belonging to the latter dynamical pattern and therefore validated the statistical analysis. Furthermore, an in silico analysis of the promoters revealed the presence of additional conserved CArG boxes upstream of the genes Nr4a1 and Rgs2. The chip assay confirmed a significant SRF signal in the Nr4a1 CArG box but not in the Rgs2 CArG box.
Tissue Lesions Due to Spirorchiid Eggs in a Loggerhead Turtle (Caretta caretta Linnaeus 1758) from Brazil: First Report Outside of the United States

Abstract Spirorchiids (family Spirorchiidae Stunkard 1921) are a group of flukes that inhabit the circulatory system of turtles. Infection by members of the family Spirorchiidae involves egg deposition in the host bloodstream and accumulation in tissues, which cause inflammatory reactions and embolisms, leading or contributing to the death of the host. Reports of spirorchiid egg lesions in loggerhead turtles (Caretta caretta Linnaeus, 1758) have only been reported from U.S. hosts. In the present report a female loggerhead sea turtle was found dead on the beach in the north part of the State of Rio de Janeiro, Brazil. During gross necropsy, no parasite egg nodule was found. But the microscopic analysis revealed a mild granulomatous inflammatory process due to eggs from the family Spirorchiidae and both Langhans giant cells and foreign-body giant cells in the heart, kidneys, intestines, lungs, and spleen. The present note is the first record of tissue lesions due to spirorchiid eggs in a loggerhead sea turtle outside the United States.
Fast on-line statistical learning on a GPGPU

On-line Machine Learning using Stochastic Gradient Descent is an inherently sequential computation. This makes it difficult to improve performance by simply employing parallel architectures. Langford et al. made a modification to the standard stochastic gradient descent approach which opens up the possibility of parallel computation. They also proved that there is no significant loss in accuracy in their approach. They did empirically demonstrate the performance gain in speed for the case of a pipelined architecture with a few processing units. In this paper we report on applying the Langford et al. approach on a General Purpose Graphics Processing Unit (GPGPU) with a large number of processing units. We accelerate the learning speed by approximately 4.5 times compared to a standard single threaded approach with comparable accuracy. We also evaluate the GPU performance for the sequential variant of the algorithm, which has not previously been reported. Finally, we investigate how changes in the number of threads, number of blocks, and amount of delay, effects the overall performance and accuracy.
Digital rectal examination: national survey of undergraduate medical training in Ireland

Objective: To assess the experience gained in digital rectal examination (DRE) by medical students in the Republic of Ireland by the completion of undergraduate training. Methods: A national survey was conducted targeting all 582 final year students from the five medical schools completing their undergraduate studies in the summer of 2005. Format was anonymous questionnaire. Experience of DRE was defined as the student having performed at least one examination on either patient or teaching mannequin. Results: In total, 396 (68%) of 582 students responded. No experience of DRE was reported in 97 (24%), with mannequin-only experience in a further 78 (20%). Of the remaining 221 (56%) who performed DRE on at least one patient, one third (74) reported no confidence in their ability to interpret their findings properly. Conclusion: Undergraduate training in DRE is limited. Training in DRE can no longer be reasonably considered part of the core curriculum taught in Irish medical schools.
Eradication of rat malignant gliomas by retroviral-mediated, in vivo delivery of the interleukin 4 gene.

Overexpression of interleukin 4 (IL-4) can impair the tumorigenicity of glioma cells, but direct evidence of its antitumor efficacy after in vivo gene transfer into malignant gliomas has not been provided. To test this, we first injected into the brain of Sprague Dawley rats a 1:1 mixture of C6 rat glioblastoma cells and psi2.L4SN20 or E86.L4SN50 retroviral producer cells (RPCs), secreting 20 and 50 ng of IL-4/5 x 10(5) cells/48 h, respectively. Twenty-seven and 56% of rats receiving injections with these low- or medium-level IL-4 RPCs, respectively, survived tumor injection, whereas control rats died in about 1 month. E86.L4SN50 RPCs coinjected with 9L gliosarcoma cells into syngeneic Fischer 344 rats yielded similar results. A novel IL-4 RPC clone expressing higher levels of IL-4, E86.L4SN200, coinjected with 9L cells increased to 75% the fraction of long-term survivors and induced tumor regression in 50% of rats when injected into established 9L gliosarcomas. Cured rats developed an immunological memory because they rejected a challenge of wild-type 9L cells into the contralateral hemisphere. Magnetic resonance imaging was used to monitor 9L and C6 gliomas and gave direct evidence for tumor rejection in treated rats. Immunohistology showed inflammatory infiltrates in IL-4-treated tumors in which CD8+ T lymphocytes were more abundant, although CD4+ T lymphocytes, B lymphocytes, and macrophages were also present. Overall, these findings suggest that IL-4 gene transfer is a new, promising approach for treating malignant gliomas.
The Role of Information Technology in Modern Production : Complement or Substitute to Other Inputs ?

Previous work has shown that the economic impact of IT varies systematically with how a firm is organized. This study investigates the role of organizational factors on an important aspect of the economics of IT: the substitution of IT capital for other inputs such as capital and labor. Much of the previous discussion of IT impact has focused on the substitution of IT for labor, yet much of the managerial literature has recently stressed the importance of finding complementarities between IT and other organizational practices. The ability to identify and leverage potential complements between IT and other factors may become increasingly important as IT investments are used less for simple cost reduction and more for creating customer value. Using firm level data for over 400 large firms we find that organizational factors play an important role in a firm’s ability to complement existing capital with IT investments. It appears that “modern organizations”, exemplified by decentralized organizational form, greater use of skilled staff and newer capital investments, are capable of such complements, while their “traditional” counterparts do not have this ability. On the other hand, we find that all forms of organizations use IT as a net substitute for labor. IT and Modern Production 1
Effects of morphine and naloxone on dorsal horn neurones in the cat.

Morphine, applied by microiontophoresis to functionally identified dorsal horn neurones in segments L5–L7 of cats (chloralose anaesthetized, decerebrated or high spinal), produced primarily a depression of the discharge of neurones responding to noxious radiant heat applied to the skin. It depressed on-going activity (12 out of 20 neurones), glutamate-evoked excitation (8/8) and the response to the noxious stimulus (13/21). The response of two additional neurones to heat was potentiated. The effects began 10–30 s from the onset of application, reached a maximum in up to 8 min and outlasted application by up to 10 min. Morphine had relatively little effect on on-going activity and glutamate-evoked excitation of neurones responding to non-noxious stimuli (n = 18). Naloxone (intravenously and iontophoretic) reversed these depressions (4/11). It is suggested that morphine may produce analgesia, at least in part, by a direct action on a specific morphine receptor in the spinal cord.
Why are the Ruijsenaars--Schneider and the Calogero--Moser hierarchies governed by the same $r$--matrix?

We demonstrate that in a certain gauge the Ruijsenaars–Schneider models admit Lax representations governed by the same dynamical r–matrix as their non–relativistic counterparts (Calogero–Moser models). This phenomenon is explained by establishing the quadratic r-matrix Poisson bracket for the Ruijsenaars– Schneider models.
NPR1 Modulates Cross-Talk between Salicylate- and Jasmonate-Dependent Defense Pathways through a Novel Function in the Cytosol Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009159.

Plant defenses against pathogens and insects are regulated differentially by cross-communicating signal transduction pathways in which salicylic acid (SA) and jasmonic acid (JA) play key roles. In this study, we investigated the molecular mechanism of the antagonistic effect of SA on JA signaling. Arabidopsis plants unable to accumulate SA produced 25-fold higher levels of JA and showed enhanced expression of the JA-responsive genes LOX2, PDF1.2, and VSP in response to infection by Pseudomonas syringae pv tomato DC3000, indicating that in wild-type plants, pathogen-induced SA accumulation is associated with the suppression of JA signaling. Analysis of the Arabidopsis mutant npr1, which is impaired in SA signal transduction, revealed that the antagonistic effect of SA on JA signaling requires the regulatory protein NPR1. Nuclear localization of NPR1, which is essential for SA-mediated defense gene expression, is not required for the suppression of JA signaling, indicating that cross-talk between SA and JA is modulated through a novel function of NPR1 in the cytosol.
16S to 23S rRNA spacer fragment length polymorphism of Salmonella enterica at subspecies and serotype levels

The variation in the lengths of the internal transcribed spacer (ITS) between 16S and 23S rRNA genes of 101 strains representing 58 serotypes of Salmonella enterica (used for Salm. choleraesuis) subsp. enterica (I), salamae (II), arizonae (IIIa), diarizonae (IIIb), houtenae (IV) and indica (VI) was used for typing by PCR amplification. Ten fragment lengths were observed by denaturing polyacrylamide gel electrophoresis on an automatic DNA sequencer resulting in 21 unique fragment patterns. Ten out of the 58 serotypes showed specific patterns but 48 serotypes were not fully differentiated. More than one ITS pattern was observed in seven serotypes. Five of the 21 fragment patterns contained representatives of more than one subspecies. Under non‐denaturing electrophoresis conditions, serotype specificity was obtained but precise ITS fragment length determination was not possible. DNA sequence comparison between ITSs of individual rrn operons is needed to further interpret ITS diversity within Salm. enterica at serotype and subspecies levels.
Reaching approximate agreement in the presence of faults

This paper considers a variant of the Byzantine Generals problem, in which processes start with arbitrary real values rather than Boolean values or values from some bounded range, and in which approximate, rather than exact, agreement is the desired goal. Algorithms are presented to reach approximate agreement in asynchronous, as well as synchronous systems. The asynchronous agreement algorithm is an interesting contrast to a result of Fischer et al, who show that exact agreement with guaranteed termination is not attainable in an asynchronous system with as few as one faulty process. The algorithms work by successive approximation, with a provable convergence rate that depends on the ratio between the number of faulty processes and the total number of processes. Lower bounds on the convergence rate for algorithms of this form are proved, and the algorithms presented are shown to be optimal.
Retrieval of meteorological parameters from ROSA on-board Megha Tropiques satellite: evaluation with COSMIC GPS RO, ERA-Interim and radiosonde data

ABSTRACT The Indian Space Research Organization (ISRO), in collaboration with Centre National d’Etudes Spatiales, France, launched radio occultation sounder for atmosphere (ROSA) on-board Megha Tropiques (MT) satellite. In this article, the retrieval of atmospheric parameters from ROSA and its evaluation with a network of in situ (radiosonde), similar satellite (Constellation Observational System for Meteorology, Ionosphere and Climate (COSMIC) GPS RO), and re-analysis (ERA-Interim) data sets are presented. The refractivity is retrieved from the bending angle as a function of impact parameter, and pressure and temperature profiles are derived from the profiles of refractivity. The algorithm has been successfully applied to COSMIC data. We have applied and validated this algorithm for the first time to ROSAon board MT. The algorithm retrieves the refractivity and pressure information from surface to 40 km whereas temperature profiles are restricted between 10 and 40 km. The ROSA algorithm refractivity, pressure, and temperature profiles compare well with independent data sets mentioned above. The mean fractional difference between ROSA and COSMIC, ERA-Interim and radiosonde refractivity and the temperature is found to be 0.1% with a standard deviation of 0.5%. It is shown that the algorithm derives the atmospheric parameters with good accuracies from the ROSA instrument and provides the atmospheric community new data from GPS RO at the verge of existing COSMIC GPS RO and in between upcoming GPS RO missions.
Microglia Stimulate the Invasiveness of Glioma Cells by Increasing the Activity of Metalloprotease-2

Gliomas represent the most frequent type of human brain tumor, and their strong invasiveness is a significant clinical problem. Microglia, the immunocompetent cells of the brain, contribute significantly to the tumor and are potential interaction partners of the glioma cells. We studied the impact of the presence of microglia on tumor cell invasion in cultured brain slices. To selectively deplete microglia, the slices were treated with clodronate-filled liposomes. When glioma cells were injected into slices devoid of endogenous microglia, the invasiveness of the tumors was significantly decreased as compared with controls. Inoculation of exogenous microglia together with glioma cells into cultured brain slices increased the infiltrative behavior of the tumor depending on the microglia/glioma cell ratio. Cell culture experiments revealed that soluble factors released from glioma cells strongly stimulate metalloprotease-2 activity in microglia. In the brain slices inoculated with glioma cells, increased activity of metalloprotease-2 was directly correlated with the abundance of microglia. Our data indicate that glioma cells stimulate microglial cells to increase breakdown of extracellular matrix and thereby promote tumor invasiveness.
Multiatlas Segmentation as Nonparametric Regression

This paper proposes a novel theoretical framework to model and analyze the statistical characteristics of a wide range of segmentation methods that incorporate a database of label maps or atlases; such methods are termed as label fusion or multiatlas segmentation. We model these multiatlas segmentation problems as nonparametric regression problems in the high-dimensional space of image patches. We analyze the nonparametric estimator's convergence behavior that characterizes expected segmentation error as a function of the size of the multiatlas database. We show that this error has an analytic form involving several parameters that are fundamental to the specific segmentation problem (determined by the chosen anatomical structure, imaging modality, registration algorithm, and label-fusion algorithm). We describe how to estimate these parameters and show that several human anatomical structures exhibit the trends modeled analytically. We use these parameter estimates to optimize the regression estimator. We show that the expected error for large database sizes is well predicted by models learned on small databases. Thus, a few expert segmentations can help predict the database sizes required to keep the expected error below a specified tolerance level. Such cost-benefit analysis is crucial for deploying clinical multiatlas segmentation systems.
Gait Modulation in C. Elegans: It's Not a Choice, It's a Reflex!

In their perspectives article, Mesce and Pierce-Shimomura (2010) make a case for the existence of two locomotion gaits in C. elegans, and for the ability of this nematode worm to choose between them. Here, we offer a counter-perspective, namely, that the variety of observed behaviors are more appropriately described as a single gait. In what follows we focus on pure forward locomotion, which is generally believed to be controlled by a dedicated circuit, distinct from the circuits that control backward locomotion and head motor behavior. With regard to our question of gaits, we are not aware of any evidence that links head swings with the generation of propulsive (forward/backward) locomotion, so these will not be considered here.
Effects of caffeine on vocal acoustic and aerodynamic measures of adult females.

PURPOSE To explore the effect of caffeine on voice, as evidenced by acoustic and aerodynamic measures, based on the fact that caffeine is considered to be a systemic dehydrating agent. METHODS The participants in this investigation were 58 females ranging in age from 18 to 35 years, who self-reported normal vocal production. The participants abstained from caffeine ingestion for 24 hours and from ingesting foods and liquids for 12 hours prior to the test. They were randomly assigned to one of two groups, control and experimental, and were individually tested. After the preliminary phase, participants in the experimental group ingested a 100 mg caffeine tablet; participants in the control group ingested placebo, and followed the same protocol as the experimental group. All participants were retested 30 minutes after ingesting caffeine or placebo. RESULTS Differences were not identified in any of the acoustic or aerodynamic measures across both groups. CONCLUSION These results suggest that a conservative (100 mg) dosage of caffeine may not have an impact on vocal acoustics and aerodynamics.