bluuebunny/crossref_metadata_2025 huggingface dataset:
General synthetic domain theory – a logical approach
Authors: REUS BERNHARD , STREICHER THOMAS
Published: July 2002

Synthetic domain theory (SDT) is a version of Domain Theory where ‘all functions are

continuous’. Following the original suggestion of Dana Scott, several approaches to SDT

have been developed that are logical or categorical, axiomatic or model-oriented in character

and that are either specialised towards Scott domains or aim at providing a general theory

axiomatising the structure common to the various notions of domains studied so far.

In Reus and Streicher (1993), Reus (1995) and Reus (1998), we have developed a logical and

axiomatic version of SDT, which is special in the sense that it captures the essence of

Domain Theory à la Scott but rules out, for example, Stable Domain Theory, as it requires

order on function spaces to be pointwise. In this article we will give a logical and axiomatic

account of a general SDT with the aim of grasping the structure common to all notions of

domains.

As in loc.cit., the underlying logic is a sufficiently expressive version of constructive type

theory. We start with a few basic axioms giving rise to a core theory on top of which we

study various notions of predomains (such as, for example, complete and well-complete

S-spaces (Longley and Simpson 1997)), define the appropriate notion of domain and verify

the usual induction principles of domain theory.

Although each domain carries a logically definable ‘specialization order’, we avoid

order-theoretic notions as much as possible in the formulation of axioms and theorems. The

reason is that the order on function spaces cannot be required to be pointwise, as this would

rule out the model of stable domains à la Berry.

The consequent use of logical language – understood as the internal language of some

categorical model of type theory – avoids the irritating coexistence of the internal and the

external view pervading purely categorical approaches. Therefore, the paper is aimed at

providing an elementary introduction to synthetic domain theory, albeit requiring some

knowledge of basic type theory.
Protecting Communities in Research: Philosophical and Pragmatic
Challenges
Authors: WEIJER CHARLES
Published: July 2002

The issue of the protection of communities in clinical
research first arose 10 years ago in studies conducted
in technologically developing countries by scientists from
technologically developed nations. The question was, which
ethical standards ought to apply, those of the Western
investigators or local standards?
Moral Agency and the Family: The Case of Living Related
Organ Transplantation
Authors: CROUCH ROBERT A. , ELLIOTT CARL
Published: July 2002

Living related organ transplantation is morally
problematic for two reasons. First, it requires surgeons
to perform nontherapeutic, even dangerous procedures on
healthy donors—and in the case of children, without
their consent. Second, the transplant donor and recipient
are often intimately related to each other, as parent and
child, or as siblings. These relationships challenge our
conventional models of medical decisionmaking. Is there
anything morally problematic about a parent allowing the
interests of one child to be risked for the sake of another?
What exactly are the interests of the prospective child
donor whose sibling will die without an organ? Is the choice
of a parent to take risks for the sake of her child truly
free, or is the specter of coercion necessarily raised?
A Characterization of GEM Distributions
Authors: GNEDIN ALEXANDER , KEROV SERGEI
Published: July 2002

Let (Xn) be a residual allocation model with i.i.d. residual fractions
Un: For W a random
variable with values in [0; 1] and independent of (Xn),
we define another sequence (Yn) by setting

(formula here)

Under minor regularity assumptions we show that (Xn) and (Yn)
have the same probability law if and only if this law is a GEM distribution. In this case, the distribution of W
and the Uns is Beta(1; θ) for some θ > 0.
On the Expected Depth of Random Circuits
Authors: ARYA SUNIL , GOLIN MORDECAI J. , MEHLHORN KURT
Published: July 2002

In this paper we analyse the expected depth of random circuits
of fixed fanin f. Such circuits
are built a gate at a time, with the f inputs of each new gate being chosen randomly from
among the previously added gates. The depth of the new gate is defined to be one more
than the maximal depth of its input gates. We show that the expected depth of a random
circuit with n gates is bounded from above by ef ln n
and from below by 2.04 … f ln n.
Cyclin B1 levels in the porcine 4-cell stage embryo
Authors: Bonk Aaron J. , Anderson Jon E. , Abeydeera Lalantha R. , Day Billy N. , Prather Randall S.
Published: July 2002

The relative quantity of cyclin B1 was determined during the development of in vitro and in vivo derived porcine 4-cell embryos by western blotting and immunolocalised during the 4-cell stage. After cleavage to the 4-cell stage cyclin B1 localised to the cytoplasm at the 5, 10, 18 and 25 time points and localised to the nucleus 33 h post 4-cell cleavage (P4CC). The relative abundance of cyclin B1 was not significantly different in in vivo or in vitro derived 4-cell stage embryos cultured in the absence of the RNA polymerase inhibitor α-amanitin. Cyclin B1 protein was not detectable in embryos cultured in medium without α-amanitin for 5, 10, 18 or 25 h P4CC followed by culture in medium with α-amanitin to 33 P4CC. These results suggest that the maternal to zygotic transition of mRNA production that occurs at the 4-cell stage of the pig embryo does not result in an increase in cyclin B1 production. In addition, cyclin B1 protein levels remained constant in the absence of embryonic genome activation at the 4-cell stage.
Intracytoplasmic sperm injection in the rat
Authors: Dozortsev D. , Wakaiama T. , Ermilov A. , Yanagimachi R.
Published: July 2002

We applied intracytoplasmic sperm injection (ICSI) to the rat comparing three different sperm injection techniques: conventional setup with a sharp needle bearing a spike (method 1), combination of partial zona dissection (PZD) needle and blunt pipette (method 2) and piezo-injection using a blunt pipette (method 3). We also investigated the timing of sperm pronuclear formation after injection. Survival rates after injection were 8%, 24% and 71% for the methods 1, 2 and 3, respectively. All surviving oocytes formed pronuclei by about 6 h after injection. Although the survival and activation rates following sperm injection using piezo-injection were high, the incidence of normal fertilisation, as evidenced by second polar body extrusion and formation of two pronuclei, was only 10%. The vast majority of the zygotes were multinucleated, although most of them subsequently underwent cleavage. Fixation and staining of injected oocytes at different times after injection revealed that replacement of sperm nuclear protamines by histones takes place by 15 min after injection, sperm head swelling occurs within 0.5–1 h after injection and pronuclei become fully developed by 7 h after injection. Although the rate of normal fertilisation in the rat following ICSI was low under the present experimental conditions, the results indicated that direct ICSI using a piezo-driven pipette would be a potentially valuable method of producing rat offspring.
The nature of the ‘nucleolus precursor body’ in early preimplantation embryos: a review of fine-structure cytochemical, immunocytochemical and autoradiographic data related to nucleolar function
Authors: Fléchon J.-E. , Kopecny V.
Published: July 2002

In mammals, the restoration of rRNA transcription after fertilisation is accompanied by a gradual differentiation of the nucleolar structure by a process called embryonic nucleogenesis. During cleavage, the nucleolar components appear sterically related to a class of nuclear bodies already detectable in pronuclei. These structures, due to their apparent function as centres of nucleolus formation, have been designated nucleolus precursor bodies (NPBs). It was found recently not only that the size and morphology of the NPBs differ among mammalian species, but that the pattern of embryonic nucleologenesis and even the molecular composition of different NPB compartments vary from one species to another. Accordingly we assumed that at least two definitely different types of NPBs exist, namely the mouse-type NPB and cow-type NPB. In the mouse-type NPB, the original compact material of the NPB remains detectable in the early functional nucleolus. This NPB core does not contain DNA or typical Ag-NOR nucleolar proteins. At the onset of rRNA transcription, the nucleolonema is formed at the periphery of the NPB. The cow-type NPB shows a homogeneous distribution of typical nucleolar proteins throughout its body from the pronucleolar to the early 8-cell stage. At the beginning of rRNA transcription, the cow-type NPB is penetrated by perinucleolar DNA and rRNA synthesis is detectable deep inside the nucleolus. In this case, the entire NPB is readily transformed into a typical nucleolus. These processes are recognisable using fine-structure analysis of preimplantation mammalian embryos. For this reason this approach is often used as a method of evaluating the state of experimental embryos; in such studies, the species differences must be taken into account.
Effect of sperm immobilisation and demembranation on the oocyte activation rate in the mouse
Authors: Kasai T. , Hoshi K. , Yanagimachi R.
Published: July 2002

To analyse the effect of the state of the sperm plasma membrane on oocyte activation rate following intracytoplasmic sperm injection (ICSI), three types of human and mouse spermatozoa (intact, immobilised and Triton X-100 treated) were individually injected into mouse oocytes. At 30, 60 and 120 min after injection, maternal chromosomes and sperm nuclei within oocytes were examined. Following human sperm injection, the fastest and the most efficient oocyte activation and sperm head decondensation occurred when the spermatozoa were treated with Triton X-100. Intact spermatozoa were the least effective in activating oocytes. Thus, the rate of mouse oocyte activation following human sperm injection is greatly influenced by the state of the sperm plasma membrane during injection. When mouse spermatozoa were injected into mouse oocytes, the rates of oocyte activation and sperm head decondensation within activated oocytes were the same irrespective of the type of sperm treatment prior to injection. We witnessed that live human spermatozoa injected into moue oocytes often kept moving very actively within the ooplasm for more than 60 min, whereas motile mouse spermatozoa usually became immotile within 20 min after injection into the ooplasm. In 0.002% Triton X-100 solution, mouse spermatozoa are immobilised faster than human spermatozoa. These facts seem to suggest that human sperm plasma membranes are physically and biochemically more stable than those of mouse spermatozoa. Perhaps the physical and chemical properties of the sperm plasma membrane vary from species to species. For those species whose spermatozoa have ‘stable’ plasma membranes, prior removal or ‘damage’ of sperm plasma membranes would increase the success rate of ICSI.
A comparison of Meteosat rainfall estimation techniques in Kenya
Authors: Tucker M R , Sear C B
Published: July 2002

Two methods for estimating ten‐day rainfall totals from Meteosat infra‐red imagery were compared for the April–June 1996 ‘long rains’ of Kenya in an area covering the eastern highlands and the Tana and Athi river basins. One of these (the Bristol ‘B4’ method) was then used for rainfall estimation for the whole of Kenya, for November 1996 and the other, the TAMSAT ‘Cold Cloud Duration’ (CCD) method was used to estimate rainfall for the whole of Kenya for November 1997 to April 1998. April–June 1996 was an unusual season with very few large rainstorms. For this comparison period the B4 method gave better estimates of actual rainfall than the TAMSAT method because it used a variable cold cloud threshold temperature and ongoing calibration against rain gauge data. Comparison of ten‐day CCD totals with rainfall for the 1997–1998 period indicated that using the TAMSAT method gave best rainfall estimates for the arid and semi‐arid areas of eastern and northern Kenya and for months other than the main rainy season months of November and April. Both methods could be used successfully to identify periods with well below or well above average rainfall even over highland areas, and they are therefore useful for providing food security early warnings. Copyright © 2001 Royal Meteorological Society
Problems and solutions for drawing fronts objectively
Authors: McCann Donald W , Whistler James P
Published: July 2002

A recent requirement charged to the Aviation Weather Center (AWC) is to produce significant weather charts for aviation users with, among other forecast products, forecast locations of significant fronts. To increase forecaster productivity, the AWC decided to evaluate the possibility that fronts should be first drawn objectively. Hewson (1998) describes the basic technique which uses a variation on the Renard & Clarke (1965) frontal locator function to find the fronts. The AWC had to overcome many problems in implementing Hewson's techniques. This paper illuminates the problems and describes the AWC solutions. As a result of the AWC's success, objective frontal analyses and forecasts are now a reality, and the productivity of forecasters increased. Copyright © 2001 Royal Meteorological Society
On some applications of finite-state automata theory to natural language
processing
Authors: MOHRI MEHRYAR
Published: July 2002

We describe new applications of the theory of automata to natural
language processing: the representation of very large scale dictionaries
and the indexation of natural language texts. They are based on new algorithms
that we introduce and describe in detail. In particular, we give pseudocodes
for the determinisation of string to string transducers, the deterministic
union of p-subsequential string to string transducers, and the
indexation by automata. We report on several experiments illustrating the
applications.
THE PSYCHOPHYSIOLOGICAL RESPONSES OF PTSD PATIENTS: HABITUATION, RESPONSES TO STRESSFUL AND NEUTRAL VIGNETTES AND ASSOCIATION WITH TREATMENT OUTCOME
Authors: Tarrier Nicholas , Sommerfield Claire , Connell John , Deakin Bill , Pilgrim Hazel , Reynolds Martina
Published: July 2002

A number of studies have demonstrated that patients suffering from PTSD show differences from appropriate controls in psychophysiological responding. This study aimed to investigate whether there were differences in habitu

ation and psychophysiological reactivity between PTSD patients and normals, and between patient subgroups depending on their symptoms and whether psychophysiological variables were associated with clinical outcome from a treatment trial. Participants were tested by measuring electrodermal activity to two sets of 15 auditory stimuli of different intensity, and to six vignettes, four neutral, one of general stress and one trauma related. Psychophysiological variables were entered into a multiple regression with clinical outcome as the dependent variable. There were no differences between patients and controls or within patients on the habituation paradigms. Patients differed from controls only on their response to the trauma related vignette. There were no differences on any within patient compar

isons. There was no association with these measures and later clinical outcome. Psychophysiological differences between PTSD patients and normal controls are very specifically related to trauma related stimuli. Patients with startle or high arousal symptoms do not show differences from those without. These measures were not related to treatment

response.
Virtual lesions and the not-so-modular brain
Authors: LLOYD DAN
Published: July 2002

Because lesions usually affect contiguous areas of the
brain, cognitive neuropsychology has generally posited
modularity of brain function, assuming that specific regions
of the brain have specific dedicated functions. However,
a review of 36 published functional neuroimaging studies
suggests that functions are distributed over multiple regions.
Or, in other words, specific brain regions are usually
multifunctional. By a technique of “virtual lesions,”
I measure the contribution that regions of the brain make
to tasks imaged in 36 PET experiments, and propose a new
and more detailed interlink between neuropsychology and
functional neuroimaging. (JINS, 2000, 6,
627–635.)
Homophone meaning generation: A new test of verbal switching
for the detection of frontal lobe dysfunction
Authors: WARRINGTON ELIZABETH K.
Published: July 2002

Executive functions in their broadest sense may be
impaired in patients with frontal lobe lesions. The
Wisconsin Card Sorting Test, perhaps the most robust test
sensitive to frontal lobe dysfunction, requires the flexibility
to switch a response pattern to meet the change in task
demands. However this task has only two category switches
and normal respondents tend to score at ceiling. Verbal
fluency tasks also incorporate a switching component and
it was hypothesized that a word generation task that maximized
a switching requirement might provide a more satisfactory
verbal measure of frontal lobe dysfunction. A new test
of homophone meaning generation that requires multiple
switches between verbal concepts (e.g., tick =
insect, correct, etc.) was devised. Normative data was
obtained from a sample of 170 control participants. Seventy-one
patients with unilateral anterior or posterior cerebral
lesions were also tested. A normal distribution of scores
was obtained in the standardization sample. The anterior
lesion groups were more impaired than the posterior groups.
There were no significant differences due to laterality.
This homophone meaning generation task is a measure of
frontal lobe dysfunction that has the advantage of psychometric
properties that permit measurement of the degree of impairment.
(JINS, 2000, 6, 643–648.)
Cognitive and linguistic correlates of children's discourse
after closed head injury: A three-year follow-up
Authors: BROOKSHIRE BONNIE L. , CHAPMAN SANDRA B. , SONG JAMES , LEVIN HARVEY S.
Published: July 2002

The discourse of 91 children who had sustained severe
(n = 68) or mild (n = 23) closed head
injury (CHI) was examined at least three years postinjury.
The groups' retellings of a narrative story were analyzed
according to two domains, information and language. In
comparison to the mild CHI group, the severe group produced
stories characterized by reduced content and information,
impaired organization, fewer words, and less complex sentences.
The relationships between discourse production and the
groups' performance on measures of language, executive
function, memory, and processing speed were examined. Correlations
were found between discourse production and general verbal
ability including verbal fluency. Correlations were also
found for discourse performance and executive function
measures associated with problem solving and working memory.
Site and extent of lesion were not useful in predicting
discourse production. These findings indicate that children
who sustain a severe closed head injury during early to
middle childhood are at risk for persisting deficits in
discourse processing and other cognitive abilities. (JINS,
2000, 6, 741–751)
Self-monitoring enhances Wisconsin Card Sorting Test performance
in patients with schizophrenia: Performance is improved
by simply asking patients to verbalize their sorting strategy
Authors: PERRY WILLIAM , POTTERAT ERIC G. , BRAFF DAVID L.
Published: July 2002

Patients with schizophrenia have Wisconsin Card Sorting
Test (WCST) deficits, which are commonly interpreted as
reflecting frontal cortex-based executive dysfunction. One
means of assessing the refractoriness of frontal-executive
impairment is to utilize a training or modification strategy
to improve WCST performance. In this study, 73 patients
with schizophrenia were assigned to 1 of 2 groups. Group
1 received the standard WCST instructions for 64 cards
(Condition 1). For the second 64-card deck, the patients
were asked to verbalize the reason that they placed the
card where they did after each sort (Condition 2). Group
2 received this modified instruction 1st (Condition 1)
and then the standard instructions for the second deck
(Condition 2). A group of normal comparison participants
was also tested using standard instructions alone. Group
2 committed significantly fewer perseverative responses
than did Group 1. Furthermore, there was no significant
difference between Group 2 (Condition 1) and the normal
participants. Group 1's performance improved when
patients were exposed to the modified instructions (Condition
2). Additionally, poor premorbid factors and disorganized
symptoms were associated with decreased benefit from the
modified instructions across both groups. Cumulatively, these
data suggest that a simple instruction may enhance executive
function and impact WCST performance in patients with
schizophrenia. (JINS, 2001, 7, 344–352.)
Performance of elderly African American and White community
residents on the CERAD Neuropsychological Battery
Authors: FILLENBAUM GERDA G. , HEYMAN ALBERT , HUBER MARC S. , GANGULI MARY , UNVERZAGT FREDERICK W.
Published: July 2002

The CERAD Neuropsychological Battery, includes 7 measures:
Verbal Fluency; Modified Boston Naming; Mini-Mental State;
Word List Learning, Recall and Recognition; Constructional
Praxis. It was originally developed to evaluate patients
with a clinical diagnosis of Alzheimer's disease,
but is increasingly used in epidemiological studies of
the incidence and prevalence of dementia in the elderly.
The current study reports norms for African American and
White representative community residents 71 years of age
and older in North Carolina, and compares performance with
that of African Americans in Indianapolis and with Whites
in the Monongahela Valley, Pennsylvania. For all 3 studies,
increased education and younger age was related to better
performance on each of the 7 measures. Sex differences,
when present, tended to favor women. Although on average
African Americans performed more poorly than Whites, with
demographic characteristics controlled, no significant
racial differences were found in the North Carolina sample.
Both African American and White participants in North Carolina
performed more poorly than their racial counterparts in
the other 2 studies, possibly because of selection-induced
differences in health and educational status. Nevertheless,
the use of an identical evaluation battery, such as the
CERAD neuropsychologic instrument, facilitates comparisons
not otherwise possible, and should be encouraged. (JINS,
2001, 7, 502–509.)
Opportunities and limitations of contingent valuation surveys to determine national park entrance fees: evidence from Costa Rica
Authors: SHULTZ STEVEN , PINAZZO JORGE , CIFUENTES MIGUEL
Published: July 2002

A contingent valuation method (CVM) survey to determine foreign and resident willingness to pay (WTP) for return visits to two different Costa Rican national parks was administered in 1995. WTP values were estimated for future entrance fees associated with proposed improvements to infrastructure and services in the Poas Volcano and the Manuel Antonio parks. Resulting logistic CVM models were statistically robust and mean WTP for entrance fees differed among the parks and were considerably higher than current fees. Results indicate that even in a developing country setting, the CVM is a useful tool to help determine park entrance fees in spite of the following methodological limitations which are recommended for further study: the need to include potential park visitors in survey samples; the lack of detailed information framing and contingent scenarios for park related WTP questions; and the threat of cultural-strategic biases when surveying residents of a developing country.
General sound classification and similarity in MPEG-7
Authors: Casey Michael
Published: July 2002

We introduce a system for generalised sound classification and similarity using a machine-learning framework. Applications of the system include automatic classification of environmental sounds, musical instruments, music genre and human speakers. In addition to classification, the system may also be used for computing similarity metrics between a target sound and other sounds in a database. We discuss the use of hidden Markov models for representing the temporal evolution of audio spectra and present results of testing the system on classification and retrieval tasks. The system has been incorporated into the MPEG-7 international standard for multimedia content description and is therefore publicly available in the form of a set of standardised interfaces and software reference tools for developers and researchers.
Child Homicide and the Law:
Implications of the Judgements of
the European Court of Human
Rights in the Case of the Children
Who Killed James Bulger
Authors: Wolff Sula , McCall Smith R. Alexander A.
Published: July 2002

The facts of the Bulger case and its legal consequences, in
particular the judgements of the European Court of Human
Rights (ECHR), are summarised. A review of the literature
on child homicide indicates that this continues to be rare,
can neither be predicted nor prevented, and suggests that the
future outlook for such offenders may be good. The
recommendations of a committee set up by Justice (1996)
for changes in legislation and procedures concerning children who have killed, are congruent with the European
Court's judgements, but still woefully at odds with public
attitudes.
STOCK RETURNS, TERM STRUCTURE, INFLATION, AND REAL ACTIVITY: AN
INTERNATIONAL PERSPECTIVE
Authors: Canova Fabio , Nicoló Gianni De
Published: July 2002

This paper analyzes the empirical interdependecies
among asset returns, real activity, and inflation from multicountry
and international points of view. We find that innovations in nominal
stock returns are not significantly related to inflation or real
activity, that the U.S. term structure of interest rates predicts both
domestic and foreign inflation rates and domestic future real
activity, and that innovations in inflation do not significantly
affect real activity. An interpretation of the dynamics and
some policy implications of the results are
provided.
rPatterns of mtDNA and microsatellite variation in an island and mainland population of guanacos in southern Chile
Authors: Sarno Ronald J. , Franklin William L. , O'Brien Stephen J. , Johnson Warren E.
Published: July 2002

The archaeological record indicates that guanacos inhabited the Patagonia of Chile and Argentina about 13,600 years ago, but were unable to migrate further south owing to the presence of glacial and water barriers that covered much of southern South America including the island of Tierra del Fuego. As environmental and ecological conditions improved, guanacos, along with other large mammals including horses, colonized the area. As a result of continued world‐wide glacial melting, ocean levels rose and Tierra del Fuego became isolated from the mainland approximately 8000 years ago. Although island populations generally exhibit lower levels of genetic variation than their counterpart mainland populations, it is difficult to predict how much less variation island populations will exhibit. An analysis of mitochondrial cytochromeband ATPase‐8 sequences and 15 nuclear microsatellite loci revealed that both populations retained appreciable genetic diversity. The island population, however, exhibited much less variation than the mainland population. Measures of genetic variation revealed modest, but significant genetic differentiation, consistent with separation of the two populations approximately 8000 years ago. The assessment of levels of genetic diversity and population differentiation among populations of the wild South American camelids is becoming increasingly important as interest mounts in their utilization as a renewable resource.
Life in the puddle: behavioural and life‐cycle adaptations in the Diptera of tropical rain pools
Authors: McLACHLAN ATHOL , LADLE RICHARD
Published: July 2002

Puddles of rain water on the surfaces of rock exposures are a little known but very common habitat for freshwater‐dwelling animals. In Africa, these are inhabited by the larvae of two taxa of fly unique to these pools. One of these includes species able to survive dry periods in situ; the other includes species that must reach adulthood and migrate to survive periods when the pool is dry. Hence, the opportunity exists for a comparative study of adaptation among these species. Since puddles are small, our principal method in the study of adaptation has been the experimental manipulation of puddles and their faunas in the wild. Using this method we were able to identify the spatial consistency of pools and their unpredictable duration during the rainy season as the main selective pressure shaping adaptation. Adaptations include diapause and adaptive adjustment of the life cycle. It is the second of these that provides the focus of our interest here.
Targeted disruption of the three Rb-related genes leads to loss of G1 control and immortalization
Authors: Sage Julien , Mulligan George J. , Attardi Laura D. , Miller Abigail , Chen SiQi , Williams Bart , Theodorou Elias , Jacks Tyler
Published: July 2002

The retinoblastoma protein, pRB, and the closely related proteins p107 and p130 are important regulators of the mammalian cell cycle. Biochemical and genetic studies have demonstrated overlapping as well as distinct functions for the three proteins in cell cycle control and mouse development. However, the role of the pRB family as a whole in the regulation of cell proliferation, cell death, or cell differentiation is not known. We generated embryonic stem (ES) cells and other cell types mutant for all three genes. Triple knock-out mouse embryonic fibroblasts (TKO MEFs) had a shorter cell cycle than wild-type, single, or double knock-out control cells. TKO cells were resistant to G1 arrest following DNA damage, despite retaining functional p53 activity. They were also insensitive to G1 arrest signals following contact inhibition or serum starvation. Finally, TKO MEFs did not undergo senescence in culture and do possess some characteristics of transformed cells. Our results confirm the essential role of the Rb family in the control of the G1/S transition, place the three Rb family members downstream of multiple cell cycle control pathways, and further the link between loss of cell cycle control and tumorigenesis.
Transgene integration into the same chromosome location can produce alleles that express at a predictable level, or alleles that are differentially silenced
Authors: Day Christopher D. , Lee Elsa , Kobayashi Janell , Holappa Lynn D. , Albert Henrik , Ow David W.
Published: July 2002

In an effort to control the variability of transgene expression in plants, we used Cre-lox mediated recombination to insert a gus reporter gene precisely and reproducibly into different target loci. Each integrant line chosen for analysis harbors a single copy of the transgene at the designated target site. At any given target site, nearly half of the insertions give a full spatial pattern of transgene expression. The absolute level of expression, however, showed target site dependency that varied up to 10-fold. This substantiates the view that the chromosome position can affect the level of gene expression. An unexpected finding was that nearly half of the insertions at any given target site failed to give a full spatial pattern of transgene expression. These partial patterns of expression appear to be attributable to gene silencing, as low gusexpression correlates with DNA methylation and low transcription. The methylation is specific for the newly integrated DNA. Methylation changes are not found outside of the newly inserted DNA. Both the full and the partial expression states are meiotically heritable. The silencing of the introduced transgenes may be a stochastic event that occurs during transformation.
Ephrin-B3 is the midline barrier that prevents corticospinal tract axons from recrossing, allowing for unilateral motor control
Authors: Kullander Klas , Croll Susan D. , Zimmer Manuel , Pan Li , McClain Joyce , Hughes Virginia , Zabski Stephanie , DeChiara Thomas M. , Klein Rüdiger , Yancopoulos George D. , Gale Nicholas W.
Published: July 2002

Growing axons follow highly stereotypical pathways, guided by a variety of attractive and repulsive cues, before establishing specific connections with distant targets. A particularly well-known example that illustrates the complexity of axonal migration pathways involves the axonal projections of motor neurons located in the motor cortex. These projections take a complex route during which they first cross the midline, then form the corticospinal tract, and ultimately connect with motor neurons in the contralateral side of the spinal cord. These obligatory contralateral connections account for why one side of the brain controls movement on the opposing side of the body. The netrins and slits provide well-known midline signals that regulate axonal crossings at the midline. Herein we report that a member of the ephrin family, ephrin-B3, also plays a key role at the midline to regulate axonal crossing. In particular, we show that ephrin-B3 acts as the midline barrier that prevents corticospinal tract projections from recrossing when they enter the spinal gray matter. We report that in ephrin-B3−/− mice, corticospinal tract projections freely recross in the spinal gray matter, such that the motor cortex on one side of the brain now provides bilateral input to the spinal cord. This neuroanatomical abnormality in ephrin-B3−/− mice correlates with loss of unilateral motor control, yielding mice that simultaneously move their right and left limbs and thus have a peculiar hopping gait quite unlike the alternate step gait displayed by normal mice. The corticospinal and walking defects in ephrin-B3−/−mice resemble those recently reported for mice lacking the EphA4 receptor, which binds ephrin-B3 as well as other ephrins, suggesting that the binding of EphA4-bearing axonal processes to ephrin-B3 at the midline provides the repulsive signal that prevents corticospinal tract projections from recrossing the midline in the developing spinal cord.
The Dlx5 and Dlx6 homeobox genes are essential for craniofacial, axial, and appendicular skeletal development
Authors: Robledo Raymond F. , Rajan Lakshmi , Li Xue , Lufkin Thomas
Published: July 2002

Dlx homeobox genes are mammalian homologs of theDrosophila Distal-less (Dll) gene. TheDlx/Dll gene family is of ancient origin and appears to play a role in appendage development in essentially all species in which it has been identified. In Drosophila, Dll is expressed in the distal portion of the developing appendages and is critical for the development of distal structures. In addition, humanDlx5 and Dlx6 homeobox genes have been identified as possible candidate genes for the autosomal dominant form of the split-hand/split-foot malformation (SHFM), a heterogeneous limb disorder characterized by missing central digits and claw-like distal extremities. Targeted inactivation of Dlx5 and Dlx6genes in mice results in severe craniofacial, axial, and appendicular skeletal abnormalities, leading to perinatal lethality. For the first time, Dlx/Dll gene products are shown to be critical regulators of mammalian limb development, as combined loss-of-function mutations phenocopy SHFM. Furthermore, spatiotemporal-specific transgenic overexpression of Dlx5, in the apical ectodermal ridge of Dlx5/6 null mice can fully rescueDlx/Dll function in limb outgrowth.
A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy
Authors: Agarwala Richa , Applegate David L. , Maglott Donna , Schuler Gregory D. , Schäffer Alejandro A.
Published: July 2002

This paper describes a fast and scalable strategy for constructing a radiation hybrid (RH) map from data on different RH panels. The maps on each panel are then integrated to produce a single RH map for the genome. Recurring problems in using maps from several sources are that the maps use different markers, the maps do not place the overlapping markers in same order, and the objective functions for map quality are incomparable. We use methods from combinatorial optimization to develop a strategy that addresses these issues. We show that by the standard objective functions of obligate chromosome breaks and maximum likelihood, software for the traveling salesman problem produces RH maps with better quality much more quickly than using software specifically tailored for RH mapping. We use known algorithms for the longest common subsequence problem as part of our map integration strategy. We demonstrate our methods by reconstructing and integrating maps for markers typed on the Genebridge 4 (GB4) and the Stanford G3 panels publicly available from the RH database. We compare map quality of our integrated map with published maps for GB4 panel and G3 panel by considering whether markers occur in the same order on a map and in DNA sequence contigs submitted to GenBank. We find that all of the maps are inconsistent with the sequence data for at least 50% of the contigs, but our integrated maps are more consistent. The map integration strategy not only scales to multiple RH maps but also to any maps that have comparable criteria for measuring map quality. Our software improves on current technology for doing RH mapping in areas of computation time and algorithms for considering a large number of markers for mapping. The essential impediments to producing dense high-quality RH maps are data quality and panel size, not computation.
Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
Authors: Loging W. Troy , Lal Anita , Siu I-Mei , Loney Tania L. , Wikstrand Carol J. , Marra Marco A. , Prange Christa , Bigner Darell D. , Strausberg Robert L. , Riggins Gregory J.
Published: July 2002

Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases can reveal RNA transcripts specifically expressed in transformed tissue. To be useful, database information must be verified and a more complete pattern of tissue expression must be demonstrated. We tested database mining plus rapid screening by fluorescent-PCR expression comparison (F-PEC) as an approach to locate candidate brain tumor antigens. Cancer Genome Anatomy Project (CGAP) data was mined for genes highly expressed in glioblastoma multiforme. From 13 mined genes, seven showed potential as possible tumor markers or antigens as determined by further expression profiling. Now that large-scale expression information is readily available for many of the commonly occurring cancers, other candidate tumor markers or antigens could be located and evaluated with this approach.

[The expression data described in this paper have been submitted to the NCBI SAGEmap database under library name SAGE_Duke_GBM_H1110, SAGE_pooled_GBM, SAGE_BB542_whitematter, and SAGE_normal_pool(6th).]
Euteleost Fish Genomes are Characterized by Expansion of Gene Families
Authors: Robinson-Rechavi Marc , Marchand Oriane , Escriva Héctor , Bardet Pierre-Luc , Zelus Dominique , Hughes Sandrine , Laudet Vincent
Published: July 2002

The presence of additional hox clusters in the zebrafish has led to the hypothesis that there was a whole genome duplication at the origin of modern fish. To investigate the generality of this assumption, we analyzed all available actinopterygian fish gene families, and sequenced nuclear receptors from diverse teleost fish. The origin and timing of duplications was systematically determined by phylogenetic analysis. More genes are indeed found in zebrafish than in mouse. This abundance is shared by all major groups of euteleost fish, but not by eels. Phylogenetic analysis shows that it may result from frequent independent duplications, rather than from an ancestral genome duplication. We predict two zebrafish paralogs for most mouse or human genes, thus expressing a note of caution in functional comparison of fish and mammalian genomes. Redundancy appears to be the rule in fish developmental genetics. Finally, our results imply that the outcome of genome projects cannot be extrapolated easily between fish species.
Human and Mouse α-Synuclein Genes: Comparative Genomic Sequence Analysis and Identification of a Novel Gene Regulatory Element
Authors: Touchman Jeffrey W. , Dehejia Anindya , Chiba-Falek Ornit , Cabin Deborah E. , Schwartz Jody R. , Orrison Bonnie M. , Polymeropoulos Mihael H. , Nussbaum Robert L.
Published: July 2002

The human α-synuclein gene (SNCA) encodes a presynaptic nerve terminal protein that was originally identified as a precursor of the non-β-amyloid component of Alzheimer's disease plaques. More recently, mutations in SNCA have been identified in some cases of familial Parkinson's disease, presenting numerous new areas of investigation for this important disease. Molecular studies would benefit from detailed information about the long-range sequence context of SNCA. To that end, we have established the complete genomic sequence of the chromosomal regions containing the human and mouse α-synuclein genes, with the objective of using the resulting sequence information to identify conserved regions of biological importance through comparative sequence analysis. These efforts have yielded ∼146 and ∼119 kb of high-accuracy human and mouse genomic sequence, respectively, revealing the precise genetic architecture of the α-synuclein gene in both species. A simple repeat element upstream of SNCA/Snca has been identified and shown to be necessary for normal expression in transient transfection assays using a luciferase reporter construct. Together, these studies provide valuable data that should facilitate more detailed analysis of this medically important gene.

[The genomic DNA sequence data described in this paper have been submitted to GenBank under accession nos. AF163864 (human) and AF163865 (mouse).]
Predicting Deleterious Amino Acid Substitutions
Authors: Ng Pauline C. , Henikoff Steven
Published: July 2002

Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT, whichsorts intolerant fromtolerant substitutions, classifies substitutions as tolerated or deleterious. A higher proportion of substitutions predicted to be deleterious by SIFT gives an affected phenotype than substitutions predicted to be deleterious by substitution scoring matrices in three test cases. UsingSIFT before mutagenesis studies could reduce the number of functional assays required and yield a higher proportion of affected phenotypes. SIFT may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.
Expression Profiling by iAFLP: A PCR-Based Method for Genome-Wide Gene Expression Profiling
Authors: Kawamoto Shoko , Ohnishi Tadashi , Kita Hiroko , Chisaka Osamu , Okubo Kousaku
Published: July 2002

The availability of comprehensive sets of genes has prompted the researchers to carry out systematic collection of gene expression data. RT–PCR has the highest specificity and sensitivity for transcript detection among all available methods. Low throughput, especially when quantitative data are desired, has precluded RT–PCR from genome-wide application. Here we report a PCR-based expression profiling method, introduced amplified fragment length polymorphism (iAFLP), that has the same specificity and sensitivity as RT–PCR and a throughput level comparable to that of DNA–microarray hybridization. In this method, restricted ends of total cDNAs from six sources were ligated with adaptors having various length of short insertions to a common sequence (polymorphic adaptors). Amplification of a pool of these differentially adapted cDNAs with a gene-specific primer and an adaptor primer allows us to quantitate the abundance of any transcript in six mRNA sources. Using three different primer colors this technique allows quantitation of expression of 864 genes across six different sources per day with a single autosequencer, which is comparable to the throughput of microarray analysis in terms of number of genes × number of sources.
The 5′-Untranslated Region of the ntp303 Gene Strongly Enhances Translation during Pollen Tube Growth, But Not during Pollen Maturation
Authors: Hulzink Raymond J.M. , de Groot Peter F.M. , Croes Anton F. , Quaedvlieg William , Twell Dave , Wullems George J. , van Herpen Marinus M.A.
Published: July 2002

Transcripts of the ntp303 gene accumulate abundantly throughout pollen development, whereas the protein only accumulates to detectable levels after pollen germination. In an attempt to explain the divergence in the accumulation profiles of the mRNA and the protein, we investigated the role of the untranslated regions (UTRs) in enhancing ntp303 translation during the transition from developing to germinating pollen. Luciferase reporter gene fusion constructs containing the ntp3035′-UTR gave rise to luciferase activity that was up to 60-fold higher during pollen tube growth than that of constructs containing different 5′-UTRs. No apparent differences in the luciferase activity of these constructs were observed during pollen development. Thentp303 5′-UTR-mediated increase in luciferase activity was not significantly influenced by coding region or 3′-UTR sequences. Furthermore, enhanced luciferase activity directed by thentp303 5′-UTR occurred predominantly at the post-transcriptional level. A series of 5′-UTR deletion constructs was created to identify putative regulatory sequences required for the high level of translation during pollen tube growth. Two predicted stem loop structures (H-I and H-II) caused a complete inhibition of the enhanced translation after their total or partial deletion. A (GAA)8repeat within the H-I stem loop structure was demonstrated to be important for the modulation of translation efficiency. The H-II stem loop structure was found to be essential for the determination of mRNA stability.
Interaction of a Potential Vacuolar Targeting Receptor with Amino- and Carboxyl-Terminal Targeting Determinants
Authors: Kirsch T. , Saalbach G. , Raikhel N. V. , Beevers L.
Published: July 2002

A protein of 80 kD from developing pea (Pisum sativum) cotyledons has previously been shown to exhibit characteristics of a vacuolar targeting receptor by means of its affinity for the amino-terminal vacuolar targeting sequence of proaleurain from barley (Hordeum vulgare). In this report we show that the same protein also binds to the amino-terminal targeting peptide of prosporamin from sweet potato (lpomoea batatas) and to the carboxyl-terminal targeting determinant of pro-2S albumin from Brazil nut (Bertholletia excelsa). The receptor protein does not bind to the carboxyl-terminal propeptide (representing the targeting sequence) of barley lectin. The binding of the 80-kD protein to the sporamin determinant involves a motif (NPIR) that has been shown to be crucial for vacuolar targeting in vivo. The binding to the carboxyl-terminal targeting determinant of pro-2S albumin appears to involve the carboxyl-terminal propeptide and the adjacent five amino acids of the mature protein. The 80-kD protein does not bind to peptide sequences that have been shown to be incompetent in directing vacuolar targeting.