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Some Measurements of Nullable and Non-Nullable Parameter Declarations in Relation to Software Malleability [article]

William Harrison, Tim Walsh, Paul Biggar
2011 arXiv   pre-print
The usual advantages put forward for including nullability declarations in the type systems of programming languages are that they improve program reliability or performance. But there is another, entirely different, reason for doing so. In the right context, this information enables the software artifacts we produce, the objects and methods, to exhibit much greater malleability. For declaratively typed languages, we can obtain greater software malleability by extending the model of method call
more » ... so that assurance of a method's availability can be provided by any non-nullable parameter, not simply the target parameter, and by allowing the method's implementation to reside in classes or objects other than the target.. This paper examines the question of whether this hypothetical improvement in software malleability is consistent with existing programming practice by examining the question of the extent to which methods in existing software have multiplicities of non-nullable parameters. The circumstance occurs frequently enough to provide an important reason to introduce declarations of nullability into programming languages.
arXiv:1108.4816v1 fatcat:4ciqfo5o4vd2repenxbfmfdjae

An experimental study of sorting and branch prediction

Paul Biggar, Nicholas Nash, Kevin Williams, David Gregg
2008 ACM Journal of Experimental Algorithmics  
Unrolling this loop not only removes the loop over-head, but is also experimentally observed to improve the average prediction accuracy by about 2% [Biggar and Gregg 2005] .  ...  We leave the precise details of performing a multi-way partition to elsewhere [LaMarca 1996; Biggar and Gregg 2005] , it is sufficient to note that we can decide which container a key should be placed  ... 
doi:10.1145/1227161.1370599 fatcat:g6cejtvaorgcziwlb7um5e6pb4

A practical solution for scripting language compilers

Paul Biggar, Edsko de Vries, David Gregg
2009 Proceedings of the 2009 ACM symposium on Applied Computing - SAC '09  
Although scripting languages are becoming increasingly popular, even mature scripting language implementations remain interpreted. Several compilers and reimplementations have been attempted, generally focusing on performance. Based on our survey of these reimplementations, we determine that there are three important features of scripting languages that are difficult to compile or reimplement. Since scripting languages are defined primarily through the semantics of their original
more » ... , they often change semantics between releases. They provide large standard libraries, which are difficult to re-use, and costly to reimplement. They provide C APIs, used both for foreignfunction-interfaces and to write third-party extensions. These APIs typically have tight integration with the original implementation. Finally, they support run-time code generation. These features make the important goal of correctness difficult to achieve. We present a technique to support these features in an ahead-oftime compiler for PHP. Our technique uses the original PHP implementation through the provided C API, both in our compiler, and an our generated code. We support all of these important scripting language features, particularly focusing on the correctness of compiled programs. Additionally, our approach allows us to automatically support limited future language changes. We present a discussion and performance evaluation of this technique, which has not previously been published. c ACM, 2009. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in SAC '09:
doi:10.1145/1529282.1529709 dblp:conf/sac/BiggarVG09 fatcat:4fzcmhzenfadpjgpk3u5rky5ky

A practical solution for achieving language compatibility in scripting language compilers

Paul Biggar, Edsko de Vries, David Gregg
2012 Science of Computer Programming  
Although scripting languages have become very popular, even mature scripting language implementations remain interpreted. Several compilers and reimplementations have been attempted, generally focusing on performance. Based on our survey of these reimplementations, we determine that there are three important features of scripting languages that are difficult to compile or reimplement. Since scripting languages are defined primarily through the semantics of their original implementations, they
more » ... ten change semantics between releases. They provide C APIs, used both for foreign-function interfaces and to write third-party extensions. These APIs typically have tight integration with the original implementation, and are used to provide large standard libraries, which are difficult to re-use, and costly to reimplement. Finally, they support run-time code generation. These features make it difficult to design a fully compatible compiler. We present a technique to support these features in an ahead-of-time compiler for PHP. Our technique uses the original PHP implementation through the provided C API, both in our compiler and in our generated code. We support all of these important scripting language features. Additionally, our approach allows us to automatically support limited future language changes. We present a discussion and performance evaluation of this technique.
doi:10.1016/j.scico.2011.01.004 fatcat:zf6wa6ipizg2bf3yxb72m7gfk4

Genetic Variants of Human T-Lymphotropic Virus Type II in American Indian Groups

ROBERT J. BIGGAR, MARIA E. TAYLOR, JAMES V. NEEL, BRIAN HJELLE, PAUL H. LEVINE, FRANCIS L. BLACK, GEORGE M. SHAW, PAUL M. SHARP, BEATRICE H. HAHN
1996 Virology  
The human T-lymphotropic virus type II (HTLV-II) is found in many New World Indian groups in North and South America and may have entered the New World from Asia with the earliest migration of ancestral Amerindians over 15,000 years ago. To characterize the phylogenetic relationships of HTLV-II strains infecting geographically diverse Indian populations, we used polymerase chain reaction to amplify HTLV-II sequences from lymphocytes of seropositive Amerindians from Brazil (Kraho, Kayapo, and
more » ... uyana), Panama (Guaymi), and the United States (the Navajo and Pueblo tribes of the southwestern states and the Seminoles of Florida). Sequence analysis of a 780-base pair fragment (located between the env gene and the second exons of tax/rex) revealed that Amerindian viruses clustered in the same two genetic subtypes (IIa and IIb) previously identified for viruses from intravenous drug users. Most infected North and Central American Indians had subtype IIb, while HTLV-II infected members of three remote Amazonian tribes clustered as a distinct group within subtype IIa. These findings suggest that the ancestral Amerindians migrating to the New World brought at least two genetic subtypes, IIa and IIb. Because HTLV-II strains from Amazonian Indians form a distinct group within subtype HTLV-IIa, these Brazilian tribes are unlikely to be the source of IIa viruses in North American drug users. Finally, the near identity of viral sequences from geographically diverse populations indicate that HTLV-II is a very ancient virus of man. ᭧
doi:10.1006/viro.1996.0043 pmid:8614983 fatcat:4vueqpkbgrceza6xmcdtjo4j7y

Stability of Maternal Reports of Lexical Comprehension in Very Young Children With Developmental Delays

Paul J. Yoder, Steven F. Warren, Heather A. Biggar
1997 American Journal of Speech-Language Pathology  
The MacArthur Communication Development Inventory: Infant Scale (CDI/I) is among the strongest measures of early lexical comprehension (Fenson et al., 1994) . The present study examined the stability of CDI/I results over a 2-week period in a sample of 17 mothers of children with developmental delays. Test-retest stability was computed for total number of words understood (i.e., summarylevel stability) and for word-by-word agreement (i.e., item-by-item stability) across a 2-week interval.
more » ... s indicated that although there was excellent summary level stability, there was, in many cases, inadequate item-by-item agreement between the two testing occasions. The degree to which mothers were consistent on an item-by-item basis varied as a function of the types of words they were reporting on, the occupational status and educational level of the mothers, and the extent to which mothers confidently interpret nonlinguistic child behavior. These data illustrate that the CDI/I can be used to identify overall vocabulary deficits and specific word classes that are under-represented, but not to identify specific words for remediation.
doi:10.1044/1058-0360.0601.59 fatcat:swpwm5dj4zdwnilaxiogrxlzlq

Hepatitis C Virus Genotype 4 in Ugandan Children and Their Mothers

Robert J. Biggar, Betty A. Ortiz-Conde, Rachel K. Bagni, Paul M. Bakaki, Cheng-Dian Wang, Eric A. Engels, Sam M. Mbulaiteye, Christopher M. Ndugwa
2006 Emerging Infectious Diseases  
Dr Biggar is a senior investigator in the Viral Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute.  ... 
doi:10.3201/eid1209.041068 pmid:17073099 pmcid:PMC3294722 fatcat:cj6ylfpf5ngxxmbe572rqgqhry

TheSchizosaccharomyces pombe rhp3+gene required for DNA repair and cell viability is functionally interchangeable with theRAD3gene ofSaccharomyces cerevisiae

Paul R. Reynolds, Stephen Biggar, Louise Prakash, Satya Prakash
1992 Nucleic Acids Research  
The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA RNA helicase activities. Mutational studies have indicated a requirement for the RAD3 helicase activities in excision repair. To examine the extent of conservation of structure and function of RAD3 during eukaryotic evolution, we have cloned the RAD3 homolog, rhp3+, from the distantly related yeast
more » ... izosaccharomyces pombe. RAD3 and rhp3 + encoded proteins are highly similar, sharing 67% identical amino acids. We show that like RAD3, rhp3+ is indispensable for excision repair and cell viability, and our studies indicate a requirement of the putative rhp3+ DNA helicase activity in DNA repair. We find that the RAD3 and rhp3+ genes can functionally substitute for one another. The level of complementation provided by the rhp3+ gene in S.cerevisiae rad3 mutants or by the RAD3 gene in S.pombe rhp3 mutants is remarkable in that both the excision repair and viability defects in both yeasts are restored to wild type levels. These observations suggest a parallel evolutionary conservation of other protein components with which RAD3 interacts in mediating its DNA repair and viability functions.
doi:10.1093/nar/20.9.2327 pmid:1534406 pmcid:PMC312349 fatcat:trxktkzs55cf3mgtl3apchr2q4

Elevated serum levels of interleukin-6 in endemic Burkitt lymphoma in Ghana

Peter Aka, Benjamin Emmanuel, Maria Candida Vila, Amar Jariwala, Francis Nkrumah, Maria V. Periago, Janet Neequaye, Christine Kiruthu, Paul H. Levine, Robert J. Biggar, Kishor Bhatia, Jeffrey M. Bethony (+1 others)
2014 Hematological Oncology  
Endemic Burkitt lymphoma (eBL) is an aggressive non-Hodgkin lymphoma with a high incidence among children in equatorial Africa [1] . Infection with Epstein-Barr virus (EBV) and Plasmodium falciparum (Pf) have been implicated as etiological factors [2] . A cohort study conducted in the West Nile district in Uganda demonstrated elevated risk of eBL in children infected with EBV during infancy [3] . Several case-control studies have confirmed that children with high exposure to malaria, based on
more » ... estionnaire and antibody measurements, have an elevated risk of eBL [4, 5] . However, how these infections cause eBL is not well understood. Pf infection is thought to influence eBL risk by impairing EBVspecific T cell immunity, which leads to EBV reactivation and an increase in EBV load [6] . Moreover, EBV secretes functional cytokine homologs, for example BCRF-1, an IL-10related peptide, which could be involved in eBL pathogenesis [7] . Interestingly, patients with acute malaria also often have elevated serum levels of cytokines, including tumor necrosis factor (TNF) α, interferon (IFN) γ, interleukin (IL)-6, and IL-10 [8]. Although there is some evidence that IL-6 serum levels in serum may be elevated before the development of AIDS-associated BL [9], the relationship between eBL and cytokines has not been evaluated before. To obtain preliminary data, we measured levels of four cytokines, TNF-α, IFN-γ, IL-6, and IL-10, in 65 children with eBL (0<16 years) enrolled at the Korle-Bu Teaching Hospital,
doi:10.1002/hon.2121 pmid:24493366 pmcid:PMC4293153 fatcat:emwgxevy2vfevfqve3srncjwty

High Levels of Epstein‐Barr Virus DNA in Saliva and Peripheral Blood from Ugandan Mother‐Child Pairs

Sam M. Mbulaiteye, Michael Walters, Eric A. Engels, Paul M. Bakaki, Christopher M. Ndugwa, Anchilla M. Owor, James J. Goedert, Denise Whitby, Robert J. Biggar
2006 Journal of Infectious Diseases  
In Africa, Epstein-Barr virus (EBV) is associated with Burkitt lymphoma. We measured levels of EBV DNA in saliva and buffy coats from 233 asymptomatic Ugandan children with sickle cell disease and their mothers by quantitative real-time polymerase chain reaction. EBV DNA was detected in saliva from 90% of the children (median [interquartile range {IQR}] level, 5.2 [4.2-6.0] log 10 copies/mL of saliva) and 79% of the mothers (median [IQR] level, 4.8 [3.7-5.6] log 10 copies/mL of saliva) ( ). EBV
more » ... DNA was detected in buffy coats P ! .001 from 86% of the children (median [IQR] level, 2.5 [2.2-2.9] log 10 copies/ peripheral white blood cells 6 1 ϫ 10 [PWBCs]) and 72% of the mothers (median [IQR] level, 2.7 [2.4-3.1] log 10 copies/ PWBCs) ( ). 6 1 ϫ 10 P p .24 Detection of EBV DNA in saliva was positively correlated with detection in buffy coats. EBV DNA was detected more frequently in saliva and buffy coats than was human herpesvirus 8 DNA. Our results indicate that EBV infection persists, with virus readily detectable in saliva and buffy coats from persons without apparent symptoms in Africa. Epstein-Barr virus (EBV) is ubiquitous, but the age at infection varies [1] . In Africa, most infections occur during early childhood and are asymptomatic [2]; however, they are associated with endemic Burkitt lymphoma, the most common tumor in African children. In the West, infections occur mostly in older children and adolescents, who frequently present with infectious mononucleosis [1]. EBV is probably transmitted via saliva, such as when mothers prechew food that is then given to babies, when people share eating utensils, and when people kiss [1].
doi:10.1086/499277 pmid:16388490 fatcat:tliuic5u3zc65gjffnjapluihy

Radiometric measurement comparisons using transfer radiometers in support of the calibration of NASA's Earth Observing System (EOS) sensors

James J. Butler, B. Carol Johnson, Steven W. Brown, Howard W. Yoon, Robert A. Barnes, Brian L. Markham, Stuart F. Biggar, Edward F. Zalewski, Paul R. Spyak, John W. Cooper, Fumihiro Sakuma, Hiroyuki Fujisada (+1 others)
1999 Sensors, Systems, and Next-Generation Satellites III  
EOS satellite instruments operating in the visible through the shortwave infrared wavelength regions (from 0.4 gm to 2.5 _.m) are calibrated prior to flight for radiance response using integrating spheres at a number of instrument builder facilities. The traceability of the radiance produced by these spheres with respect to international standards is the responsibility of the instrument builder, and different calibration techniques are employed by those builders. The National Aeronautics and
more » ... ce Administration's (NASA's) Earth Observing System (EOS) Project Science Office, realizing the importance of preflight calibration and cross-calibration, has sponsored a number of radiometric measurement comparisons, the main purpose of which is to validate the radiometric scale assigned to the integrating spheres by the instrument builders. This paper describes the radiometric measurement comparisons, the use of stable transfer radiometers to perform the measurements, and the measurement approaches and protocols used to validate integrating sphere radiances. Stable transfer radiometers from the in Japan, have participated in these comparisons. The approaches used in the comparisons include the measurement of multiple integrating sphere lamp levels, repeat measurements of select lamp levels, the use of the stable radiometers as external sphere monitors, and the rapid reporting of measurement results. Results from several comparisons are presented. The absolute radiometric calibration standard uncertainties required by the EOS satellite instruments are typically in the ±3% to ±5% range. Preliminary results reported during eleven radiometric measurement comparisons held between February 1995 and May 1998 have shown the radiance of integrating spheres agreed to within ±2.5% from the average at blue wavelengths and to within ±1.7% from the average at red and near infrared wavelengths. This level of agreement lends confidence in the use of the transfer radiometers in validating the radiance scales assigned by EOS instrument calibration facilities to their integrating sphere sources. , "Volume 37. The _J © X X XX X
doi:10.1117/12.373186 fatcat:5tzfr25g55afreehvubj4oi244

Radiometric characterization of field radiometers in support of the 1997 Lunar Lake, Nevada, experiment to determine surface reflectance and top-of-atmosphere radiance

Steven W. Brown, B.Carol Johnson, Howard W. Yoon, James J. Butler, Robert A. Barnes, Stuart Biggar, Paul Spyak, Kurtis Thome, Edward Zalewski, Mark Helmlinger, Carol Bruegge, Stephen Schiller (+4 others)
2001 Remote Sensing of Environment  
The UA VNIR is an eight-channel filter radiometer with a detector employing three Si photodiodes (p-on-n type) arranged in a light trapping configuration (Biggar, 1998; Biggar & Slater, 1993) .  ...  to Lunar Lake, Nevada, in which international remote sensing research groups measure the surface reflectance of the playa from the air and the ground during periods of satellite overflights (Slater, Biggar  ... 
doi:10.1016/s0034-4257(01)00215-2 fatcat:ro3gorxsczhotbkac3ceszagnu

MOESM1 of Age and geographic patterns of Plasmodium falciparum malaria infection in a representative sample of children living in Burkitt lymphoma-endemic areas of northern Uganda

Marlena Maziarz, Tobias Kinyera, Isaac Otim, Paul Kagwa, Hadijah Nabalende, Ismail Legason, Martin Ogwang, Samuel Kirimunda, Benjamin Emmanuel, Steven Reynolds, Patrick Kerchan, Moses Joloba (+7 others)
2017 Figshare  
Additional file 1.
doi:10.6084/m9.figshare.c.3721723_d1.v1 fatcat:2is4u2b4dvck5ef4uk3j6f3wr4

Evaluating the Causal Link Between Malaria Infection and Endemic Burkitt Lymphoma in Northern Uganda: A Mendelian Randomization Study

Ismail D. Legason, Ruth M. Pfeiffer, Krizia-Ivana Udquim, Andrew W. Bergen, Mateus H. Gouveia, Samuel Kirimunda, Isaac Otim, Eric Karlins, Patrick Kerchan, Hadijah Nabalende, Ariunaa Bayanjargal, Benjamin Emmanuel (+12 others)
2017 EBioMedicine  
Plasmodium falciparum (Pf) malaria infection is suspected to cause endemic Burkitt Lymphoma (eBL), but the evidence remains unsettled. An inverse relationship between sickle cell trait (SCT) and eBL, which supports that between malaria and eBL, has been reported before, but in small studies with low power. We investigated this hypothesis in children in a population-based study in northern Uganda using Mendelian Randomization. Methods: Malaria-related polymorphisms (SCT, IL10, IL1A, CD36,
more » ... and IFNAR1) were genotyped in 202 eBL cases and 624 controls enrolled during 2010-2015. We modeled associations between genotypes and eBL or malaria using logistic regression. Findings: SCT was associated with decreased risk of eBL (adjusted odds ratio [OR] 0·37, 95% CI 0·21-0·66; p = 0·0003). Decreased risk of eBL was associated with IL10 rs1800896-CT (OR 0·73, 95% CI 0·50-1·07) and -CC genotypes (OR 0·53, 95% CI 0·29-0·95, p trend = 0·019); IL1A rs2856838-AG (OR 0·56, 95% CI 0·39-0·81) and -AA genotype (OR 0·50, 95% CI 0·28-1·01, p trend = 0·0016); and SEMA3C rs4461841-CT or -CC genotypes (OR 0·57, 95% CI 0·35-0·93, p = 0·0193). SCT and IL10 rs1800896, IL1A rs2856838, but not SEMA3C rs4461841, polymorphisms were associated with decreased risk of malaria in the controls. Interpretation: Our results support a causal effect of malaria infection on eBL. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).
doi:10.1016/j.ebiom.2017.09.037 pmid:29033373 pmcid:PMC5704046 fatcat:ndzuqhzktffvnnvlximuyoyfyi

Age and geographic patterns of Plasmodium falciparum malaria infection in a representative sample of children living in Burkitt lymphoma-endemic areas of northern Uganda

Marlena Maziarz, Tobias Kinyera, Isaac Otim, Paul Kagwa, Hadijah Nabalende, Ismail D. Legason, Martin D. Ogwang, Samuel Kirimunda, Benjamin Emmanuel, Steven J. Reynolds, Patrick Kerchan, Moses M. Joloba (+7 others)
2017 Malaria Journal  
Falciparum malaria is an important risk factor for African Burkitt lymphoma (BL), but few studies have evaluated malaria patterns in healthy BL-age children in populations where both diseases are endemic. To obtain accurate current data, patterns of asymptomatic malaria were investigated in northern Uganda, where BL is endemic. Methods: Between 2011 and 2015, 1150 apparently healthy children under 15 years old were sampled from 100 villages in northern Uganda using a stratified, multi-stage,
more » ... ster survey design. Falciparum malaria prevalence (pfPR) was assessed by questionnaire, rapid diagnostic test (RDT) and thick film microscopy (TFM). Weighted pfPR and unadjusted and adjusted associations of prevalence with covariates were calculated using logistic models and survey methods. Results: Based on 1143 children successfully tested, weighted pfPR was 54.8% by RDT and 43.4% by TFM. RDT sensitivity and specificity were 97.5 and 77.8%, respectively, as compared to TFM, because RDT detect malaria antigens, which persist in peripheral blood after clinical malaria, thus results based on RDT are reported. Weighted pfPR increased from 40% in children aged under 2 years to 61.8% in children aged 6-8 years (odds ratio 2.42, 95% confidence interval (CI) 1.26-4.65), then fell slightly to 49% in those aged 12-15 years. Geometric mean parasite density was 1805.5 parasites/µL (95% CI 1344.6-2424.3) among TFM-positive participants, and it was higher in children aged <5 years at 5092.9/µL (95% CI 2892.7-8966.8) and lower in those aged ≥10 years at 983.8/µL (95% CI 472.7-2047.4; P = 0.001). Weighted pfPR was lower in children residing in sub-regions employing indoor residual spraying (IRS) than in those residing in non-IRS sub-regions (32.8 versus 65.7%; OR 0.26, 95% CI 0.14, 0.46). However, pfPR varied both within IRS (3.2-55.3%) and non-IRS sub-regions (29.8-75.8%; Pheterogeneity <0.001). pfPR was inversely correlated with a child's mother's income (P = 0.011) and positively correlated with being enrolled in the wet season (P = 0.076), but sex was irrelevant.
doi:10.1186/s12936-017-1778-z pmid:28320389 pmcid:PMC5360076 fatcat:vz4roo57mzh7bahzbropvucj2u
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