bluuebunny/crossref_metadata_2025 huggingface dataset:
Scale domains of abundance amongst species of mammalian Carnivora
Authors: SMALLWOOD K. SHAWN
Published: July 2002

The spatial requirements of populations ought to be central to developing conservation strategies and ecological theory, but they are difficult to identify from the published collection of reported population estimates. Transforming population estimates into density and log values may have clouded recognition of the discontinuous relationship that exists between abundance estimates and the areas within which they were made. I used abundance estimates of terrestrial mammalian Carnivora to identify scale domains of abundance. In scale domain A, the study areas were too small to include all the individuals of the population, and abundance estimates increased propor-tionally with study area size. Scale domain B included high variation in abundance estimates, but these estimates no longer increased with increasing size of study area as they did in domain A. I refer to the smallest area in the scale domain B as the 'threshold area' (the minimum area known to support a population of the particular species). The abundance in scale domain B averaged 52 individuals amongst all but three outlier species. Scale domains C and D were also identified, and included much larger study areas and substantially larger abundance estimates.

The threshold area is the first empirically-derived representation of the minimum space used by populations of each species. However, nearly half of all carnivore abundance estimates were made in areas smaller than the threshold area, and only 4% could be used to represent transitions between scale domains B, C and D. The remainder varied within domains B, C and D due to variation in environmental conditions and research methods. Most comparisons of density between sites and between species have been made without considering whether the estimates represented the true population or some collection of individuals more or less abundant than the population. Threshold area can be used as a standard area against which to estimate and compare population density, in lieu of more appropriately comparing estimates of region-wide density, which generally do not yet exist. Also, threshold area could be predicted with reasonable error rates based on a typical species' body mass, brain mass and home range size. Therefore, conservation biologists may now have a tool to identify the minimum habitat areas needed to conserve populations of carnivore species, and theoretical ecologists can relate ecological space at the population level to allometric variables.
Adaptive-growth-type 3D representation for configuration
design
Authors: TAURA TOSHIHARU , NAGASAKA ICHIRO
Published: July 2002

In this paper, the design of geometrical shapes
of function carriers and their layout in given space is
called configuration design. The constraint satisfaction
problem in configuration design may be difficult to solve
due to the lack of tight constraints and the countless
combinations of the layout; a diversity of solutions that
satisfy the constraints should be allowed. Therefore, to
allow such diversity, we directed our attention to developmental
processes in biology and proposed an adaptive-growth-type
3D representation based on evolutionary algorithms. Here,
the adaptive-growth-type means the shape expressed in the
process, which develops through interaction with an outside
environment, like shape generation of a living organism
in the natural world. The usefulness of the representation
was verified by applying it to the component layout problem
in the early stage of satellite design.
Surveillance of small round structured virus (SRSV) infection
in England and Wales, 1990–5
Authors: DEDMAN D. , LAURICHESSE H. , CAUL E. O. , WALL P. G.
Published: July 2002

Data from the national surveillance scheme for general outbreaks

of intestinal disease, and the
national laboratory reporting scheme were used to describe the epidemiology
of small round
structured virus (SRSV) infections in England and Wales. Between 1990 and
1995, there were
7492 laboratory reports of SRSV. Rates of reported illness were highest
among infants, young
children and the elderly. During 1992–5, some 707 SRSV outbreaks
were reported. Outbreaks
in hospital wards and residential facilities for the elderly accounted
for 76% of the total, and
annual numbers increased more than sixfold over the study period. There
were wide regional
variations in the numbers of SRSV outbreaks and laboratory reports. Both
sporadic cases and
outbreaks in the community are likely to be underestimated, but these passive
surveillance
systems provide an insight into the burden of SRSV infection among the
institutionalized
elderly.
Diarrhoea prevention in Bolivia through point-of-use water
treatment and safe storage: a promising new strategy
Authors: QUICK R. E. , VENCZEL L. V. , MINTZ E. D. , SOLETO L. , APARICIO J. , GIRONAZ M. , HUTWAGNER L. , GREENE K. , BOPP C. , MALONEY K. , CHAVEZ D. , SOBSEY M. , TAUXE R. V.
Published: July 2002

A novel water quality intervention that consists of point-of-use
water disinfection, safe storage
and community education was field tested in Bolivia. A total of 127 households
in two
periurban communities were randomized into intervention and control groups,
surveyed and
the intervention was distributed. Monthly water quality testing and weekly
diarrhoea
surveillance were conducted. Over a 5-month period, intervention households
had 44% fewer
diarrhoea episodes than control households (P=0·002).
Infants <1 year old (P=0·05) and
children 5–14 years old (P=0·01) in intervention
households had significantly less diarrhoea
than control children. Campylobacter was less commonly isolated from intervention
than
control patients (P=0·02). Stored water in intervention
households was less contaminated with
Escherichia coli than stored water in control households (P<0·0001).
Intervention households
exhibited less E. coli contamination of stored water and less
diarrhoea than control households.
This promising new strategy may have broad applicability for waterborne
disease prevention.
Psychosocial influences: Critiques, findings, and research needs
Authors: RUTTER MICHAEL
Published: July 2002

Nongenetic factors have a major influence on psychopathology. Knowledge on specific
psychosocial risk and protective mechanisms is more limited because of inadequate attention to
measurement issues, person effects on the environment, and the possibility of genetic mediation.
Nevertheless, a range of research strategies may be used to provide rigorous tests of causal
hypotheses; these have shown the importance of environmentally mediated risks. Challenges for
the future include greater use of such research strategies, improved measures of psychosocial
risks that can be applied to large samples, investigation of origins of risks, identification of
causes of time trends in levels of psychopathology, delineation of psychosocial effects on
lifetime liability, understanding of environmental effects on the organism, appreciation of
processes involved in developmental programming, and understanding of individual differences
in susceptibility.
Problem behavior: The double symptom of adolescence
Authors: SIEGEL ALEXANDER W. , SCOVILL LORI C.
Published: July 2002

In this article we address several issues regarding problem or antisocial behavior in

adolescents. First, we discuss conceptualizations of adolescent problem behavior to answer the

question “What do we think we know so far?” Then, we briefly characterize

current interventions designed to reduce these behaviors, and their relative success in doing so.

Next, we examine earlier attempts to prevent and ameliorate problem behavior (including juvenile

delinquency), situating them in the historical context of America from the turn of the century to

World War II. Here, we attempt to answer the questions “How did we get to where we

are?” and “How can we learn from the past?” Following this, we try to

answer the question “Where do we go from here?” and articulate some research

and policy implications relevant to developmental psychopathology that arise from these

considerations. We argue that problem behavior is viewed most productively in its double aspect,

which John Hughlings Jackson called a “double symptom,” with the positive aspect

of the symptom reflecting adolescents' attempts to satisfy their developmental needs.
Talking about self and other: Emergence of an internal state lexicon in young children with

Down syndrome
Authors: BEEGHLY MARJORIE , CICCHETTI DANTE
Published: July 2002

The ability to talk about the internal states (IS) of self and other is an age-typical

development of early childhood that is thought to reflect young children's emergent

self–other understanding. This study examined the emergence of an IS lexicon in a

cross-sectional sample of young children with Down syndrome (DS) and a cognitively and

demographically comparable group of normally developing (ND) children. Children's IS

lexicons were derived from transcripts of their spontaneous utterances during two laboratory

contexts: a mother–child emotions picture book task and semistructured play. Children

with DS produced significantly fewer IS words and fewer IS word types than their MA-matched

counterparts. Controlling for corpus size, children with DS also were less likely to attribute

internal states to themselves and were more context bound in their use of IS language. In

addition, children with DS also differed from ND children in the semantic content of their IS

language, with proportionately higher rates of affective words and lower rates for words about

volition, ability, and cognition. For both the DS and ND groups, individual differences in IS

language production were significantly related to general expressive language skills. However,

dissociations were observed for the relation between children's IS word production and

nonverbal symbolic play skills in the two groups. These findings suggest some degree of

disorganization at the interface among symbolic domains for children with DS. Because IS

language is critical to the regulation of social interaction and an early index of self–other

differentiation and understanding, children with DS may be at risk for later compromises in

self-organization.
Prenatal and perinatal influences on risk for psychopathology in childhood and
adolescence
Authors: ALLEN NICHOLAS B. , LEWINSOHN PETER M. , SEELEY JOHN R.
Published: July 2002

The relationship between a range of prenatal and perinatal events and risk for
psychopathology in offspring was examined. Prenatal and perinatal events investigated included
maternal experiences, health, and substance use during pregnancy, obstetric complications,
feeding practices, and infant health during the first year of life. Offspring diagnosis was based on
structured interviews conducted with 579 adolescents on two occasions. Risk for later
psychopathology was associated with a number of prenatal and perinatal factors. Major
depression was associated with not being breast fed and maternal emotional problems during the
pregnancy. Anxiety was chiefly associated with fever and illness during the first year of life and
maternal history of miscarriage and stillbirth. Disruptive behavior disorder was associated with
poor maternal emotional health during the pregnancy and birth complications. Risk for substance
use disorder was associated with maternal use of substances during the pregnancy. Mediating
effects of maternal depression, maternal–child conflict, and physical symptoms in the
child, and moderating effects of gender of child and parental education were also evaluated. The
limitations of this study are discussed and future research directions are suggested.
The role of child maltreatment and attachment style in adolescent relationship
violence
Authors: WEKERLE CHRISTINE , WOLFE DAVID A.
Published: July 2002

Utilizing attachment theory as a basis for conceptualizing close relationships among
adolescents, this study investigated two important relationship risk factors (child maltreatment,
and adolescent self-perceived insecure attachment style) as predictors of
“offender” and “victim” experiences in youth relationships. In
addition to considering the influence of these risk factors, we further considered their interaction
in predicting conflict in close relationships. Of interest was the extent to which attachment styles
may function as a moderator of the relationship between childhood abuse and current abuse in
teen close relationships. High school students (N = 321) in grades 9 and 10 completed
questionnaires tapping their histories of maltreatment, currently viewed styles of attachment, and
conflict in close relationships over the past 6 months. Maltreatment alone emerged as the most
consistent predictor, accounting for 13–18% of the variance in male's physically,
sexually, and verbally abusive behaviors; in contrast, it was not highly predictive of
female's abusive behaviors. Maltreatment was predictive of victimization experiences for
both males and females. Attachment style did not substantially add to the prediction of
relationship conflict beyond maltreatment; however, avoidant attachment style emerged
repeatedly as a significant predictor of female abusiveness and victimization. Attachment
self-ratings were found to function as a moderator of child maltreatment in predicting primarily
male coercive behavior towards a relationship partner as well as predicting male's
experience of coercion from a partner. Thus, the presence of childhood maltreatment and
adolescent self-perceived insecure attachment style applies predominantly to male youth. The
implication of these gender differences for understanding relationship violence is discussed.
Neighborhood influences and child development: A prospective study of substance
abusers' offspring
Authors: LUTHAR SUNIYA S. , CUSHING GRETTA
Published: July 2002

In this 2-year prospective study, psychopathology and competence among drug
abusers' offspring were examined in relation to characteristics of their neighborhoods. The
sample consisted of 77 children of cocaine and opioid addicts with a mean age of 12.3 years at
baseline and 14.2 years at follow-up. Outcomes examined included psychiatric diagnoses,
dimensional symptom indices, and aspects of everyday behavioral competence. Links involving
neighborhood variables varied by gender, wherein boys reflected greater deterioration than girls
when neighborhoods had high crime rates and high proportions of low-income households.
Conversely, girls appeared to benefit more than boys from the presence of professional adults in
the community. Overall, neighborhood indicators accounted for more variability in changes in
child adjustment over time than did indices of maternal psychopathology. Findings are discussed
in terms of developmental changes in the salience of exosystemic and familial forces, and
implications for interventions are outlined.
On the bisimulation proof method
Authors: SANGIORGI DAVIDE
Published: July 2002

The most popular method for establishing bisimilarities

among processes is to exhibit bisimulation relations. By definition,
[Rscr ] is a bisimulation relation if [Rscr ] progresses to
[Rscr ] itself, i.e., pairs of processes in [Rscr ]
can match each other's actions and their derivatives are again in
[Rscr ].

We study generalisations of the method aimed at reducing the size of
the relations to be
exhibited and hence relieving the proof work needed to establish bisimilarity
results. We
allow a relation [Rscr ] to progress to a different relation [Fscr ] ([Rscr ]),
where
[Fscr ] is a function on relations. Functions that can be safely used in
this way
(i.e., such that if [Rscr ] progresses to [Fscr ] ([Rscr ]), then
[Rscr ]
only includes pairs of bisimilar processes) are sound. We give
a simple
condition that ensures soundness. We show that the class of sound functions
contains
non-trivial functions and we study the closure properties of the class
with respect to various
important function constructors, like composition, union and iteration.
These properties
allow us to construct sophisticated sound functions – and hence sophisticated
proof
techniques for bisimilarity – from simpler ones.

The usefulness of our proof techniques is supported by various non-trivial
examples
drawn from the process algebras CCS and π-calculus. They include the
proof of the unique
solution of equations and the proof of a few properties of the replication
operator. Among
these, there is a novel result that justifies the adoption of a simple
form of prefix-guarded
replication as the only form of replication in the π-calculus.
The numerical analysis of bifurcation problems with application to fluid mechanics
Authors: Cliffe K. A. , Spence A. , Tavener S. J.
Published: July 2002

In this review we discuss bifurcation theory in a Banach space setting using
the singularity theory developed by Golubitsky and Schaeffer to classify bifurcation
points. The numerical analysis of bifurcation problems is discussed
and the convergence theory for several important bifurcations is described for
both projection and finite difference methods. These results are used to provide
a convergence theory for the mixed finite element method applied to the
steady incompressible Navier–Stokes equations. Numerical methods for the
calculation of several common bifurcations are described and the performance
of these methods is illustrated by application to several problems in fluid mechanics.
A detailed description of the Taylor–Couette problem is given, and
extensive numerical and experimental results are provided for comparison and
discussion.
On the relation between the wet delay and the integrated precipitable water vapour in the European atmosphere
Authors: Emardson T Ragne , Derks Henrico J P
Published: July 2002

A ground‐based network of Global Positioning System (GPS) receivers can be used to determine the excess propagation path of the GPS signals. Using surface pressure data it is possible to derive the excess path caused by water vapour. This quantity is often referred to as the wet delay. We have studied the relationship between the wet delay and the integrated precipitable water vapour (IPWV), based on more than 120 000 radiosonde profiles from 38 sites in Europe. We have studied four different models based on the surface temperature, the latitude of the site, and the time of the year in different combinations. The accuracies of the models have been evaluated and also compared with the accuracy resulting from the use of published model parameters derived from radiosonde data acquired in the United States. The models using the surface temperature data yielded the smallest relative root mean square errors of 1.14% and 1.15% respectively. We find that the accuracy can sometimes be further improved, typically down to 1.02%, by adjusting the values of the model parameters to the area or site of interest. Copyright © 2000 Royal Meteorological Society
The dry intrusion perspective of extra‐tropical cyclone development
Authors: Browning K A
Published: July 2002

The dry intrusion is a coherent region of air descending from near tropopause‐level. It often has a clear signature in satellite imagery, especially in the water vapour channel, where it is seen as a ‘dark zone’. Parts of dry intrusions are characterised by high potential vorticity and, upon approaching a low‐level baroclinic zone, rapid cyclogenesis may be expected to ensue. The leading edges of dry intrusions are defined by cold θw‐fronts (moisture fronts). In some places the dry intrusion undercuts rearward‐ascending warm air to give an ana‐cold front. In other places it overruns the warm air to produce an upper cold θw‐front in advance of the surface cold frontHere the dry intrusion is associated with the generation of potential instability and its eventual release as showers or thunderstorms. Identification of dry intrusions provides the forecaster with additional nowcasting evidence that is especially helpful when issuing severe weather warnings. The identification of water vapour dark zones associated with dry intrusions can also form the basis of methods for validating NWP models. Through their relationship to high potential vorticity, they can provide guidance for bogussing NWP models in situations of potentially severe weather. This article provides an introduction to the structure and behaviour of dry intrusions and their relationship to other aspects of extra‐tropical cyclones. Copyright © 2004 Royal Meteorological Society
Natural language question answering:
the view from here
Authors: HIRSCHMAN L. , GAIZAUSKAS R.
Published: July 2002

As users struggle to navigate the wealth of on-line information now available, the
need for automated question answering systems becomes more urgent. We need
systems that allow a user to ask a question in everyday language and receive an
answer quickly and succinctly, with sufficient context to validate the answer. Current
search engines can return ranked lists of documents, but they do not deliver answers
to the user.

Question answering systems address this problem. Recent successes have been
reported in a series of question-answering evaluations that started in 1999 as part
of the Text Retrieval Conference (TREC). The best systems are now able to answer
more than two thirds of factual questions in this evaluation.
PREDICTORS OF THERAPEUTIC FAILURE IN SLOT-MACHINE PATHOLOGICAL GAMBLERS FOLLOWING BEHAVIOURAL TREATMENT
Authors: Echeburúa Enrique , Fernández-Montalvo Javier , Báez Concepción
Published: July 2002

The aim of this paper was to determine the features of pathological gamblers who dropped out of the
treatment or relapsed within a one year follow-up period. The sample consisted of 69 patients selected according to
DSM-IV criteria. Results indicated that the only difference between the patients who dropped out of treatment and the
ones who completed was the level of state-anxiety. The former were more anxious than the latter. Predictive variables
for the therapeutic failure were the dissatisfaction with the treatment, the high level of alcohol consumption, and the
neuroticism as a personality variable. Implications of the study for clinical practice and future research in this field
are commented upon.
Old and New Neuropsychology Make a Mixed Bag
Authors: Donders Jacobus
Published: July 2002

The second edition of Clinician's Guide to
Neuropsychological Assessment is intended to be a graduate
level textbook dealing with the practice of neuropsychology.
The number of chapters has been expanded considerably, compared
to the first edition of this book. Most of the new contributions
are fairly up to date with the recent literature and pertain
to areas of applied neuropsychology that have shown considerable
growth over the past few years. In contrast, many of the
purportedly revised chapters that were also present in the first
edition are disappointing. For example, the chapter on
“Principles of Neuropsychological Interpretation”
appears to be an almost verbatim reprint of its 1994 counterpart
and fails to review any of the literature that has since then
developed with regard to issues such as reliability of change
in test scores (Sawrie et al., 1996), effects of financial
incentives (Binder & Rohling, 1996), or construct validity
of commonly used tests (Goldman et al., 1996).
A new verbal learning and memory test for English-
and Spanish-speaking older people
Authors: GONZÁLEZ HECTOR M. , MUNGAS DAN , REED BRUCE R. , MARSHALL SARAH , HAAN MARY N.
Published: July 2002

Word-list verbal learning and memory tests with appropriate
normative data can be highly sensitive to cognitive decline,
but there are significant limitations of such tests available
for use with older Hispanic and non-Hispanic people living
in the US. The purpose of this study was to (1) create
a new word-list learning and memory test in both English
and Spanish and, (2) validate it with respect to sensitivity
to cognitive impairment, and (3) develop statistical corrections
for the effects of significant demographic variables, including
ethnicity, language of administration, age, education,
and gender. A community dwelling sample of 801 English-
and Spanish-speaking older people was employed. Recall
on learning trials and the delayed recall trial of the
word-list learning test were strongly related to the Mini-Mental
State Examination (MMSE), moderately related to age, and
weakly related to gender and education. The relationship
of word-list variables and the MMSE did not significantly
differ across ethnicity/language groups. Regression coefficients
for demographic variables were used in a statistical correction
formula to adjust raw word-list scores, and then to develop
specific percentile cut-off values. (JINS, 2001,
7, 544–555.)
AN INTERVIEW WITH FRANCO MODIGLIANI
Authors: Barnett William A. , Solow Robert
Published: July 2002

Franco Modigliani's contributions in economics and finance have transformed both fields. Although many other major contributions in those fields have come and gone, Modigliani's contributions seem to grow in importance with time. His famous 1944 article on liquidity preference has not only remained required reading for generations of Keynesian economists but has become part of the vocabulary of all economists. The implications of the life-cycle hypothesis of consumption and saving provided the primary motivation for the incorporation of finite lifetime models into macroeconomics and had a seminal role in the growth in macroeconomics of the overlapping generations approach to modeling of Allais, Samuelson, and Diamond. Modigliani and Miller's work on the cost of capital transformed corporate finance and deeply influenced subsequent research on investment, capital asset pricing, and recent research on derivatives. Modigliani received the Nobel Memorial Prize for Economics in 1985.

In macroeconomic policy, Modigliani has remained influential on two continents. In the United States, he played a central role in the creation of a the Federal Reserve System's large-scale quarterly macroeconometric model, and he frequently participated in the semiannual meetings of academic consultants to the Board of Governors of the Federal Reserve System in Washington, D.C. His visibility in European policy matters is most evident in Italy, where nearly everyone seems to know him as a celebrity, from his frequent appearances in the media. In the rest of Europe, his visibility has been enhanced by his publication, with a group of distinguished European and American economists, of “An Economists' Manifesto on Unemployment in the European Union,” which was signed by a number of famous economists and endorsed by several others.

This interview was conducted in two parts on different dates in two different locations, and later unified. The initial interview was conducted by Robert Solow at Modigliani's vacation home in Martha's Vineyard. Following the transcription of the tape from that interview, the rest of the interview was conducted by William Barnett in Modigliani's apartment on the top floor of a high-rise building overlooking the Charles River near Harvard University in Cambridge, Massachusetts. Those concluding parts of the interview in Cambridge continued for the two days of November 5–6, 1999 with breaks for lunch and for the excellent espresso coffee prepared by Modigliani in an elaborate machine that would be owned only by someone who takes fine coffee seriously.

Although the impact that Modigliani has had on the economics and finance professions is clear to all members of those professions, only his students can understand the inspiration that he has provided to them. However, that may have been adequately reflected by Robert Shiller at Yale University in correspondence regarding this interview, when he referred to Modigliani as: “my hero.”
Analysis of the transcriptional program induced by Raf in epithelial cells
Authors: Schulze Almut , Lehmann Kerstin , Jefferies Harold B.J. , McMahon Martin , Downward Julian
Published: July 2002

Activation of the Raf/MAP kinase pathway is a critical event in tumorigenesis induced by RAS and other oncogenes, a major role of this signaling system being the regulation of cellular transcription factors. To address the contribution of MAP kinase mediated transcriptional changes to the transformed phenotype, we used an inducible form of Raf to analyze early changes in the transcription of some 6000 genes following activation of the kinase in a normal human breast epithelial cell line. Of the more than 120 significant changes in mRNA level detected, genes promoting cell proliferation, invasiveness, and angiogenesis featured prominently. Some of the most strongly induced genes encoded growth factors of the EGF family: Autocrine activation of the EGF receptor was shown to be responsible for the ability of Raf activation to protect these cells from apoptosis induced by detachment of cells from extracellular matrix (anoikis), which is a critical component of the transformed phenotype.
Functional selectivity of recombinant mammalian SWI/SNF subunits
Authors: Kadam Shilpa , McAlpine Glenn S. , Phelan Michael L. , Kingston Robert E. , Jones Katherine A. , Emerson Beverly M.
Published: July 2002

The SWI/SNF family of chromatin-remodeling complexes plays a key role in facilitating the binding of specific transcription factors to nucleosomal DNA in diverse organisms from yeast to man. Yet the process by which SWI/SNF and other chromatin-remodeling complexes activate specific subsets of genes is poorly understood. We show that mammalian SWI/SNF regulates transcription from chromatin-assembled genes in a factor-specific manner in vitro. The DNA-binding domains (DBDs) of several zinc finger proteins, including EKLF, interact directly with SWI/SNF to generate DNase I hypersensitivity within the chromatin-assembled β-globin promoter. Interestingly, we find that two SWI/SNF subunits (BRG1 and BAF155) are necessary and sufficient for targeted chromatin remodeling and transcriptional activation by EKLF in vitro. Remodeling is achieved with only the BRG1–BAF155 minimal complex and the EKLF zinc finger DBD, whereas transcription requires, in addition, an activation domain. In contrast, the BRG1–BAF155 complex does not interact or function with two unrelated transcription factors, TFE3 and NF-κB. We conclude that specific domains of certain transcription factors differentially target SWI/SNF complexes to chromatin in a gene-selective manner and that individual SWI/SNF subunits play unique roles in transcription factor–directed nucleosome remodeling.
Regulation of cellular growth by the Drosophila target of rapamycin dTOR
Authors: Zhang Hongbing , Stallock James P. , Ng Joyce C. , Reinhard Christoph , Neufeld Thomas P.
Published: July 2002

The TOR protein kinases (TOR1 and TOR2 in yeast; mTOR/FRAP/RAFT1 in mammals) promote cellular proliferation in response to nutrients and growth factors, but their role in development is poorly understood. Here, we show that the Drosophila TOR homolog dTOR is required cell autonomously for normal growth and proliferation during larval development, and for increases in cellular growth caused by activation of the phosphoinositide 3-kinase (PI3K) signaling pathway. As in mammalian cells, the kinase activity of dTOR is required for growth factor-dependent phosphorylation of p70 S6 kinase (p70S6K) in vitro, and we demonstrate that overexpression of p70S6K in vivo can rescue dTOR mutant animals to viability. Loss of dTOR also results in cellular phenotypes characteristic of amino acid deprivation, including reduced nucleolar size, lipid vesicle aggregation in the larval fat body, and a cell type-specific pattern of cell cycle arrest that can be bypassed by overexpression of the S-phase regulator cyclin E. Our results suggest that dTOR regulates growth during animal development by coupling growth factor signaling to nutrient availability.
Diethylstilbestrol regulates trophoblast stem cell differentiation as a ligand of orphan nuclear receptor ERRβ
Authors: Tremblay Gilles B. , Kunath Tilo , Bergeron Denis , Lapointe Line , Champigny Céline , Bader Jo-Ann , Rossant Janet , Giguère Vincent
Published: July 2002

The orphan nuclear receptor ERRβ is expressed in undifferentiated trophoblast stem cell lines and extraembryonic ectoderm, and genetic ablation of ERRβ results in abnormal trophoblast proliferation and precocious differentiation toward the giant cell lineage. Here, we show that the synthetic estrogen diethylstilbestrol (DES) promotes coactivator release from ERRβ and inhibits its transcriptional activity. Strikingly, treatment of trophoblast stem cells with DES led to their differentiation toward the polyploid giant cell lineage. In addition, DES-treated pregnant mice exhibited abnormal early placenta development associated with an overabundance of trophoblast giant cells and an absence of diploid trophoblast. These results define a novel pathway for DES action and provide evidence for steroidlike control of trophoblast development.
Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism
Authors: Mitsui Shigeru , Yamaguchi Shun , Matsuo Takuya , Ishida Yoshiki , Okamura Hitoshi
Published: July 2002

E4BP4, a basic leucine zipper transcription factor, contains a DNA-binding domain closely related to DBP, HLF, and TEF, which are PAR proteins. Here, we show that the phase of e4bp4 mRNA rhythm is opposite to that of the dbp, hlf, and tefrhythms in the suprachiasmatic nucleus (SCN), the mammalian circadian center, and the liver. The protein levels of E4BP4 and DBP also fluctuate in almost the opposite phase. Moreover, all PAR proteins activate, whereas E4BP4 suppresses, the transcriptional activity of the reporter gene containing a common binding sequence in transcriptional assays in vitro. An electrophoretic mobility shift assay demonstrated that E4BP4 is not able to dimerize with the PAR proteins, but is able to compete for the same binding sites with them. Furthermore, we showed sustained low e4bp4 and high dbp mRNA levels inmCry-deficient mice. These results indicate that the E4BP4 and PAR proteins are paired components of a reciprocating mechanism wherein E4BP4 suppresses the transcription of target genes during the time of day when E4BP4 is abundant, and the PAR proteins activate them at another time of day. E4BP4 and the PAR proteins may switch back and forth between the on-off conditions of the target genes.
Loss of Werner syndrome protein function promotes aberrant mitotic recombination
Authors: Prince Polly R. , Emond Mary J. , Monnat Raymond J.
Published: July 2002

The chromosome 8p11–12 Werner syndrome (WRN ) locus encodes a RecQ helicase protein of unknown function that possesses both 3′ → 5′ helicase and 3′ → 5′ exonuclease activities. We show that WRN cell lines display a marked reduction in cell proliferation following mitotic recombination, and generate few viable gene conversion-type recombinants. These findings indicate that WRN plays a role in mitotic recombination, and that a loss of WRN function may promote genetic instability and disease via recombination-initiated mitotic arrest, cell death, or gene rearrangement.
COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis
Authors: Schindelman Gary , Morikami Atsushi , Jung Jee , Baskin Tobias I. , Carpita Nicholas C. , Derbyshire Paul , McCann Maureen C. , Benfey Philip N.
Published: July 2002

To control organ shape, plant cells expand differentially. The organization of the cellulose microfibrils in the cell wall is a key determinant of differential expansion. Mutations in the COBRA(COB) gene of Arabidopsis, known to affect the orientation of cell expansion in the root, are reported here to reduce the amount of crystalline cellulose in cell walls in the root growth zone. The COB gene, identified by map-based cloning, contains a sequence motif found in proteins that are anchored to the extracellular surface of the plasma membrane through a glycosylphosphatidylinositol (GPI) linkage. In animal cells, this lipid linkage is known to confer polar localization to proteins. The COB protein was detected predominately on the longitudinal sides of root cells in the zone of rapid elongation. Moreover, COB RNA levels are dramatically upregulated in cells entering the zone of rapid elongation. Based on these results, models are proposed for the role of COB as a regulator of oriented cell expansion.
Identification of novel small RNAs using comparative genomics and microarrays
Authors: Wassarman Karen M. , Repoila Francis , Rosenow Carsten , Storz Gisela , Gottesman Susan
Published: July 2002

A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of theEscherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.
The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4
Authors: Larschan Erica , Winston Fred
Published: July 2002

Previous studies demonstrated that the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex facilitates the binding of TATA-binding protein (TBP) during transcriptional activation of the GAL1 gene ofSaccharomyces cerevisiae. TBP binding was shown to require the SAGA components Spt3 and Spt20/Ada5, but not the SAGA component Gcn5. We have now examined whether SAGA is directly required as a coactivator in vivo by using chromatin immunoprecipitation analysis. Our results demonstrate that SAGA is physically recruited in vivo to the upstream activation sequence (UAS) regions of the galactose-inducibleGAL genes. This recruitment is dependent on both induction by galactose and the Gal4 activation domain. Furthermore, we demonstrate that another well-characterized activator, Gal4–VP16, also recruits SAGA in vivo. Finally, we provide evidence that a specific interaction between Spt3 and TBP in vivo is important for Gal4 transcriptional activation at a step after SAGA recruitment. These results, taken together with previous studies, demonstrate a dependent pathway for the recruitment of TBP to GAL gene promoters consisting of the recruitment of SAGA by Gal4 and the subsequent recruitment of TBP by SAGA.
A Gene-enriched BAC Library for Cloning Large Allele-specific Fragments from Maize: Isolation of a 240-kb Contig of the bronze Region
Authors: Fu Huihua , Dooner Hugo K.
Published: July 2002

A generic bacterial artificial chromosome (BAC) library from a complex plant genome like maize may not be suitable for some types of genomic analysis, for example, for establishing correlations between the genetic and the physical organization of a given chromosome region. Previously, we carried out extensive genetic analysis of thebronze (Bz) region in Zea mays using a W22 inbred line carrying the Bz-McC allele; however, BAC libraries of that line are neither available nor under construction. Here, we report the isolation of large, adjacent BAC clones of this region from a partial BAC library of W22. We developed a BAC vector suitable for cloning NotI fragments and used it to clone size-fractionated genomic DNA that had been cut to completion with the methylation-sensitive, rare-cutting enzyme NotI. This strategy resulted in a very significant enrichment of large genic DNA. From a library of about 20,000 BACs, containing just two-thirds of a maize genome, we isolated 16 BAC clones of the 110-kb distal Bzfragment and 10 BAC clones of the 130-kb proximal Bz fragment. This recovery means that our strategy resulted in a 15- to 24-fold enrichment of specific sequences. The order of the BAC clones in the 240-kb contig, predetermined from an internal NotI site in theBz-McC allele was confirmed by hybridization with sequences from sites previously mapped proximal and distal to Bz and by sequencing. To show the general utility of our approach and the value of our partial BAC library, we also isolated BAC clones of other sequences, such as tub4 and the complex R-r allele, contained in the same size fraction of DNA. This is the first report of the use of a BAC vector to clone allele-specific large DNA fragments from a plant with a large genome, circumventing the need to construct a complete BAC library.
Alfresco—A Workbench for Comparative Genomic Sequence Analysis
Authors: Jareborg Niclas , Durbin Richard
Published: July 2002

Comparative analysis of genomic sequences provides a powerful tool for identifying regions of potential biologic function; by comparing corresponding regions of genomes from suitable species, protein coding or regulatory regions can be identified by their homology. This requires the use of several specific types of computational analysis tools. Many programs exist for these types of analysis; not many exist for overall view/control of the results, which is necessary for large-scale genomic sequence analysis. Using Java, we have developed a new visualization tool that allows effective comparative genome sequence analysis. The program handles a pair of sequences from putatively homologous regions in different species. Results from various different existing external analysis programs, such as database searching, gene prediction, repeat masking, and alignment programs, are visualized and used to find corresponding functional sequence domains in the two sequences. The user interacts with the program through a graphic display of the genome regions, in which an independently scrollable and zoomable symbolic representation of the sequences is shown. As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of theUTY locus is presented.
An Efficient and Robust Statistical Modeling Approach to Discover Differentially Expressed Genes Using Genomic Expression Profiles
Authors: Thomas Jeffrey G. , Olson James M. , Tapscott Stephen J. , Zhao Lue Ping
Published: July 2002

We have developed a statistical regression modeling approach to discover genes that are differentially expressed between two predefined sample groups in DNA microarray experiments. Our model is based on well-defined assumptions, uses rigorous and well-characterized statistical measures, and accounts for the heterogeneity and genomic complexity of the data. In contrast to cluster analysis, which attempts to define groups of genes and/or samples that share common overall expression profiles, our modeling approach uses known sample group membership to focus on expression profiles of individual genes in a sensitive and robust manner. Further, this approach can be used to test statistical hypotheses about gene expression. To demonstrate this methodology, we compared the expression profiles of 11 acute myeloid leukemia (AML) and 27 acute lymphoblastic leukemia (ALL) samples from a previous study (Golub et al. 1999) and found 141 genes differentially expressed between AML and ALL with a 1% significance at the genomic level. Using this modeling approach to compare different sample groups within the AML samples, we identified a group of genes whose expression profiles correlated with that of thrombopoietin and found that genes whose expression associated with AML treatment outcome lie in recurrent chromosomal locations. Our results are compared with those obtained using t-tests or Wilcoxon rank sum statistics.
Capturing Whole-Genome Characteristics in Short Sequences Using a Naïve Bayesian Classifier
Authors: Sandberg Rickard , Winberg Gösta , Bränden Carl-Ivar , Kaske Alexander , Ernberg Ingemar , Cöster Joakim
Published: July 2002

Bacterial genomes have diverged during evolution, resulting in clearcut differences in their nucleotide composition, such as their GC content. The analysis of complete sequences of bacterial genomes also reveals the presence of nonrandom sequence variation, manifest in the frequency profile of specific short oligonucleotides. These frequency profiles constitute highly specific genomic signatures. Based on these differences in oligonucleotide frequency between bacterial genomes, we investigated the possibility of predicting the genome of origin for a specific genomic sequence. To this end, we developed a naïve Bayesian classifier and systematically analyzed 28 eubacterial and archaeal genomes. We found that sequences as short as 400 bases could be correctly classified with an accuracy of 85%. We then applied the classifier to the identification of horizontal gene transfer events in whole-genome sequences and demonstrated the validity of our approach by correctly predicting the transfer of both the superoxide dismutase (sodC) and the bioC gene from Haemophilus influenzaeto Neisseria meningitis, correctly identifying both the donor and recipient species. We believe that this classification methodology could be a valuable tool in biodiversity studies.
A Highly Reproducible, Linear, and Automated Sample Preparation Method for DNA Microarrays
Authors: Dorris David R. , Ramakrishnan Ramesh , Trakas Dionisios , Dudzik Frank , Belval Richard , Zhao Connie , Nguyen Allen , Domanus Marc , Mazumder Abhijit
Published: July 2002

DNA microarrays are powerful tools to detect changes in transcript abundance in multiple samples in parallel. However, detection of differential transcript levels requires a reproducible sample (target) preparation method in addition to a high-performance microarray. Therefore, we optimized a target-preparation method that converts the poly(A)+ RNA fraction of total RNA into complementary DNA, then generates biotin-labeled complementary RNA from the cDNA. We measured the efficiency of incorporation of biotin-containing nucleotides by an enzymatic digestion, followed by resolution via analytical high-performance liquid chromatography (HPLC). When the target was hybridized to a sensitive and reproducible microarray platform, low coefficients of variation in both hybridization intensities and differential expression ratios across target preparations were observed. Nearly identical hybridization intensities and expression ratios are observed regardless of whether poly(A)+-enriched RNA or total RNA is used as the starting material. We show the ability to discern biological and production variability through the use of different lots of commercial samples as visualized by hierarchical clustering. Automation of the target-preparation procedure shows equivalence to the manual procedure, reproducible yields of target, and low variability as measured by hybridization to microarrays. Most importantly, RNA mixing experiments show a linear and quantitative amplification in probe hybridization signals for >6000 genes across the entire signal range.