Analysis of memory use for improved design and compile-time allocation of local memory

Trace analysis techniques are used to study memory referencing behavior for the purpose of designing local memories and determining how to allocate them for data and instructions. In an attempt to assess the inherent behavior of the source code, the trace analysis system described here reduced the effects of the compiler and host architecture on the trace by using a technical called flattening. The variables in the trace, their associated single-assignment values, and references are histogrammed on the basis of various parameters describing memory referencing behavior. Bounds are developed specifying the amount of memory space required to store all live values in a particular histogram class. The reduction achieved in main memory traffic by allocating local memory is specified for each class

The interpretation of noun noun compounds

This thesis looks at conceptual combination, in particular it investigates how noun noun compounds are interpreted. Several themes run throughout the work. Real compounds (e.g. coat hanger, crab apple) are compared to novel ones (e.g. banjo cactus, zip violin). Also, compounds are examined in each of the possible permutations of artefacts (A) (e.g. coat, banjo) and natural kinds (N) (e.g. crab, cactus), (AA, AN, NA and NN).Experiments 1 - 4 examine noncompositionality in noun noun compounds. Possible sources of noncompositionality are investigated using both feature listing and feature rating tasks. Although some differences were found, results were similar between different types of compound, evidence of noncompositionality being found in each. The results also confirm that most of the meaning of a noun noim compound is derived from the second constituent (noun2).Experiments 5 and 6 look at two different types of compoimd interpretation - slot filling and property mapping. In experiment 5, slot filling is found to be the preferred interpretation type overall, but property mapping is more common in compounds composed of two natural kinds (NN). Experiment 6 examines possible factors influencing the choice between slot filling and property mapping interpretations. It was found that constituent similarity plays an important role, and also that this interacts with whether or not the constituents have important properties which clash. Experiment 7 looks at compound identification. Results suggest that the first constituent (nounl) may be critical in such tasks. Experiment 8 compares the importance of nounl and noun2 in determining the type of interpretation given to a compound. Neither position is found to be more influential than the other, although relational information does seem to be associated with specific nouns in each position. Throughout the thesis findings are related to current theories of conceptual combination, such as prototype models, the concept specialisation model and theories of compound interpretation by analogy

Spectral imaging of thermal damage induced during microwave ablation in the liver

Induction of thermal damage to tissue through delivery of microwave energy is frequently applied in surgery to destroy diseased tissue such as cancer cells. Minimization of unwanted harm to healthy tissue is still achieved subjectively, and the surgeon has few tools at their disposal to monitor the spread of the induced damage. This work describes the use of optical methods to monitor the time course of changes to the tissue during delivery of microwave energy in the porcine liver. Multispectral imaging and diffuse reflectance spectroscopy are used to monitor temporal changes in optical properties in parallel with thermal imaging. The results demonstrate the ability to monitor the spatial extent of thermal damage on a whole organ, including possible secondary effects due to vascular damage. Future applications of this type of imaging may see the multispectral data used as a feedback mechanism to avoid collateral damage to critical healthy structures and to potentially verify sufficient application of energy to the diseased tissue.Comment: 4pg,6fig. Copyright 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other work

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts

Improved pressure contour analysis for estimating cardiac stroke volume using pulse wave velocity measurement.

peer reviewedBACKGROUND: Pressure contour analysis is commonly used to estimate cardiac performance for patients suffering from cardiovascular dysfunction in the intensive care unit. However, the existing techniques for continuous estimation of stroke volume (SV) from pressure measurement can be unreliable during hemodynamic instability, which is inevitable for patients requiring significant treatment. For this reason, pressure contour methods must be improved to capture changes in vascular properties and thus provide accurate conversion from pressure to flow. METHODS: This paper presents a novel pressure contour method utilizing pulse wave velocity (PWV) measurement to capture vascular properties. A three-element Windkessel model combined with the reservoir-wave concept are used to decompose the pressure contour into components related to storage and flow. The model parameters are identified beat-to-beat from the water-hammer equation using measured PWV, wave component of the pressure, and an estimate of subject-specific aortic dimension. SV is then calculated by converting pressure to flow using identified model parameters. The accuracy of this novel method is investigated using data from porcine experiments (N = 4 Pietrain pigs, 20-24.5 kg), where hemodynamic properties were significantly altered using dobutamine, fluid administration, and mechanical ventilation. In the experiment, left ventricular volume was measured using admittance catheter, and aortic pressure waveforms were measured at two locations, the aortic arch and abdominal aorta. RESULTS: Bland-Altman analysis comparing gold-standard SV measured by the admittance catheter and estimated SV from the novel method showed average limits of agreement of +/-26% across significant hemodynamic alterations. This result shows the method is capable of estimating clinically acceptable absolute SV values according to Critchely and Critchely. CONCLUSION: The novel pressure contour method presented can accurately estimate and track SV even when hemodynamic properties are significantly altered. Integrating PWV measurements into pressure contour analysis improves identification of beat-to-beat changes in Windkessel model parameters, and thus, provides accurate estimate of blood flow from measured pressure contour. The method has great potential for overcoming weaknesses associated with current pressure contour methods for estimating SV

Whey- vs Casein-Based Enteral Formula and Gastrointestinal Function in Children With Cerebral Palsy.

Objectives: Children with severe cerebral palsy (CP) commonly have gastrointestinal (GI) dysfunction. Whey-based enteral formulas have been postulated to reduce gastroesophageal reflux (GOR) and accelerate gastric emptying (GE). The authors investigated whether whey-based (vs casein-based) enteral formulas reduce GOR and accelerate GE in children who have severe CP with a gastrostomy and fundoplication. Methods: Thirteen children received a casein-based formula for 1 week and either a 50% whey whole protein (50% WWP) or a 100% whey partially hydrolyzed protein (100% WPHP) formula for 1 week. Reflux episodes, gastric half-emptying time (GE t1/2), and reported pain and GI symptoms were measured. Results: Whey formulas emptied significantly faster than casein (median [interquartile range (IQR)] GE t1/2, 33.9 [25.3-166.2] min vs 56.6 [46-191] min; P = .033). Reflux parameters were unchanged. GI symptoms were lower in children who received 50% WWP (visual analog symptom score, median [IQR], 0[0-11.8]) vs 100% WPHP (13.0 [2.5-24.8]) (P = .035). Conclusion: This pilot study shows that in children who have severe CP with a gastrostomy and fundoplication, GE of the whey-based enteral formula is significantly faster than casein. The acceleration in GE does not alter GOR frequency, and there appears to be no effect of whey vs casein in reducing acid, nonacid, and total reflux episodes. The results indicate that enteral formula selection may be particularly important for children with severe CP and delayed GE. (JPEN J Parenter Enteral Nutr. 2012;36:118S-123S

Cloning of metacaspase gene expressed in the opportunistic human pathogenic fungus, Aspergillus fumigatus

How to cite this article: Ayatollahi Mousavi SA, Robson GD. Cloning of metacaspase gene expressed in the opportunistic human pathogenic fungus, Aspergillus fumigatus. Jundishapur J Microbiol. 2010; 3(2): 71-8. Received: January 2010 Accepted: March 2010 Introduction and objective: Caspases belong to a distinct class of cysteine proteases which also includes hemoglobinases, gingipains, clostripains, and separases, the proteases involved in chromosome segregation in mitosis and meiosis. Two families of predicted Caspase Homoglobinase Fold (CHF)-proteases were identified and shown to be more closely related to the caspases than to other proteases of this class and hence dubbed paracaspases and metacaspases. The aim of present study was to isolate genes particularly caspase-related ones up-regulated in the earliest stages of the stationary phase (up to four hours) and using clones to perform a PCR on cDNA prepared from exponential and stationary phase mRNA. Materials and methods: After the use of the clorimetric assay to get evidence of caspase activity, both strands of cDNA were used for cloning the PCR products. The whole plasmid and freeze-dried material were sent for automated sequencing. By searching in NCBI homepage, particularly Blast part, all the alignment sequences were shown and then after similar genes were recognized as well. Results: There was no sign of any cDNA in the midlog and 4h stationary phases which shows no RNA synthesis in those phases. The extended sequence of the gene was found to have a high level of identity (87%) with a metacaspase from Schizosaccharomyces pombe through a BLASTX search. Conclusion: This information may be used to fabricate microarrays which would enable a genome-wide analysis of gene expression of Aspergillus fumigatus as it enters and during the stationary phase

Esophageal impedance baselines in infants before and after placebo and proton pump inhibitor therapy

Author version made available in accordance with the publisher's policy.ABSTRACT Background Esophageal impedance monitoring records changes in conductivity. During esophageal rest impedance baseline values may represent mucosal integrity. The aim of this study was to assess the influence of acid suppression on impedance baselines in a placebo controlled setting. Material and Methods Impedance recordings from 40 infants (0-6months) enrolled in randomized placebo controlled trials of proton pump inhibitor (PPI) were retrospectively analyzed. Infants underwent 24hr pH-impedance monitoring prior to and after two weeks of double blind therapy with placebo or a PPI. Typical clinical signs of gastroesophageal reflux (GER) were recorded and I-GERQ-R questionnaire was completed. Key results Median (IQR) impedance baseline increased on PPI treatment (from 1217 (826-1514) to 1903 (1560-2194) Ohm, p<0.001) but not with placebo (from 1445 (1033-1791) to 1650 (1292-1983) Ohm, p=0.13). Baselines before treatment inversely correlate with the number of GER, acid GER, weakly acid GER, acid exposure and symptoms. The change in baseline on treatment inversely correlates with acid exposure and acid GER. Patients with initial low baselines have no improved symptomatic response to treatment. Conclusions and Inferences Impedance baselines are influenced by GER and increase significantly more with PPI therapy than with placebo. Clinical impact of this observation remains undefined as targeting therapy at infants with low baselines does not improve symptomatic response to treatment

The Spring 1985 high precision baseline test of the JPL GPS-based geodetic system

The Spring 1985 High Precision Baseline Test (HPBT) was conducted. The HPBT was designed to meet a number of objectives. Foremost among these was the demonstration of a level of accuracy of 1 to 2:10 to the 7th power, or better, for baselines ranging in length up to several hundred kilometers. These objectives were all met with a high degree of success, with respect to the demonstration of system accuracy in particular. The results from six baselines ranging in length from 70 to 729 km were examined for repeatability and, in the case of three baselines, were compared to results from colocated VLBI systems. Repeatability was found to be 5:10 to the 8th power (RMS) for the north baseline coordinate, independent of baseline length, while for the east coordinate RMS repeatability was found to be larger than this by factors of 2 to 4. The GPS-based results were found to be in agreement with those from colocated VLBI measurements, when corrected for the physical separations of the VLBI and CPG antennas, at the level of 1 to 2:10 to the 7th power in all coordinates, independent of baseline length. The results for baseline repeatability are consistent with the current GPA error budget, but the GPS-VLBI intercomparisons disagree at a somewhat larger level than expected. It is hypothesized that these differences may result from errors in the local survey measurements used to correct for the separations of the GPS and VLBI antenna reference centers