Program development using abstract interpretation (and the ciao system preprocessor)

The technique of Abstract Interpretation has allowed the development of very sophisticated global program analyses which are at the same time provably correct and practical. We present in a tutorial fashion a novel program development framework which uses abstract interpretation as a fundamental tool. The framework uses modular, incremental abstract interpretation to obtain information about the program. This information is used to validate programs, to detect bugs with respect to partial specifications written using assertions (in the program itself and/or in system librarles), to genérate and simplify run-time tests, and to perform high-level program transformations such as múltiple abstract specialization, parallelization, and resource usage control, all in a provably correct way. In the case of validation and debugging, the assertions can refer to a variety of program points such as procedure entry, procedure exit, points within procedures, or global computations. The system can reason with much richer information than, for example, traditional types. This includes data structure shape (including pointer sharing), bounds on data structure sizes, and other operational variable instantiation properties, as well as procedure-level properties such as determinacy, termination, non-failure, and bounds on resource consumption (time or space cost). CiaoPP, the preprocessor of the Ciao multi-paradigm programming system, which implements the described functionality, will be used to illustrate the fundamental ideas.

A tutorial on program development and optimization using the Ciao preprocessor

We present in a tutorial fashion CiaoPP, the preprocessor of the Ciao multi-paradigm programming system, which implements a novel program development framework which uses abstract interpretation as a fundamental tool. The framework uses modular, incremental abstract interpretation to obtain information about the program. This information is used to validate programs, to detect bugs with respect to partial specifications written using assertions (in the program itself and/or in system libraries), to generate and simplify run-time tests, and to perform high-level program transformations such as multiple abstract specialization, parallelization, and resource usage control, all in a provably correct way. In the case of validation and debugging, the assertions can refer to a variety of program points such as procedure entry, procedure exit, points within procedures, or global computations. The system can reason with much richer information than, for example, traditional types. This includes data structure shape (including pointer sharing), bounds on data structure sizes, and other operational variable instantiation properties, as well as procedure-level properties such as determinacy, termination, non-failure, and bounds on resource consumption (time or space cost).

Modulation of Ca2+ entry by polypeptides of the inositol 1,4,5-trisphosphate receptor (IP3R) that bind transient receptor potential (TRP): Evidence for roles of TRP and IP3R in store depletion-activated Ca2+ entry

Homologues of Drosophilia transient receptor potential (TRP) have been proposed to be unitary subunits of plasma membrane ion channels that are activated as a consequence of active or passive depletion of Ca2+ stores. In agreement with this hypothesis, cells expressing TRPs display novel Ca2+-permeable cation channels that can be activated by the inositol 1,4,5-trisphosphate receptor (IP3R) protein. Expression of TRPs alters cells in many ways, including up-regulation of IP3Rs not coded for by TRP genes, and proof that TRP forms channels of these and other cells is still missing. Here, we document physical interaction of TRP and IP3R by coimmunoprecipitation and glutathione S-transferase-pulldown experiments and identify two regions of IP3R, F2q and F2g, that interact with one region of TRP, C7. These interacting regions were expressed in cells with an unmodified complement of TRPs and IP3Rs to study their effect on agonist- as well as store depletion-induced Ca2+ entry and to test for a role of their respective binding partners in Ca2+ entry. C7 and an F2q-containing fragment of IP3R decreased both forms of Ca2+ entry. In contrast, F2g enhanced the two forms of Ca2+ entry. We conclude that store depletion-activated Ca2+ entry occurs through channels that have TRPs as one of their normal structural components, and that these channels are directly activated by IP3Rs. IP3Rs, therefore, have the dual role of releasing Ca2+ from stores and activating Ca2+ influx in response to either increasing IP3 or decreasing luminal Ca2+.

The Ran/TC4 GTPase-binding domain: identification by expression cloning and characterization of a conserved sequence motif.

Ran/TC4 is an essential, nuclear GTPase implicated in the initiation of DNA replication, entry into and exit from mitosis, and in nuclear RNA and protein transport through the nuclear pore complex. This diversity of functions suggests that Ran interacts with a large number of down-stream targets. Using an overlay assay, we detected a family of putative target proteins that associate with GTP-bound Ran. The sequence of only one such protein, HTF9a/RanBP1, is known. We have now cloned two additional Ran-binding proteins, allowing identification of a distinctive, highly conserved sequence motif of approximately 150 residues. This motif represents a minimal Ran-binding domain that stabilizes the GTP-bound state of Ran. The isolated domain also functions as a coactivator of Ran-GTPase-activating protein. Mutation of a conserved residue within the Ran-binding domain of HTF9a protein drastically reduced Ran binding. Ran-binding proteins coimmunoprecipitated with epitope-tagged Ran from cell lysates, suggesting that these proteins may associate in vivo. A previously uncharacterized Caenorhabditis elegans gene could encode a protein (96 kDa) possessing two Ran-binding domains. This open reading frame also contains similarities to nucleoporins, suggesting a functional link between Ran and nuclear pore complexes.

Mapping the determinants in owl monkey CD4 and CCR5 that allow entry of early-stage HIV-1 Env variants

Thesis (Master's)--University of Washington, 2016-06

Reforms and entry:some evidence from the Indian manufacturing sector

Traditional research in the context of product market entry has explored the strategic reactions of incumbent firms when threatened by the possibility of entry, and have identified industry-specific factors that affect entry rates. However, following de Soto (1989), there has been increasing emphasis on regulatory and institutional factors governing entry rates, especially in the context of developing countries. Using three-digit industry-level data from India, for the 1984–97 period, we examine the phenomenon of entry in the Indian context. Our empirical results suggest that during the 1980s industry-level factors largely explained variations in entry rates, but that, following the economic federalism brought about by the post-1991 reforms, variations in entry rates during the 1990s were explained largely by state-level institutional and legacy factors. Past productivity growth affects net entry rates as well.

Pre-entry organisational identification:considering the theoretical and managerial implications of future members’ identification with an organisation

From a Social Identity Theory perspective, organisational identification arises through a cognitive process of self-categorisation. As a consequence a person need not have a formal relationship with an organisation in order to identify with it. In this conceptual paper, the authors draw on this proposal to argue that future members are capable of identifying with an organisation prior to entry, and that this initial pre-entry identification could contribute to a person’s subsequent post-entry organisational identification. The paper further suggests that because no distinction need be drawn between organisational identification in current and future members, we might expect to find the same antecedents of identification in both instances. The group engagement model (Tyler and Blader 2003) is called on to propose that when a future member experiences pride in, and respect from, an organisation before they join, this should positively influence their pre-entry organisational identification. The authors explore the managerial implications of these propositions, and argue that an organisation’s actions and practices that have been shown to influence a post-entry organisational identification should have an equivalent impact on future members’ organisational identification when observed during the pre-entry period. Two examples of such practices, organisational support and organisational communication, are used to illustrate this suggestion and a number of ways are discussed through which these practices may be experienced by a person before they join an organisation.

Entry characteristics and academic performance of students in a master of pharmacy degree program in the United Kingdom

Objective. Evaluate the characteristics of a cohort of Master of Pharmacy (MPharm) students upon entry and examine any associations between entry qualifications, type of school attended, socioeconomic deprivation, age and academic performance in the MPharm programme. Methods. A retrospective cohort analysis of data recorded on Aston University’s central database for each individual exiting the MPharm programme during the five year period 2005-6 – 2009-10 (n=644). Results. Entrants were disproportionately drawn from socioeconomically deprived areas and independent (private) schools. Achievement prior to admission was related to the type of school attended but not to deprivation. Performance on the programme was not related to type of school or deprivation but was strongly correlated with prior achievements. Conclusions. Prior achievement is the most important predictor of performance on the MPharm programme but the superior prior achievement of independent school pupils is not seen at the point of graduation. This may have implications for admissions policies.

Multimodal field data entry:performance and usability issues

Mobile technologies have yet to be widely adopted by the Architectural, Engineering, and Construction (AEC) industry despite being one of the major growth areas in computing in recent years. This lack of uptake in the AEC industry is likely due, in large part, to the combination of small screen size and inappropriate interaction demands of current mobile technologies. This paper discusses the scope for multimodal interaction design with a specific focus on speech-based interaction to enhance the suitability of mobile technology use within the AEC industry by broadening the field data input capabilities of such technologies. To investigate the appropriateness of using multimodal technology for field data collection in the AEC industry, we have developed a prototype Multimodal Field Data Entry (MFDE) application. This application, which allows concrete testing technicians to record quality control data in the field, has been designed to support two different modalities of data input speech-based data entry and stylus-based data entry. To compare the effectiveness or usability of, and user preference for, the different input options, we have designed a comprehensive lab-based evaluation of the application. To appropriately reflect the anticipated context of use within the study design, careful consideration had to be given to the key elements of a construction site that would potentially influence a test technician's ability to use the input techniques. These considerations and the resultant evaluation design are discussed in detail in this paper.

Investment liberalisation, technology take-off and export markets entry:does foreign ownership structure matter?

Before and after its accession to the WTO in 2001, China has undergone a far-reaching investment liberalisation. As part of this, existing restrictions on foreign ownership structure and mandatory export and technology transfer requirements imposed on foreign firms have been lifted in a number of industries. Against this background we identify the causal effects of foreign acquisitions on export market entry and technology take-off and evaluate whether the level of foreign ownership plays a role in stimulating these changes. Using doubly robust propensity score reweighted bivariate probit regressions to control for the selection bias associated with firm level foreign acquisition incidences, we uncover strong but heterogeneous positive effects on export activity for all types of foreign ownership structure. We also find that minority foreign owned acquisition targets experience higher likelihood of R&D, providing evidence that joint ventures can contribute positively to China's "science and technology take-off".

Late Entry into HIV Care: Estimated Impact on AIDS Mortality Rates in Brazil, 2003-2006

Background: Worldwide, a high proportion of HIV-infected individuals enter into HIV care late. Here, our objective was to estimate the impact that late entry into HIV care has had on AIDS mortality rates in Brazil. Methodology/Principal Findings: We analyzed data from information systems regarding HIV-infected adults who sought treatment at public health care facilities in Brazil from 2003 to 2006. We initially estimated the prevalence of late entry into HIV care, as well as the probability of death in the first 12 months, the percentage of the risk of death attributable to late entry, and the number of avoidable deaths. We subsequently adjusted the annual AIDS mortality rate by excluding such deaths. Of the 115,369 patients evaluated, 50,358 (43.6%) had entered HIV care late, and 18,002 died in the first 12 months, representing a 16.5% probability of death in the first 12 months (95% CI: 16.3-16.7). By comparing patients who entered HIV care late with those who gained timely access, we found that the risk ratio for death was 49.5 (95% CI: 45.1-54.2). The percentage of the risk of death attributable to late entry was 95.5%, translating to 17,189 potentially avoidable deaths. Averting those deaths would have lowered the 2003-2006 AIDS mortality rate by 39.5%. Including asymptomatic patients with CD4(+) T cell counts >200 and <= 350 cells/mm(3) in the group who entered HIV care late increased this proportion by 1.8%. Conclusions/Significance: In Brazil, antiretroviral drugs reduced AIDS mortality by 43%. Timely entry would reduce that rate by a similar proportion, as well as resulting in a 45.2% increase in the effectiveness of the program for HIV care. The World Health Organization recommendation that asymptomatic patients with CD4(+) T cell counts <= 350 cells/mm(3) be treated would not have a significant impact on this scenario.

Listeria monocytogenes in two different poultry facilities: Manual and automatic evisceration

Listeriosis is a serious foodborne disease caused by Listeria monocytogenes, a pathogen often found in food processing plants. Poultry meat and its derivatives may harbor L. monocytogenes even if good manufacturing practices are implanted in abattoirs. Little information exists in Brazil on the frequency of L. monocytogenes contamination, even though the country is considered the top poultry meat exporter in the world. This study attempted to compare 2 exporters poultry facilities following same the standards but differing only in manual (plant M) or automatic (plant A) evisceration. Eight hundred fifty-one samples from food, food contact and non-food contact surfaces, water, and workers` hands were collected from cage to finished products over a 1-yr period. In plant A, 20.1% of the samples were positive for L. monocytogenes, whereas in plant M, 16.4% was found. The greatest incidence of contamination with the pathogen in plant A was found in non- food contact surfaces (27.3%), while in plant M, it was found in products (19.4%). The most prevalent serovars were 1/2a or 3a (plant M) and 4b, 4d, or 4e (plant A). Despite having proper hygiene and good manufacturing practices, controlling the entry and persistence of L. monocytogenes in processing facilities remains a formidable task.

Regional Effects of Port Infrastructure: A Spatial CGE Application to Brazil

This article attempts to elucidate one of the mechanisms that link trade barriers, in the form of port costs, and subsequent growth and regional inequality. Prior attention has focused on inland or link costs, but port costs can be considered as a further barrier to enhancing trade liberalization and growth. In contrast to a highway link, congestion at a port may have severe impacts that are spread over space and time whereas highway link congestion may be resolved within several hours. Since a port is part of the transportation network, any congestion/disruption is likely to ripple throughout the hinterland. In this sense, it is important to model properly the role nodal components play in the context of spatial models and international trade. In this article, a spatial computable general equilibrium (CGE) model that is integrated to a transport network system is presented to simulate the impacts of increases in port efficiency in Brazil. The role of ports of entry and ports of exit are explicitly considered to grasp the holistic picture in an integrated interregional system. Measures of efficiency for different port locations are incorporated in the calibration of the model and used as the benchmark in our simulations. Three scenarios are evaluated: (1) an overall increase in port efficiency in Brazil to achieve international standards; (2) efficiency gains associated with decentralization in port management in Brazil; and (3) regionally differentiated increases in port efficiency to reach the boundary of the national efficiency frontier.

Phosphate Binder Impact on Bone Remodeling and Coronary Calcification - Results from the BRiC Study

Background and Aims: Calcium-containing phosphate binders have been shown to increase the progression of vascular calcification in hemodialysis patients. This is a prospective study that compares the effects of calcium acetate and sevelamer on coronary calcification (CAC) and bone histology. Methods: 101 hemodialysis patients were randomized for each phosphate binder and submitted to multislice coronary tomographies and bone biopsies at entry and 12 months. Results: The 71 patients who concluded the study had similar baseline characteristics. On follow-up, the sevelamer group had higher levels of intact parathyroid hormone (498 +/- 352 vs. 326 +/- 236 pg/ml, p = 0.017), bone alkaline phosphatase (38 +/- 24 vs. 28 +/- 15 U/l, p = 0.03) and deoxypyridinoline (135 +/- 107 vs. 89 +/- 71 nmol/l, p = 0.03) and lower LDL cholesterol (74 +/- 21 vs. 91 +/- 28 mg/dl, p = 0.015). Phosphorus (5.8 +/- 1.0 vs. 6 +/- 1.0 mg/dl, p = 0.47) and calcium (1.27 +/- 0.07 vs. 1.23 +/- 0.08 mmol/l, p = 0.68) levels did not differ between groups. CAC progression (35 vs. 24%, p = 0.94) and bone histological diagnosis at baseline and 12 months were similar in both groups. Patients of the sevelamer group with a high turnover at baseline had an increase in bone resorption (eroded surface, ES/BS = 9.0 +/- 5.9 vs. 13.1 +/- 9.5%, p = 0.05), whereas patients of both groups with low turnover at baseline had an improvement in bone formation rate (BFR/BS = 0.015 +/- 0.016 vs. 0.062 +/- 0.078, p = 0.003 for calcium and 0.017 +/- 0.016 vs. 0.071 +/- 0.084 mu m(3)/mu m(2)/day, p = 0.010 for sevelamer). Conclusions: There was no difference in CAC progression or changes in bone remodeling between the calcium and the sevelamer groups. Copyright (C) 2008 S. Karger AG, Basel

Image quality assessment and medical physics evaluation of different portable dental X-ray units

Introduction: Recently developed portable dental X-ray units increase the mobility of the forensic odontologists and allow more efficient X-ray work in a disaster field, especially when used in combination with digital sensors. This type of machines might also have potential for application in remote areas, military and humanitarian missions, dental care of patients with mobility limitation, as well as imaging in operating rooms. Objective: To evaluate radiographic image quality acquired by three portable X-ray devices in combination with four image receptors and to evaluate their medical physics parameters. Materials and methods: Images of five samples consisting of four teeth and one formalin-fixed mandible were acquired by one conventional wall-mounted X-ray unit, MinRay (R) 60/70 kVp, used as a clinical standard, and three portable dental X-ray devices: AnyRay (R) 60 kVp, Nomad (R) 60 kVp and Rextar (R) 70 kVp, in combination with a phosphor image plate (PSP), a CCD, or a CMOS sensor. Three observers evaluated images for standard image quality besides forensic diagnostic quality on a 4-point rating scale. Furthermore, all machines underwent tests for occupational as well as patient dosimetry. Results: Statistical analysis showed good quality imaging for all system, with the combination of Nomad (R) and PSP yielding the best score. A significant difference in image quality between the combination of the four X-ray devices and four sensors was established (p < 0.05). For patient safety, the exposure rate was determined and exit dose rates for MinRay (R) at 60 kVp, MinRay (R) at 70 kVp, AnyRay (R), Nomad (R) and Rextar (R) were 3.4 mGy/s, 4.5 mGy/s, 13.5 mGy/s, 3.8 mGy/s and 2.6 mGy/s respectively. The kVp of the AnyRay (R) system was the most stable, with a ripple of 3.7%. Short-term variations in the tube output of all the devices were less than 10%. AnyRay (R) presented higher estimated effective dose than other machines. Occupational dosimetry showed doses at the operator`s hand being lowest with protective shielding (Nomad (R): 0.1 mu Gy). It was also low while using remote control (distance > 1 m: Rextar (R) < 0.2 mu Gy, MinRay (R) < 0.1 mu Gy). Conclusions: The present study demonstrated the feasibility of three portable X-ray systems to be used for specific indications, based on acceptable image quality and sufficient accuracy of the machines and following the standard guidelines for radiation hygiene. (C) 2010 Elsevier Ireland Ltd. All rights reserved.