bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of exposure to community violence and developmental problems among inner-city
youth
Authors: GORMAN–SMITH DEBORAH , TOLAN PATRICK
Published: July 2002

While research has well documented that urban youth are exposed to increasing rates of
community violence, little is known about what increases risk for violence exposure, what
protects children from exposure to violence, and what factors reduce the most negative outcomes
associated with witnessing violence. This study expands on current research by evaluating the
relations between exposure to violence, family relationship characteristics and parenting
practices, and aggression and depression symptoms. Data were drawn from a sample of 245
African-American and Latino boys and their caregivers from economically disadvantaged
inner-city neighborhoods in Chicago. Rates of exposure could not be predicted from family
relationship and parenting characteristics, although there was a trend for discipline to be related.
Exposure to community violence was related to increases in aggressive behavior and depression
over a 1-year period even after controlling for previous status. Future studies should continue to
evaluate the role of exposure to violence on the development of youth among different
neighborhoods and communities. Implications for intervention and policy are discussed.
Hugoniot-type conditions and weak solutions to
the phase-field system
Authors: DANILOV V. G. , OMEL'YANOV G. A. , RADKEVICH E. V.
Published: July 2002

We consider a new concept of weak solutions to the phase-field
equations with a small
parameter ε characterizing the length of interaction. For the standard
situation of a single
free interface, this concept (in contrast with the common one) leads to
the well-known
Stefan–Gibbs–Thomson problem as ε→0. For the case
of a large number M(ε) (M(ε)→∞ as
ε→0)
of free interfaces, which corresponds to the ‘wave-train’
interpretation of a ‘mushy
region’, this concept allows us to obtain the limit problem as ε→0.
Full abstraction, totality and PCF
Authors: PLOTKIN GORDON
Published: July 2002

Inspired by a question of Riecke, we consider the
interaction of totality and full abstraction,
asking whether full abstraction holds for Scott's model of cpos and
continuous functions if
one restricts to total programs and total observations. The answer is negative,
as there are
distinct operational and denotational notions of totality. However, when
two terms are each
total in both senses, they are totally equivalent operationally
iff they are totally equivalent in
the Scott model. Analysing further, we consider sequential and parallel
versions of PCF and
several models: Scott's model of continuous functions, Milner's
fully abstract model of PCF
and their effective submodels. We investigate how totality differs between
these models.
Some apparently rather difficult open problems arise that essentially concern
whether the
sequential and parallel versions of PCF have the same expressive power,
in the sense of total
equivalence.
‘Degrees of Foreignness’ and the Construction of Identity in French border regions during the inter-war period
Authors: Lawrence Paul , Baycroft Timothy , Grohmann Carolyn
Published: July 2002

This paper presents a comparative study of the development of national and regional identities in three different border regions of France: the Basses-Alpes, the Moselle and French Flanders. It demonstrates that in spite of political, economic and social differences between the regions, the presence of the border and interaction with foreigners in specifically border regions similarly influenced identity formation in interwar France. In each case hierarchies or degrees of foreignness were developed, and a specific form of national identity came to be dominant which was determined more by a differentiation from ‘others’ than through an identification with shared, centre-generated national images.
Putting Patients First in Organ Allocation: An Ethical Analysis
of the U.S. Debate
Authors: CHILDRESS JAMES F.
Published: July 2002

Organ allocation policy involves a mixture of ethical,
scientific, medical, legal, and political factors, among others.
It is thus hard, and perhaps even impossible, to identify and
fully separate ethical considerations from all these other factors.
Yet I will focus primarily on the ethical considerations embedded
in the current debate in the United States about organ allocation
policy. I will argue that it is important to put patients
first—in the language of the title of one of the major
public hearings—but even then significant ethical questions
will remain about exactly how to put patients first.
Disease Gene Patenting: The Clinician's Dilemma
Authors: MAGNUS DAVID
Published: July 2002

One strategy for defenders of gene patenting is
to adopt a constructivist interpretation of genetic testing
to avoid the “product of nature doctrine.”
I argue that accepting this view (which seems to be the
approach of the U.S. Office of Patents and Trademarks)
results in an intolerable dilemma for physicians. They
must either infringe patents or fail to act on all the
medically relevant information they possess (malpractice).
Linear and Hereditary Discrepancy
Authors: DOERR BENJAMIN
Published: July 2002

Let A be an m × n matrix and
q := [lfloor ]log2(m)[rfloor ]+1. In this article we improve the well-known
bound lindisc(A) [les ] 2 herdisc(A) and show that

formula here

As with the previous proofs relating to this problem, ours is constructive. We will give an
on-line algorithm and analyse it using game theory.
Multi-Coloured Hamilton Cycles in Random Edge-Coloured Graphs
Authors: COOPER COLIN , FRIEZE ALAN
Published: July 2002

We define a space of random edge-coloured graphs [Gscr ]n,m,κ which correspond
naturally to edge κ-colourings of Gn,m. We show that there exist constants
K0, K1 [les ] 21 such that,
provided m [ges ] K0n log n and
κ [ges ] K1n, then a random edge-coloured graph contains a
multi-coloured Hamilton cycle with probability tending to 1 as the number of vertices n
tends to infinity.
On the Density of Universal Sum-Free Sets
Authors: SCHOEN TOMASZ
Published: July 2002

A set A is called universal sum-free if, for every finite
0–1 sequence χ = (e1, …, en),
either

(i) there exist i, j, where 1[les ]j<i[les ]n,
such that ei = ej = 1 and
i − j∈A, or

(ii) there exists t∈N such that, for 1[les ]i[les ]n,
we have t + i∈A if and only if
ei = 1.

It is proved that the density of each universal sum-free set is zero, which settles a
problem of Cameron.
Iron supplementation during pregnancy
Authors: Breymann Christian
Published: July 2002

Iron deficiency and iron supplementation are well known but unresolved issues of perinatal care. Approximately one thousand articles listed in Medline® over the last ten years focus on iron and pregnancy. Clearly, there are many unresolved questions regarding perinatal iron deficiency and iron supplementation.
Hyaluronic acid enhances induction of the acrosome reaction of human sperm through interaction with the PH-20 protein
Authors: Sabeur Khalida , Cherr Gary N. , Yudin Ashley I. , Overstreet James W.
Published: July 2002

When capacitated human sperm were treated with hyaluronic acid (HA) for 30 min prior to the addition of progesterone or solubilised human zonae pellucidae, there was a significant increase in the percentage of acrosome reactions. Progesterone treatment alone increased acrosome reactions from 10.5% to 21.8% and pretreatment with 100 µg/ml HA resulted in 33.0% acrosome reactions. With zonae pellucidae treatment alone the increase was from 9.0% to 23.5% and with HA pretreatment it was 48.8%. HA treatment alone had no direct effect on acrosome reactions, and the enhancing effect of HA was not removed when sperm were washed prior to the addition of either acrosome reaction agonist. Experiments with sperm 5 min after HA treatment demonstrated that enhancement of acrosome reactions was apparent as early as 1 min after addition of zonae and within 5 min after addition of progesterone. When sperm were pretreated with Fab fragments of anti-PH-20 IgG, then with HA and then with progesterone or zonae pellucidae, there was no enhancement of the acrosome reaction. Fab treatment did not induce acrosome reactions and did not interfere with the action of either agonist in the absence of HA. Sperm that were treated with HA had significantly higher intracellular calcium levels, and pretreatment with Fab reduced this increase to 42.7%. Addition of progesterone to HA-treated sperm was followed by another large increase in intracellular calcium, which was lower when sperm were pretreated with Fab. These results suggest that HA interacts with the PH-20 protein to increase basal levels of intracellular calcium and thereby potentiates the acrosome reaction. The data support the hypothesis that HA in the cumulus matrix may act to prime the fertilising sperm for induction of the acrosome reaction by constituents of the cumulus and/or zona pellucida.
Hyaluronic acid and the cumulus extracellular matrix induce increases in intracellular calcium in macaque sperm via the plasma membrane protein PH-20
Authors: Cherr Gary N. , Yudin Ashley I. , Li Ming-Wen , Vines Carol A. , Overstreet James W.
Published: July 2002

The hyaluronic acid (HA)-rich extracellular matrix (ECM) of the cumulus oophorus is known to facilitate fertilisation. It has been suggested that HA may enhance fertilisation in a number of species, and in macaque sperm, HA has been shown to increase the number of acrosome reactions that follow sperm binding to the zona pellucida. In this study, we investigated the effects of HA on intracellular Ca2+ in capacitated cynomolgus macaque sperm. Fluorometry studies using the intracellular Ca2+ indicator Fluo-3 showed that addition of 100 μg/ml of HA induced a rapid increase in intracellular Ca2+. This Ca2+ increase (approximately 2–3 times above basal levels) was inhibited by preincubation of sperm with Fab fragments of anti-recombinant PH-20 IgG. The frequency of acrosome reactions in sperm exposed to HA was not above control levels. A synthetic gel was prepared with similar viscosity to the cumulus and with HA trapped in its matrix. Video imaging of individual sperm was used to demonstrate that capacitated sperm swimming into the HA gel had increased intracellular Ca2+ levels. Preincubation of sperm with Fab fragments of anti-PH-20 IgG inhibited the increased intracellular Ca2+ levels induced by the HA gel. Sperm in control gel (no HA) did not show increased intracellular Ca2+, while sperm in gel containing anti-PH-20 IgG showed increased Ca2+ (positive control). Sperm loaded with Fluo-3 were allowed to interact with cynomologus macaque cumulus masses, and sperm within the cumulus ECM clearly showed increased intracellular Ca2+ that was inhibited when sperm were preincubated in anti-PH-20 Fab. Fluorescein isothiocyanate (FITC)-HA was found to bind to sperm over the acrosomal region, corresponding to PH-20 localisation, and this binding could be inhibited by preincubation of sperm with anti-PH-20 fragments. The results of this study show that HA increases intracellular Ca2+ in macaque sperm through interaction with plasma membrane PH-20. We propose that HA binding to plasma membrane PH-20 induces an aggregation of receptors that in turn results in intracellular signalling. As a result, sperm have higher basal CA2+ levels and are more responsive to induction of the acrosome reaction after binding to the zona pellucida.
Precipitation estimations from geostationary orbit and prospects for METEOSAT Second Generation
Authors: Levizzani V , Schmetz J , Lutz H J , Kerkmann J , Alberoni P P , Cervino M
Published: July 2002

For over two decades operational rainfall estimations from geostationary satellites have represented an ambitious aspiration of scientists and an identified need of operational meteorologists. A wide variety of infrared and combined visible and infrared methods have been proposed for the identification of suitable relationships between satellite‐observed cloud top radiative features and rainfall at the ground. Microwave‐based retrievals, however, correlate rainfall and internal cloud microphysical features more successfully. The most significant limitation, however, is the indirect character of the retrieval that correlates microphysical and dynamical cloud characteristics with rain amounts at ground level. METEOSAT Second Generation signals a new era for geostationary satellites with its new 12 channel imager SEVIRI and 15 minute full‐disk image repeat cycle. SEVIRI is expected to contribute significantly to a better characterisation of clouds and atmospheric stability by means of improved infrared calibration, radiometric performances, imaging frequency and multispectral image analysis. The significant increase of multispectral cloud observations is expected to provide new data for the improvement of rainfall estimations from geostationary orbit. The anticipated progress from enhanced imaging frequency and multispectral data for the definition of new techniques is discussed. Considerations for operational applications, chiefly for nowcasting, are also provided as they are the main goal of the satellite. Future developments and synergies with other geostationary and polar orbiting instruments, passive and active, are finally considered as the ultimate strategy for more accurate instantaneous rainfall estimations at all latitudes. Copyright © 2001 Royal Meteorological Society
Reliable Change formula query
Authors: HINTON-BAYRE ANTON
Published: July 2002

In a recent article, Temkin et al. (1999) contrasted
four models for detecting significant change in individual
performance on neuropsychological tests. Two of these models
relied on the calculation of the Reliable Change Index
(RCI) by Jacobson and Truax (1991), with and without a
correction for practice associated with repeated testing.
The other two models were based on simple linear regression
and multiple regression, respectively. The models were
contrasted based on the width of 90% prediction intervals
(PI) and normal-distribution-based prediction accuracy
of classifying unusual cases. Participants were tested
twice (Time 1 and Time 2), on seven common neuropsychological
measures. Prediction accuracy was based on the discrepancy
between obtained and predicted Time 2 scores.
Does literacy have an effect on stick construction tasks?
Authors: MATUTE ESMERALDA , LEAL FERNANDO , ZARABOZO DANIEL , ROBLES ANTONIA , CEDILLO CONCEPCIÓN
Published: July 2002

Since constructional apraxia is often concomitant
with brain lesions, the study of constructional tasks in
the non-brain-damaged population might be useful in helping
to disentangle other causal factors. This paper explores
the performance of illiterate individuals (N =
29) as compared to that of semiliterates (N =
21) and literates (N = 23) in order to see the
effect of reading and writing abilities on constructional
tasks. Each participant was asked to construct 4 figures
based upon models having varying degrees of complexity.
A global criterion of lack of fidelity and several analytic
criteria (related to distortion, rotation, and disarticulation
errors) were used to evaluate performance. Although illiterates
generally made more errors than semiliterates and semiliterates
more than literates, only some of these differences were
statistically significant. Significant differences were
found for lack of global fidelity and disarticulation errors
when all 4 figures were considered together. Subtler data
emerged with respect to single figures. (JINS,
2000, 6, 668–672.)
Neuropsychological characteristics of five children with
the Landau-Kleffner syndrome: Dissociation of auditory
and phonological discrimination
Authors: KORKMAN MARIT , GRANSTRÖM MARJA-LIISA , APPELQVIST KATI , LIUKKONEN ELINA
Published: July 2002

The Landau-Kleffner Syndrome (LKS) is characterized
by acquired receptive aphasia and EEG abnormality with
onset between the ages of 3 and 8 years. This study presents
neuropsychological assessments in 5 children with LKS.
The aims were (1) to specify the neuropsychological deficits
characteristic of these children; and (2) to clarify the
nature of the receptive aphasia by comparing nonverbal
and verbal auditory discrimination. Receptive aphasia was
present in all children. Retardation, poor motor coordination,
hyperkinesia, and conduct problems were frequent but variable.
All children exhibited a dissociation between the discrimination
of environmental sounds and phonological auditory discrimination,
the latter being more impaired than the former. This suggests
that the primary deficit of the receptive aphasia is an
impairment of auditory phonological discrimination rather
than a generalized auditory agnosia. (JINS, 1998,
4, 566–575.)
Brain activation and pupil response during covert performance
of the Stroop Color Word task
Authors: BROWN GREGORY G. , KINDERMANN SANDRA S. , SIEGLE GREG J. , GRANHOLM ERIC , WONG ERIC C. , BUXTON RICHARD B.
Published: July 2002

Patterns of brain activation associated with covert
performance of the Stroop Color–Word task were studied
in young, healthy, adult volunteers using blood oxygen
level dependent (BOLD) functional magnetic resonance imaging
(fMRI). Comparisons of the incongruous Stroop condition
were made with both color naming and word reading baselines.
Areas of the left and right anterior cingulate, the right
precuneus, and the left pars opercularis displayed larger
BOLD signal responses during the incongruous Stroop condition
than during baseline conditions. Activation of BOLD signals
in these areas was highly repeatable. In a second experiment,
pupil diameter was used to assess cognitive load in 7 individuals
studied during overt and covert performance of both Stroop
and color naming conditions. Cognitive load was similar
in overt and covert response conditions. Results from the
BOLD study indicate that brain regions participating in
selective visual attention and in the selection of motor
programs involved in speech were activated more by the
Stroop task than by the baseline tasks. The neural substrate
involved in the resolution of the perceptual and motor
conflicts elicited by the Stroop Color–Word task
does not appear to be a single brain region. Rather, a
network of brain regions is implicated, with separate regions
within this system supporting distinct functions. (JINS,
1999, 5, 308–319.)
A model of rural conflict: violence and land reform policy in Brazil
Authors: ALSTON LEE J. , LIBECAP GARY D. , MUELLER BERNARDO
Published: July 2002

This paper analyzes the underlying determinants of rural land conflicts in Brazil involving squatters, landowners, the federal government, the courts and INCRA, the land reform agency. A model is presented whereby squatters and landowners strategically choose to engage in violence. Landowners use violence as a means of increasing the likelihood of successful eviction of squatters, and squatters use violence to increase the probability that the farm will be expropriated in their favor as part of the government's land reform program. The model's predictions are tested using state level data for Brazil for 22 states from 1988 through 1995. It is shown that the government's land reform policy, which is based on expropriation and settlement projects, paradoxically may be encouraging both sides to engage in more violence, rather than reducing conflicts.
Developing an Autism
Assessment Service II: Analysis
of the First 81 Cases Seen
Authors: Moore Vanessa , Titcomb Josie , Johnson Chris , Cronk Elaine , Baker Sue , Thysson Laura , Rolles Chris
Published: July 2002

This paper presents an analysis of the first 81 cases seen in the
recently
established assessment service for children with autism and related
disorders in Southampton. The children presenting for assessment are
described in terms of a number of biographical, educational, behavioural,

and medical features and the characteristics of our sample are compared

with published findings. The future development of the service is
considered in the light of current developments and common features and

concerns of the families seen.
FINANCIAL INTERMEDIATION AND AGGREGATE FLUCTUATIONS:
A QUANTITATIVE ANALYSIS
Authors: Cooper Russell , Ejarque João
Published: July 2002

We investigate the quantitative behavior of business-cycle models in which the
intermediation process acts either as a source of fluctuations or as a
propagator of real shocks. In neither case do we find convincing evidence that
the intermediation process is an important element of aggregate fluctuations.
For an economy driven by intermediation shocks, consumption is not smoother than
output, investment is negatively correlated with output, variations in the
capital stock are quite large, and interest rates are procyclical. The model
economy thus fails to match unconditional moments for the U.S. economy. We also
structurally estimate parameters of a model economy in which intermediation and
productivity shocks are present, allowing for the intermediation process to
propagate the real shock. The unconditional correlations are closer to those
observed only when the intermediation shock is relatively
unimportant.
A MIXED BLESSING
Authors: Gylfason Thorvaldur , Herbertsson Tryggvi Thor , Zoega Gylfi
Published: July 2002

This paper diagnoses the symptoms of the Dutch disease in a two-sector
stochastic endogenous growth model. A productive, low-skill-intensive
primary sector causes the currency to appreciate in real terms, thus
hampering the development of a high-skill-intensive secondary sector and
thereby reducing growth. Moreover, the volatility of the primary sector
generates real-exchange-rate uncertainty and may thus reduce investment and
learning in the secondary sector and hence also growth. Cross-sectional and
panel regressions based on data for 125 countries in the period 1960–1992
confirm a statistically significant inverse relationship between the size of
the primary sector and economic growth, but not between the volatility of
the real exchange rate and growth.
DNA evidence for elephant social behaviour breakdown in Queen Elizabeth National Park, Uganda
Authors: Nyakaana Silvester , Abe Eve L. , Arctander Peter , Siegismund Hans R.
Published: July 2002

Elephant social structure is matrilineal, with family units composed only of maternally related females and their juvenile offspring, while adult males are mostly solitary and seldom congregate into bachelor herds. In such a social structure, we expect females in the same family unit to have the same mitochondrial genome, which may or may not differ from that of individuals in other family units in the population. Such social structuring also results in the mating males and females having different allele frequencies at nuclear microsatellite loci. This is manifested as an excess of heterozygotes relative to the expected Hardy‐Weinberg proportions, a phenomenon which maintains genetic variation within the population by minimizing inbreeding. We analyzed mitochondrial nucleotide sequences and allele frequencies at four microsatellite loci in nine family units of the African elephant (Loxodonta africana) in Queen Elizabeth National Park and found more than one distinct mitochondrial genotype in three of the family units and no significant excess heterozygosity at microsatellite loci in eight of the families. We interpreted these findings as an indication of a breakdown in social structure of this population caused by social stress due to factors like excessive poaching that has taken place in this national park over the last three decades. Ecological and management implications of these findings for elephant populations are discussed.
Photobiological uncertainties in the Archaean and post-Archaean world
Authors: Cockell Charles S.
Published: July 2002

The notion that ultraviolet (UV) fluxes, and thus biologically weighted irradiances, were higher on Archaean Earth than on present-day Earth has been a pervasive influence on thinking concerning the nature of early Earth. It directly influences calculations concerning protection strategies that may or may not have been required by early life. Our knowledge of the Earth's changing UV radiation climate over time depends upon our knowledge of a diversity of factors, the magnitudes of which are uncertain. Here these uncertainties are explored. During the Archaean Era, calculations of the surface photobiological environment span a three order of magnitude difference in DNA-damage weighted irradiances with consequences for our assumptions concerning the environment for exposed surface life and the role of UV radiation as a mutagen. These differences are primarily caused by uncertainties in the concentrations of trace gases and the partial pressures of carbon dioxide and nitrogen that affect scattering in the atmosphere. To a lesser extent, the luminosity of the Sun in the UV region is also a factor. During the Proterozoic and Phanerozoic, when we know that an ozone column existed, these uncertainties drop to two orders of magnitude and are primarily caused by poor knowledge about the frequency and atmospheric effects of potentially ozone-depleting agents such as volcanism, impact events and supernovae explosions as well as the effects of global temperatures on ozone concentrations and thus surface UV irradiance. Changes in other atmospheric constituents during this time have less of an effect on photobiological consequences, which include a Palaeozoic oxygen pulse. Understanding the cause of photobiological uncertainties and their consequences constitutes a current challenge for atmospheric chemists and photobiologists.
Mutation of a Drosophila gamma tubulin ring complex subunit encoded by discs degenerate-4 differentially disrupts centrosomal protein localization
Authors: Barbosa Vitor , Yamamoto Rochele R. , Henderson Daryl S. , Glover David M.
Published: July 2002

We have cloned the Drosophila gene discs degenerate-4 (dd4) and find that it encodes a component of the γ-tubulin ring complex (γTuRC) homologous to Spc98 of budding yeast. This provides the first opportunity to study decreased function of a member of the γ-tubulin ring complex, other than γ-tubulin itself, in a metazoan cell. γ-tubulin is no longer at the centrosomes but is dispersed throughout dd4 cells and yet bipolar metaphase spindles do form, although these have a dramatically decreased density of microtubules. Centrosomin (CNN) remains in broad discrete bodies but only at the focused poles of such spindles, whereas Asp (abnormal spindleprotein) is always present at the presumptive minus ends of microtubules, whether or not they are focused. This is consistent with the proposed role of Asp in coordinating the nucleation of mitotic microtubule organizing centers. The centrosome associated protein CP190 is partially lost from the spindle poles in dd4cells supporting a weak interaction with γ-tubulin, and the displaced protein accumulates in the vicinity of chromosomes. Electron microscopy indicates not only that the poles of dd4 cells have irregular amounts of pericentriolar material, but also that they can have abnormal centrioles. In six dd4 cells subjected to serial sectioning centrioles were missing from one of the two poles. This suggests that in addition to its role in nucleating cytoplasmic and spindle microtubules, the γTuRC is also essential to the structure of centrioles and the separation of centrosomes.
The function of Xenopus Bloom's syndrome protein homolog (xBLM) in DNA replication
Authors: Liao Shuren , Graham Jeanine , Yan Hong
Published: July 2002

The Bloom's syndrome gene (BLM) plays a pivotal role in the maintenance of genomic stability in somatic cells. It encodes a DNA helicase (BLM) of the RecQ family, but the exact function of BLM remains elusive. To study this question, we have cloned the BLM homolog of the frog Xenopus laevis (xBLM) and have raised antibodies to it. Immunodepletion of xBLM from a Xenopusegg extract severely inhibits the replication of DNA in reconstituted nuclei. Moreover, the inhibition can be rescued by the addition of the recombinant xBLM protein. These results provide the first direct evidence that BLM plays an important role in DNA replication, suggesting that Bloom's syndrome may be the consequence of defective DNA replication.
Interactions with Costal2 and Suppressor of fused regulate nuclear translocation and activity of Cubitus interruptus
Authors: Wang Gelin , Amanai Kazuhito , Wang Bing , Jiang Jin
Published: July 2002

The Hedgehog (Hh) family of secreted proteins controls many aspects of growth and patterning in animal development. InDrosophila, Hh acts by preventing the formation of a truncated repressor form of Cubitus interruptus (Ci) and stimulating the transcriptional activity of full-length Ci. Here, we provide evidence that Costal2 (Cos2) and Suppressor of Fused [Su(fu)] inhibit Ci by tethering it in the cytoplasm, whereas Hh induces nuclear translocaltion of Ci through Fused (Fu). We have identified a 125 amino acid domain in the C-terminal part of Ci that mediates response to Cos2 inhibition. We show that Cos2 binds Ci, prevents its nuclear import, and inhibits its activity via this domain. We also provide evidence that Su(fu) regulates Ci through two distinct mechanisms: (1) Su(fu) blocks Ci nuclear import through the N-terminal region of Ci , and (2) it inhibits the activity of Ci through a mechanism independent of Ci nuclear translocation. Finally, we show that Cos2 is required for transducing high levels of Hh signaling activity, and it does so by alleviating the blockage of Ci activity imposed by Su(fu).
Ablation of the Retinoblastoma gene family deregulates G1 control causing immortalization and increased cell turnover under growth-restricting conditions
Authors: Dannenberg Jan-Hermen , van Rossum Agnes , Schuijff Leontine , te Riele Hein
Published: July 2002

The retinoblastoma suppressor pRB belongs to the family of so-called pocket proteins, which also includes p107 and p130. These proteins may functionally overlap in cell cycle control and tumor suppression. We have generated an isogenic set of embryonic stem (ES) cell lines carrying single or compound loss-of-function mutations in theRb gene family, including a cell line completely devoid of all three pocket proteins. None of the knockout combinations affected the growth characteristics of ES cells; however, concomitant ablation of all three pocket proteins strongly impaired their differentiation capacity. For the generated genotypes, primary mouse embryonic fibroblasts (MEFs) also were obtained. While inactivation ofRb alone did not alleviate the senescence response of MEFs, pRB/p107-deficient MEFs, after having adapted to in vitro culturing, continued to proliferate at modest rate. Additional ablation of p130 rendered MEFs completely insensitive to senescence-inducing signals and strongly increased their proliferation rate. Although triple-knockout MEFs retained anchorage dependence, they lacked proper G1control and showed increased cell turnover under growth-inhibiting conditions.
Functional interactions between BRCA1 and the checkpoint kinase ATR during genotoxic stress
Authors: Tibbetts Randal S. , Cortez David , Brumbaugh Kathryn M. , Scully Ralph , Livingston David , Elledge Stephen J. , Abraham Robert T.
Published: July 2002

The BRCA1 gene encodes a tumor suppressor that is mutated in 50% of familial breast cancers. The BRCA1 protein has been implicated in the DNA damage response, as DNA damage induces the phosphorylation of BRCA1 and causes its recruitment into nuclear foci that contain DNA repair proteins. The ataxia-telangiectasia-mutated (ATM) gene product controls overall BRCA1 phosphorylation in response to γ-irradiation (IR). In this study, we show that BRCA1 phosphorylation is only partially ATM dependent in response to IR and ATM independent in response to treatment with UV light, or the DNA replication inhibitors hydroxyurea (HU) and aphidicolin (APH). We provide evidence that the kinase responsible for this phosphorylation is the ATM-related kinase, ATR. ATR phosphorylates BRCA1 on six Ser/Thr residues, including Ser 1423, in vitro. Increased expression of ATR enhanced the phosphorylation of BRCA1 on Ser 1423 following cellular exposure to HU or UV light, whereas doxycycline-induced expression of a kinase-inactive ATR mutant protein inhibited HU- or UV light-induced Ser 1423 phosphorylation in GM847 fibroblasts, and partially suppressed the phosphorylation of this site in response to IR. Thus, ATR, like ATM, controls BRCA1 phosphorylation in vivo. Although ATR isolated from DNA-damaged cells does not show enhanced kinase activity in vitro, we found that ATR responds to DNA damage and replication blocks by forming distinct nuclear foci at the sites of stalled replication forks. Furthermore, ATR nuclear foci overlap with the nuclear foci formed by BRCA1. The dramatic relocalization of ATR in response to DNA damage points to a possible mechanism for its ability to enhance the phosphorylation of substrates in response to DNA damage. Together, these results demonstrate that ATR and BRCA1 are components of the same genotoxic stress-responsive pathway, and that ATR directly phosphorylates BRCA1 in response to damaged DNA or stalled DNA replication.
casanova encodes a novel Sox-related protein necessary and sufficient for early endoderm formation in zebrafish
Authors: Kikuchi Yutaka , Agathon Antoine , Alexander Jonathan , Thisse Christine , Waldron Steven , Yelon Deborah , Thisse Bernard , Stainier Didier Y.R.
Published: July 2002

Early endoderm formation in zebrafish requires at least three loci that function downstream of Nodal signaling but upstream of the early endodermal marker sox17: bonnie and clyde (bon), faust (fau), and casanova (cas). cas mutants show the most severe phenotype as they do not form any gut tissue and lack all sox17 expression. Activation of the Nodal signaling pathway or overexpression of Bon or Fau/Gata5 fails to restore anysox17 expression in cas mutants, demonstrating thatcas plays a central role in endoderm formation. Here we show that cas encodes a novel member of the Sox family of transcription factors. Initial cas expression appears in the dorsal yolk syncytial layer (YSL) in the early blastula, and is independent of Nodal signaling. In contrast, endodermal expression ofcas, which begins in the late blastula, is regulated by Nodal signaling. Cas is a potent inducer of sox17 expression in wild-type embryos as well as in bon and fau/gata5mutants. Cas is also a potent inducer of sox17 expression inMZoep mutants, which cannot respond to Nodal signaling. In addition, ectopic expression of cas in presumptive mesodermal cells leads to their transfating into endoderm. Altogether, these data indicate that Cas is the principal transcriptional effector of Nodal signaling during zebrafish endoderm formation.
Oct4 distribution and level in mouse clones: consequences for pluripotency
Authors: Boiani Michele , Eckardt Sigrid , Schöler Hans R. , McLaughlin K. John
Published: July 2002

Somatic cell clones often fail at a developmental stage coincident with commencement of differentiation. The transcription factor Oct4 is expressed during cleavage stages and is essential for the differentiation of the blastocyst. Oct4 expression becomes restricted to the inner cell mass and epiblast. After gastrulation Oct4 is active only in germ cells and is silent in somatic cells. Here,Oct4 and an Oct4–GFP transgene were used as markers for which gene reprogramming could be directly related to the developmental potential of somatic cell clones. Cumulus cell clones initiated Oct4 expression at the correct stage but showed an incorrect spatial expression in the majority of blastocysts. The ability of clones to form outgrowths was reduced, and the outgrowths had low or even undetectable levels of Oct4 RNA or GFP. The quality of GFP signals in blastocysts correlated with the ability to generate outgrowths that maintain GFP expression and the frequency of embryonic stem (ES) cell derivation. Abnormal Oct4 expression in clones is either directly or indirectly caused by reprogramming errors and is indicative of a general failure to reset the genetic program. The abnormal Oct4 expression may be associated with aberrant expression of other crucial developmental genes, leading to abnormalities at various embryonic stages. Regardless of other genes, the variations observed in Oct4 levels alone account for the majority of failures currently observed for somatic cell cloning.
Genie—Gene Finding in Drosophila melanogaster
Authors: Reese Martin G. , Kulp David , Tammana Hari , Haussler David
Published: July 2002

A hidden Markov model-based gene-finding system calledGenie was applied to the genomic Adh region inDrosophila melanogaster as a part of the Genome Annotation Assessment Project (GASP). Predictions from three versions of theGenie gene-finding system were submitted, one based on statistical properties of coding genes, a second included EST alignment information, and a third that integrated protein sequence homology information. All three programs were trained on the providedDrosophila training data. In addition, promoter assignments from an integrated neural network were submitted. The gene assignments overlapped >90% of the 222 annotated genes and 26 possibly novel genes were predicted, of which some might be overpredictions. The system correctly identified the exon boundaries of 70% of the exons in cDNA-confirmed genes and 77% of the exons with the addition of EST sequence alignments. The best of the three Geniesubmissions predicted 19 of the annotated 43 gene structures entirely correct (44%). In the promoter category, only 30% of the transcription start sites could be detected, but by integrating this program as a sensor into Genie the false-positive rate could be dropped to 1/16,786 (0.006%). The results of the experiment on the long contiguous genomic sequence revealed some problems concerning gene assembly in Genie. The results were used to improve the system. We show that Genie is a robust hidden Markov model system that allows for a generalized integration of information from different sources such as signal sensors (splice sites, start codon, etc.), content sensors (exons, introns, intergenic) and alignments of mRNA, EST, and peptide sequences. The assessment showed that Genie could effectively be used for the annotation of complete genomes from higher organisms.
PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
Authors: Schwartz Scott , Zhang Zheng , Frazer Kelly A. , Smit Arian , Riemer Cathy , Bouck John , Gibbs Richard , Hardison Ross , Miller Webb
Published: July 2002

PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. Positions along the horizontal axis can be labeled with features such as exons of genes and repetitive elements, and colors can be used to clarify and enhance the display. The web site also provides a plot of the locations of those segments in both species (similar to a dot plot). PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of information that can be inferred (e.g., protein-coding regions andcis-regulatory elements) depend on the level of conservation and the time and divergence rate since the separation of the species. Gene regulatory elements are often detectable as similar, noncoding sequences in species that diverged as much as 100–300 million years ago, such as humans and mice, Caenorhabditis elegans andC. briggsae, or Escherichia coli andSalmonella spp. PipMaker supports analysis of unfinished or “working draft” sequences by permitting one of the two sequences to be in unoriented and unordered contigs.
Phylogenetic Origin of Human Chromosomes 7, 16, and 19 and their Homologs in Placental Mammals
Authors: Richard Florence , Lombard Martine , Dutrillaux Bernard
Published: July 2002

The origin of human chromosomes (HSA) 7, 16, and 19 was studied by comparing data obtained from chromosome banding, chromosome painting, and gene mapping in species belonging to 11 orders of placental mammals (Eutherians). This allowed us to propose the reconstruction of their presumed ancestral forms. The HSA7 homologs were composed of two parts, the largest forming an acrocentric. The smallest formed one arm of a small submetacentric; the other arm was composed of sequences homologous to the short arm of HSA16 (HSA16p). The sequences homologous to the long arm of HSA16 (HSA16q) were associated with sequences homologous to the long arm of HSA19 (HSA19q) and formed another submetacentric. From their origin, these chromosomes underwent the following rearrangements to give rise to current human chromosomes: centromeric fission of the two submetacentrics in ancestors of all primates (∼80 million years ago); fusion of the HSA19p and HSA19q sequences, originating the current HSA19, in ancestors of all simians (∼55 million years ago); fusions of the HSA16p and HSA16q sequences, originating the current HSA16 and the two components of HSA7 before the separation of Cercopithecoids and Hominoids (∼35 million years ago); and finally, pericentric and paracentric inversions of the homologs to HSA7 after the divergence of orangutan and gorilla, respectively. Thus, compared with HSA16 and HSA19, HSA7 is a fairly recent chromosome shared by man and chimpanzee only.
Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes
Authors: McGuire Abigail Manson , Hughes Jason D. , Church George M.
Published: July 2002

Regulatory motifs can be found by local multiple alignment of upstream regions from coregulated sets of genes, or regulons. We searched for regulatory motifs using the program AlignACE together with a set of filters that helped us choose the motifs most likely to be biologically relevant in 17 complete microbial genomes. We searched the upstream regions of potentially coregulated genes grouped by three methods: (1) genes that make up functional pathways; (2) genes homologous to regulons from a well-studied species (Escherichia coli); and (3) groups of genes derived from conserved operons. This last group is based on the observation that genes making up homologous regulons in different species are often assorted into coregulated operons in different combinations. This allows partial reconstruction of regulons by looking at operon structure across several species. Unlike other methods for predicting regulons, this method does not depend on the availability of experimental data other than the genome sequence and the locations of genes. New, statistically significant motifs were found in the genome sequence of each organism using each grouping method. The most significant new motif was found upstream of genes in the methane-metabolism functional group inMethanobacterium thermoautotrophicum. We found that at least 27% of the known E. coli DNA-regulatory motifs are conserved in one or more distantly related eubacteria. We also observed significant motifs that differed from the E. coli motif in other organisms upstream of sets of genes homologous to known E. coli regulons, including Crp, LexA, and ArcA in Bacillus subtilis; four anaerobic regulons in Archaeoglobus fulgidus (NarL, NarP, Fnr, and ModE); and the PhoB, PurR, RpoH, and FhlA regulons in other archaebacterial species. We also used motif conservation to aid in finding new motifs by grouping upstream regions from closely related bacteria, thus increasing the number of instances of the motif in the sequence to be aligned. For example, by grouping upstream sequences from three archaebacterial species, we found a conserved motif that may regulate ferrous ion transport that was not found in individual genomes. Discovery of conserved motifs becomes easier as the number of closely related genome sequences increases.
Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels
Authors: Lin Jimmy , Gerstein Mark
Published: July 2002

We built whole-genome trees based on the presence or absence of particular molecular features, either orthologs or folds, in the genomes of a number of recently sequenced microorganisms. To put these genomic trees into perspective, we compared them to the traditional ribosomal phylogeny and also to trees based on the sequence similarity of individual orthologous proteins. We found that our genomic trees based on the overall occurrence of orthologs did not agree well with the traditional tree. This discrepancy, however, vanished when one restricted the tree to proteins involved in transcription and translation, not including problematic proteins involved in metabolism. Protein folds unite superficially unrelated sequence families and represent a most fundamental molecular unit described by genomes. We found that our genomic occurrence tree based on folds agreed fairly well with the traditional ribosomal phylogeny. Surprisingly, despite this overall agreement, certain classes of folds, particularly all-beta ones, had a somewhat different phylogenetic distribution. We also compared our occurrence trees to whole-genome clusters based on the composition of amino acids and di-nucleotides. Finally, we analyzed some technical aspects of genomic trees—e.g., comparing parsimony versus distance-based approaches and examining the effects of increasing numbers of organisms. Additional information (e.g. clickable trees) is available from http://bioinfo.mbb.yale.edu/genome/trees.
SAGEmap: A Public Gene Expression Resource
Authors: Lash Alex E. , Tolstoshev Carolyn M. , Wagner Lukas , Schuler Gregory D. , Strausberg Robert L. , Riggins Gregory J. , Altschul Stephen F.
Published: July 2002

We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of this resource, SAGEmap, are located at http://www.ncbi.nlm.nih.gov/sage andftp://ncbi.nlm.nih.gov/pub/sage, respectively. We herein describe SAGE data submission procedures, the construction and characteristics of SAGE tags to gene assignments, the derivation and use of a novel statistical test designed specifically for differential-type analyses of SAGE data, and the organization and use of this resource.
Genomic Sequence Analysis of the Mouse Naip Gene Array
Authors: Endrizzi Matthew G. , Hadinoto Vey , Growney Joseph D. , Miller Webb , Dietrich William F.
Published: July 2002

A mouse locus called Lgn1 determines differences in macrophage permissiveness for the intracellular replication ofLegionella pneumophila. The only regional candidate genes for this phenotype difference lie within a cluster of closely linked paralogs of the Neuronal Apoptosis Inhibitory Protein (Naip) gene. Previous genetic and physical mapping of the Lgn1phenotype narrowed it to an interval containing only Naip2and Naip5, suggesting that there is not complete functional overlap among the mouse Naip loci. In order to gather more information about polymorphisms among the Naipgenes of the 129 mouse haplotype, we have determined the genomic sequence of a substantial portion of the 129 Naip gene array. We have constructed an evolutionary model for the expansion of theNaip gene array from a single progenitor Naip gene. This model predicts the presence of two distinct families ofNaip paralogs: Naip1/2/3 and Naip4/5/6/7. Unlike the divergences among all the other Naip paralogs, the splits among Naip4, Naip5, Naip6, andNaip7 occurred relatively recently. The high degree of sequence conservation within the Naip4/5/6/7 family increases the likelihood of functional overlap among these genes.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF242431-AF242435.]