bluuebunny/crossref_metadata_2025 huggingface dataset:
Eradication of vancomycin resistant Enterococcus faecium
from a paediatric oncology unit and prevalence of
colonization in hospitalized and community-based children
Authors: NOURSE C. , BYRNE C. , MURPHY H. , KAUFMANN M. E. , CLARKE A. , BUTLER K.
Published: July 2002

We previously reported an outbreak of vancomycin resistant enterococci (VRE) in a paediatric
oncology unit in December 1995 which was associated with widespread environmental
contamination of the unit with VRE. We undertook this study to evaluate the effectiveness of
the infection control policy instituted subsequent to the outbreak and to investigate the
underlying prevalence of VRE colonization in hospitalized, outpatient and community-based
children. We sought to establish the molecular similarity of VRE isolates from the study. Stool
specimens were obtained from outpatients at risk of VRE, hospital inpatients and from healthy
community-based children. VRE colonization was eradicated from the inpatient unit within 11
months, but in outpatients, 16 months after the outbreak, 4 of 137 (2·9%) attending oncology
outpatients, 5 of 65 (7·7%) with cystic fibrosis and 1 of 12 (8·3%) with liver disease were
found to be colonized with VRE. The isolates were all Enterococcus faecium, Van A phenotype
except one E. casseliflavus of the Van C phenotype. All were unique in SmaI DNA
macrorestriction patterns with the exception of two isolates, which were similar to the original
outbreak strain and three further isolates of a single strain but which differed from the
outbreak strain. Of 315 hospital inpatients, 2·5% were colonized with VRE of the Van C
resistance phenotype but VRE was not detected in 116 healthy, community-based children. We
conclude that effective strategies can successfully control spread of VRE but despite a low
prevalence of VRE colonization in hospital patients and in community-based children,
outbreaks can occur when infection control practices are not optimal. Continued vigilance to
detect VRE and limit spread within hospitals is therefore necessary.
An extension of Zermelo's model for ranking by paired comparisons
Authors: CONNER G. R. , GRANT C. P.
Published: July 2002

In 1929, Zermelo proposed a probabilistic model for ranking by paired comparisons and
showed that this model produces a unique ranking of the objects under consideration when
the outcome matrix is irreducible. When the matrix is reducible, the model may yield only
a partial ordering of the objects. In this paper, we analyse a natural extension of Zermelo's
model resulting from a singular perturbation. We show that this extension produces a ranking
for arbitrary (nonnegative) outcome matrices and retains several of the desirable properties
of the original model. In addition, we discuss computational techniques and provide examples
of their use.
Multidimensional inverse source problems of
underwater acoustics
Authors: ALEKSEEV G. V.
Published: July 2002

We consider linear and nonlinear inverse source
problems of sound radiation in an unbounded
domain which models an oceanic waveguide. The method for analysing their
solvability is
based on analytical properties of generalized acoustic potentials and the
theory of extremal
problems.
From ML to Ada: Strongly-typed language
interoperability via source translation
Authors: TOLMACH ANDREW , OLIVA DINO P.
Published: July 2002

We describe a system that supports source-level integration of
ML-like functional language
code with ANSI C or Ada83 code. The system works by translating the functional
code into
type-correct, ‘vanilla’ C or Ada; it offers simple, efficient,
type-safe inter-operation between
new functional code components and ‘legacy’ third-generation-language
components. Our
translator represents a novel synthesis of techniques including user-parameterized
specification
of primitive types and operators; removal of polymorphism by code specialization;
removal of
higher-order functions using closure datatypes and interpretation; and
aggressive optimization
of the resulting first-order code, which can be viewed as encoding the
result of a closure
analysis. Programs remain fully typed at every stage of the translation
process, using only
simple, standard type systems. Target code runs at speeds comparable to
the output of current
optimizing ML compilers, even though handicapped by a conservative garbage
collector.
ICT in varied language learning environments:
Selected papers from EUROCALL 1999
Authors: CHANIER THIERRY
Published: July 2002

This special issue offers a selection of papers presented at the 1999
annual EUROCALL conference, held last September in Besançon, France. Although
CALL has a deep rooted tradition in France, EUROCALL’99 was the first large scale
international CALL conference to take place in this country. Initiated by the
European Association for Computer Assisted Language Learning and the French
speaking CALL journal ALSIC (2000), the conference attracted more than 370
full participants coming from 30 countries.
Measuring the outcomes of care in older people: a non-critical review of patient-based measures.III. Pain, physical disability and handicap, and social health instruments
Authors: Kliempt P , Ruta D , McMurdo M
Published: July 2002

Introduction

This is the last in a series of three papers reviewing 69 patient-based outcome measures that have been developed specifically for use in older people, or that have been administered to populations that include older people. The previous papers described how the measures were identified, and provided brief descriptions

of measures of general health status and quality of life, instruments assessing mental status, measures of depression, and measures of psychological wellbeing. In this paper we describe six pain measures, 12 measures of physical disability and handicap, and eight measures of social health (see Tables 1–3). References in the text which include a copy of the questionnaire are marked with a # sign. Otherwise, a copy can be obtained from the address provided. It is recommended, however, before using any of the questionnaires to contact the authors to obtain permission to use them.
Pain management in old age: an update
Authors: Hardy Paul A.J.
Published: July 2002

A previous review dealt with the management of chronic pain in old age and attempted
to provide an up-to-date account of management at that time. The present
review will try to avoid going over the same ground but will discuss more recent
developments in pain medicine, with an emphasis on those aspects relevant to the
management of older patients.
The role of day hospitals in rehabilitation
Authors: Curless Richard
Published: July 2002

Introduction

Day hospitals for older people typically provide a multidisciplinary service for
a heterogeneous group of patients based largely upon a health care model. The broad
objectives of day hospital attendance are now widely accepted (Figure
1). There is wide variation, nationally and locally, in the types of service provision.
Little information is available to support evidence-based day hospital practice,
partly due to the lack of an established methodology to evaluate current practice
and allow comparison of different types of community-based rehabilitation and support.
This review will confine itself to day hospitals for older people; day care and day
hospitals for psychiatry of old age will not be discussed in any detail.
Ethical and legal issues in the care of people with dementia
Authors: Jones RG
Published: July 2002

This paper addresses some ethical and legal issues which arise in the UK in the
care of people with dementia, focusing on the law in England and Wales – updating
and revising the 1997 and earlier version. The ‘end
of medical ethics’ continues to be debated, with an attendant
fear of doctors’ responsibility and authority being fatally eroded by administrators
and cost controllers, concerned only with budgets and ‘bureaucratic parsimony’.
Aging, disease and the autonomic nervous system
Authors: Collins Kenneth J
Published: July 2002

Autonomic disorders in old age can be attributed to several main features associated with aging: the intrinsic neurobiological changes that occur with age, degenerative changes in effector organs innervated by autonomic nerves, and secondary involvement of the autonomic nervous system (ANS) in disease processes. As in most areas of clinical geriatrics, the distinction between disorders ascribed to ‘normal’ aging and those attributable to diseases of old age is difficult to make with any degree of certainty. Neurobiological changes with age have become the subject of intense investigation in recent years, with improvements in techniques for assessing autonomic nerve structure and function. This has included a better understanding of neurotransmitter and receptor transformations during development and aging. The versatility of the ANS, or ‘plasticity’, involves interactions with target organs, e.g. via nerve growth factor (NGF) and with other neurons, and it is as vital to the mature and aging autonomic neuron as it is during development. Some neurotrophic features of aging in the ANS and in disease processes in old age are considered in this paper.
We are not screening properly for disabling diabetic complications in elderly people with diabetes
Authors: Shawis TN , Bacon MT
Published: July 2002

We read with interest the review article by Paul V Knight and Alan McKenzie on diabetes in the elderly. They highlight the fact that close examination of the feet or fundoscopy is often not performed. We have audited the care of elderly diabetic patients on our acute wards using the BGS guidline for diabetic care.
Decidability of fourth-order matching
Authors: PADOVANI VINCENT
Published: July 2002

Higher Order Matching consists of solving finite sets of equations of
the form u =βηv, where
u, v are simply typed terms of λ-calculus, and v is a closed term. Whether this problem is
decidable is an open question. In this paper its decidability is proved when the free variables
of all equations are of order at most 4 – we actually extend this result to a more general
situation in which in addition to equations, disequations are also considered.
On the semantics of place/transition Petri nets
Authors: MESEGUER JOSÉ , MONTANARI UGO , SASSONE VLADIMIRO
Published: July 2002

Place/transition (PT) Petri nets are one of the most widely
used models of concurrency.
However, they still lack, in our view, a satisfactory semantics: on the
one
hand the ‘token
game’ is too intensional, even in its more abstract interpretations
in terms of nonsequential
processes and monoidal categories; on the other hand, Winskel's basic
unfolding
construction, which provides a coreflection between nets and finitary prime
algebraic
domains, works only for safe nets. In this paper we extend Winskel's
result to PT nets. We
start with a rather general category PTNets of PT nets, we introduce a
category DecOcc of
decorated (nondeterministic) occurrence nets and we define adjunctions
between PTNets and
DecOcc and between DecOcc and Occ, the category of occurrence nets.
The role of DecOcc
is to provide natural unfoldings for PT nets, i.e., acyclic safe nets
where a notion of family is
used to relate multiple instances of the same place. The unfolding
functor from PTNets to
Occ reduces to Winskel's when restricted to safe nets. Moreover,
the standard coreflection
between Occ and Dom, the category of finitary prime algebraic domains,
when composed
with the unfolding functor above, determines a chain of adjunctions
between PTNets and Dom.
The British Conservative Party from Churchill to Heath: Doctrine or Men?
Authors: ADDISON PAUL
Published: July 2002

John Ramsden, The Age of Churchill and Eden 1940–1957 (London: Longman, 1995), 350pp., £57.50, ISBN 0-582-50463-5; The Winds of Change: Macmillan to Heath 1957-1975 London: Longman, 1996), 485pp., £70.00, ISBN 0-582-227570-9.
Prospects for hormonal contraception in the male
Authors: Anderson RA
Published: July 2002

Female-dependent methods of contraception have been the subject of considerable scientific advance since the introduction of the combined contraceptive pill, offering effective and male-independent contraception, but there is an emerging emphasis that men should be more involved in family planning. The supremacy of modern, female methods in the developed world obscures the fact that one-third of all couples worldwide rely on a male-dependent method of contraception, mostly the condom or withdrawal, methods that have been used since antiquity. Potential methods of male contraception include withdrawal of the gonadotrophic support to the testis, interference with spermatogenesis within the seminiferous tubules, or with post-testicular functions. Effects on maturation within the epididymis can be induced by chloro-6-deoxy sugars or plant-derived glycosides. Although advances in assisted conception, particularly associated with intracytoplasmic sperm injection (ICSI), have demonstrated the functional competence of the nucleus and centriole of testicular spermatozoa and other less mature forms, it has been suggested that normal passage through the male reproductive tract is necessary for conventional conception. Advances in both testicular and post-testicular methods of contraception have been hampered by toxicity and remain in preclinical testing, reflecting the limited extent of (and thus the need for) scientific knowledge in this area. While progress in these areas is fully acknowledged, the pretesticular hormonal approach is currently at a considerably more advanced stage of development with prospects for a real product becoming increasingly likely on a realistic time-scale. This review will therefore confine itself to this, the hormonal approach.
Response to “Germ Line Therapy to Cure Mitochondrial
Disease: Protocol and Ethics of In Vitro Ovum Nuclear Transplantation”
by Donald S. Rubenstein, David C. Thomasma, Eric A. Schon,
and Michael J. Zinaman (CQ Vol. 4, No. 3)
Authors: Watt Helen
Published: July 2002

Germ-line therapy has long been regarded with great
caution both by scientists and by ethicists. Even those
who do not reject germ-line therapy in principle have tended
to reject it in practice as carrying unacceptable risks
in our current state of knowledge. For this reason, a recent
paper by Rubenstein, Thomasma, Shon, and Zinaman is unusual
in putting forward a serious proposal for the use of germ-line
therapy in the foreseeable future.
What Actually Happened
Authors: KUCZEWSKI MARK G.
Published: July 2002

The transplant coordinator scheduled a meeting
that included numerous members of the multidisciplinary
team, among them the transplant surgeon, a social worker,
a psychologist, and an ethics consultant. The ethics consultant
outlined the ethical issues and made a recommendation.
The consultant argued that the question whether the patient
should again be listed as a transplant candidate really
came down to the kind of environment that could be provided
during aftercare. That is, if a rather structured living
environment—one more structured and supportive than
the previous independent living facility—could be
found for the patient, then retransplantation might be
warranted. But without such an environment, the patient
would again probably fail to adhere to the medical and
psychological treatment regimen necessary for a successful
life as a transplant recipient. The psychologist, who had
been working closely with the ethics consultant, concurred
in this opinion.
Random Finite Topologies and their Thresholds
Authors: MACLEAN C. F. , O'CONNELL NEIL
Published: July 2002

For each integer n, there is a natural family of probability distributions on the set of
topologies on a set of n elements, parametrized by an integer variable, m. We will describe
how these are constructed and analysed, and find threshold functions (for m in terms of n)
for various topological properties; we focus attention on connectivity and the size of the
largest component.
Imperfections in Random Tournaments
Authors: BARBOUR A. D. , GODBOLE ANANT P. , QIAN JINGHUA
Published: July 2002

A tournament T on a set V of n

players is an orientation of the edges of the complete graph

Kn on V; T will be

called a random tournament if the directions of these edges

are determined by a sequence

{Yj[ratio ]j = 1, …,

(n2)} of independent coin flips. If

(y, x) is an edge in a (random) tournament, we say that y

beats x. A set A ⊂ V,

|A| = k, is said to be beaten

if there exists a player y ∉ A such that

y beats x for each x ∈ A. If

such a y does not exist, we say that A is

unbeaten. A (random) tournament on V is said to have

property Sk if each k-element

subset of V is beaten. In this paper, we use the

Stein–Chen method to show that the probability distribution of

the number W0 of unbeaten k-subsets of

V can be well-approximated by that of a Poisson random

variable with the same mean; an improved condition for the existence

of tournaments with property Sk is

derived as a corollary. A multivariate version of this result is

proved next: with Wj representing the

number of k-subsets that are beaten by precisely j

external vertices, j = 0, 1, …, b, it is shown
that

the joint distribution of (W0,

W1, …, Wb) can
be

approximated by a multidimensional Poisson vector with independent

components, provided that b is not too large.
On Medians of Lattice Distributions and a Game with Two Dice
Authors: GRINSTEAD CHARLES M.
Published: July 2002

Let D1 and D2 be two dice with
k and l integer faces, respectively, where k and
l are
two positive integers. The game Gn consists
of tossing each die n times and summing the
resulting faces. The die with the higher total wins the game. We examine
the question of
which die wins game Gn more often, for large values
of n. We also give an example of a
set of three dice which is non-transitive in game Gn

for infinitely many values of n.
Compound Poisson Approximation for Dissociated
Random Variables via Stein's Method
Authors: EICHELSBACHER PETER , ROOS MAŁGORZATA
Published: July 2002

In the present paper we consider compound Poisson approximation by Stein's method
for dissociated random variables. We present some applications to problems in system
reliability. In particular, our examples have the structure of an incomplete
U-statistics. We mainly apply techniques from Barbour and Utev, who gave new bounds
for the solutions of the Stein equation in compound Poisson approximation in two recent papers.
Residential leisure towns in England towards the end of the eighteenth century
Authors: Schwarz Leonard
Published: July 2002

Apart from a few obvious exceptions, the definition of a ‘leisure town’ in eighteenth-century England remains problematic. Using a list of the employers of manservants registered for taxation in 1780 this paper isolates the fifty-three ‘residential leisure towns’ outside Middlesex and Surrey where there were thirty or more such employers. It is suggested that the employment of manservants is, within limits, a useful indicator of a certain type of gentility and that the spread of such towns outside the Home Counties was very limited at this time.
Antenatal treatment of fetal immune thrombocytopenias
Authors: Skupski Daniel W , Bussel James B
Published: July 2002

Advances in both imaging techniques and in treatments for immune thrombocytopenias affecting the fetus have allowed for more accurate antenatal predictions of severe disease and effective antenatal treatments for those fetuses who are at risk of sequelae. This article will review current knowledge of the diagnosis and treatment of affected fetuses in alloimmune thrombocytopenia and in immune thrombocytopenic purpura.
Publications on financial history 1998
Authors: NOIRET SERGE
Published: July 2002

This bibliography
covers publications that appeared during 1998. It follows previous criteria, being divided into two
broad areas: general literature on financial history in section I, and specialised material in section
2. Section 2 is subdivided chronologically and, further, by geographical area (the complete
classification scheme was published in Volume I, Part 2, pp. 157–60). Where there are no entries
for a particular section, the heading has been omitted. Abbreviations have been kept to a minimum but
standard abbreviations such as J. for Journal, Q. for Quarterly,
Rev. for Review/Revue, have been used throughout. Short titles are used for
references to edited volumes within the section in which they are listed, elsewhere they are cited in
full. Articles published in books ‘edited by’ are mentioned only if the bibliographer
accessed the relevant index before the deadline for publication (August 1998). Doctoral theses and
Working Papers are not included.

The bibliographer is pleased to receive suggestions of any kind
at his e-mail address: 
GHOSTS, AESTHETICISM, AND “VERNON LEE”
Authors: Leighton Angela
Published: July 2002

“TO RAISE A REAL SPECTRE of the antique is a craving of our own century” (104) writes “Vernon Lee” in her early collection of essays on aesthetics, Belcaro. The nineteenth century is indeed, as Julia Briggs has pointed out, an age which craves ghost stories of all kinds. Sceptical of the supernatural yet nostalgic for it (Briggs 19), the age turns to ghost stories to assuage its lost faith. Ghosts, if nothing else, might still glimmer in the empty spaces of a universe vacated by the gods but not yet filled with the space journeys of science and science fiction. Their questionable shapes thus continue to shape the questions of an age seeking reassurance, even if that reassurance comes in a spasm of terror. And terror, however subtly or ingeniously aroused, whether by the self-induced fantasies of James’s governess or the calculated self-hauntings of Stevenson’s Jekyll, remains the primary motivation and aim of the ghost story. Fear of the unknown, whether within or without, provides the last bastion of a supernaturalism under threat from the encroaching “materialism” (Briggs 24) of the modern world. The ghost story not only indulges the unstable, if sometimes deeply conventional order of fantasy at the expense of “naturalistic art” (Cavaliero 7); it also indulges the wish to believe in another, more fearful world, beyond the material order of things. The specter focuses this trouble of belief. It is there and not there. It outlines emptiness but also fills it up, embodying and disembodying its own reality at the same time.
ROBERT AND ELIZABETH BARRETT BROWNING: AN ANNOTATED BIBLIOGRAPHY FOR 1997
Authors: Donaldson Sandra M. , Bisignano Dominic , Brotton Melissa
Published: July 2002

The following abbreviations appear in this year’s bibliography:

BSNBrowning Society Notes

DAI Dissertation Abstracts International

N&QNotes and Queries

NCLNineteenth Century Literature

RESReview of English Studies

SBHCStudies in Browning and His Circle

VLCVictorian Literature and Culture

VPVictorian Poetry

VRVictorian Review

An asterisk* indicates that we have not seen the item. Cross references with citation numbers between 51 and 70 followed by a colon (e.g., C68:) refer to William S. Peterson’s Robert and Elizabeth Barrett Browning: An Annotated Bibliography, 1951–1970 (New York: Browning Institute, 1974); higher numbers refer to Robert Browning: A Bibliography 1830–1950, compiled by L. N. Broughton, C. S. Northup, and Robert Pearsall (Ithaca: Cornell UP, 1953).
WALUCHOW’S DEFENSE OF INCLUSIVE POSITIVISM
Authors: Himma Kenneth Einar
Published: July 2002

In “The Model of Rules I,”1 Ronald Dworkin argues that judges are often bound by principles that do not derive their authority from having been formally promulgated by a judge or legislature in accordance with a rule of recognition. But, on Dworkin’s view, the existence of such principles is inconsistent with positivism’s pedigree thesis, according to which propositions are legally valid solely in virtue of having been promulgated in accordance with a rule of recognition. Thus, Dworkin concludes that positivism is false.
Reliable Change formula query: A statistician's comments
Authors: ABRAMSON IAN S.
Published: July 2002

Dr. Hinton-Bayre has correctly noted a discrepancy here between
the Jacobson and Temkin procedures. His comparison of prediction
bounds both confirms this and suggests too that the differences
are minor.
Performance of 7- to 95-year-old individuals in a Chinese
version of the category fluency test
Authors: CHAN AGNES S. , POON MAGGIE W.
Published: July 2002

A version of the category fluency test including
the categories of animal and transportation, was administered
to 316 Chinese native speakers ranging in age from 7 to
95. Results indicated that the number of items generated
in the category fluency test increases with age from childhood
to adulthood with a peak performance in adults aged from
19 to 30, and then declines subsequently into late life.
All participants, regardless of their age, generated more
animal than transportation names. Educational level, but
not gender, was a significant factor affecting their performance.
The participants in all age groups committed very few intrusion
and perseveration errors. The results of the present study
were in general consistent with those reported in the western
countries. Thus, it seems to be appropriate to apply the
category fluency test, which was originally developed in
western countries, for clinical use in Hong Kong. (JINS,
1999, 5, 525–533.)
Resilience in social and economic systems: a concept that fails the cost–benefit test?
Authors: HANLEY NICK
Published: July 2002

One of the first lessons that students of cost-benefit analysis (CBA) learn is to ask whether projects or policies which they are studying generate additional benefits or costs, relative to the status quo. They are also told to be very careful in defining the project/policy which is the subject of their analysis. In my view, the ecological concept of resilience fails the CBA test, when applied to the study of economic and social systems, because it offers no additional insights to those we have already, and appears to be poorly defined.
Paradigms for the new string instrument: digital and materials technology
Authors: LIVINGSTON HUGH
Published: July 2002

The applications of technology in instrument design contribute to the resulting sound on many levels, particularly in

the context of new evolutions representing the traditional instruments of our culture. Materials technology is seldom

given consideration in the description of Western string instruments, but our choices of woods, metals and synthetics

can dramatically alter the sound without altering the substance of instrumental performance. In the design of modified

string instruments which mimic features of natural acoustic predecessors, new technology is applied on many levels.

A taxonomy is proposed for the past, present and future of instrument design. Due consideration is given to the music

which results from the new sound world, especially that involving interactive electronic processing. The advantages

and disadvantages of directions in instrument design for the future are evaluated within the proposed schema. Some

extended techniques on the cello are proposed to be further extended with electronics, and audio examples and descriptions are provided. A model for future collaborations between composer, performer and engineer is proposed.
Cyberspace memes
Authors: Milicevic Mladen
Published: July 2002

This paper addresses the issues concerning the impact of music on cyberspace globalisation. It points out that Internet access is limited to only one per cent of the wealthiest human population. It also looks into the future of cyberspace music and predicts that most of the cyberspace activities are going to be unleashing one of many of humanity's predispositions – the predisposition to steal. Cyberspace represents a perfect medium for concealing a person's identity and for the masking of any of the responsibility that is expected from socially acceptable human behaviour. With these aspects in mind, the paper concentrates on the Internet's distribution of pirated software and the trading of MP3 files. The paper also focuses on commercial music whose economic impact on the development of music technology allows ‘academic musicians’ to appropriate most of the tools that otherwise would not have been developed for ‘academic’ use.
Analysis of Crosstalk, a work by Michael Vaughan
Authors: FISCHMAN RAJMIL
Published: July 2002

This article presents a full analysis of Crosstalk – a
piece for tape by Michael Vaughan (1989). The methodological approach
employed here develops its concepts and techniques from those of Music
Semiology and Spectromorphology. The former provides the concept and method
of semiological neutral inference – as applied by Nattiez
(1982, 1990). The latter – developed by Smalley (1986) – offers
tools and a terminology for the characterisation of timbre and temporal
functionality within the musical work.
SOME INTRANATIONAL EVIDENCE ON OUTPUT-INFLATION TRADE-OFFS
Authors: Hess Gregory D. , Shin Kwanho
Published: July 2002

In a seminal paper, Robert E.
Lucas, Jr. provided the theoretical relationship
between aggregate demand and
real output based on relative price confusion
at the individual market level.
Subsequently, an alternative New Keynesian aggregate supply relationship
was derived and it was demonstrated
that the two theories can be distinguished
on the basis of how both the rate of inflation and
the volatility of relative prices
affect its slope.
By emphasizing the first
implication of New Keynesian theory,
strong evidence was obtained supporting this model
using international data.
We also concentrate on the second
difference between the two theories.
We derive the individual market-level
equilibrium relationship
for the Lucas model, i.e., the disaggregate supply curve.
We estimate
the crucial parameters of the relationship
between aggregate nominal demand shocks and real output
using U.S. intranational state and industry data.
We find that the Lucas model
omits important New Keynesian features of the data.
Promoter opening by ς54 and ς70 RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control
Authors: Guo Yuli , Lew Chih Min , Gralla Jay D.
Published: July 2002

Transcription control at the melting step is not yet understood. Here, band shift, cross-linking, and transcription experiments on diverse DNA probes were used with two bacterial RNA polymerase holoenzymes that differ in how they regulate melting. Data indicated that both ς54 and ς70 holoenzymes assume a default closed form that cannot establish single-strand binding. Upon activation the enzymes are converted to an open form that can bind simultaneously to the upstream fork junction and to the melted transcription start site. The key difference is that ς54imposes tighter regulation by creating a complex molecular switch at −12/−11; the current data show that this switch can be thrown by activator. In this case an ATP-bound enhancer protein causes ς54 to alter its cross-linking pattern near −11 and also causes a reorganization of holoenzyme: DNA interactions, detected by electrophoretic mobility-shift assay. At a temperature-dependent ς70 promoter, elevated temperature alone can assist in triggering conformational changes that enhance the engagement of single-strand DNA. Thus, the two ς factors modify the same intrinsic opening pathway to create quite different mechanisms of transcriptional regulation.
A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNAMet is an important translation initiation intermediate in vivo
Authors: Asano Katsura , Clayton Jason , Shalev Anath , Hinnebusch Alan G.
Published: July 2002

Translation initiation factor 2 (eIF2) bound to GTP transfers the initiator methionyl tRNA to the 40S ribosomal subunit. The eIF5 stimulates GTP hydrolysis by the eIF2/GTP/Met-tRNAiMet ternary complex on base-pairing between Met-tRNAiMet and the start codon. The eIF2, eIF5, and eIF1 all have been implicated in stringent selection of AUG as the start codon. The eIF3 binds to the 40S ribosome and promotes recruitment of the ternary complex; however, physical contact between eIF3 and eIF2 has not been observed. We show that yeast eIF5 can bridge interaction in vitro between eIF3 and eIF2 by binding simultaneously to the amino terminus of eIF3 subunit NIP1 and the amino-terminal half of eIF2β, dependent on a conserved bipartite motif in the carboxyl terminus of eIF5. Additionally, the amino terminus of NIP1 can bind concurrently to eIF5 and eIF1. These findings suggest the occurrence of an eIF3/eIF1/eIF5/eIF2 multifactor complex, which was observed in cell extracts free of 40S ribosomes and found to contain stoichiometric amounts of tRNAiMet. The multifactor complex was disrupted by the tif5-7A mutation in the bipartite motif of eIF5. Importantly, the tif5-7A mutant is temperature sensitive and displayed a substantial reduction in translation initiation at the restrictive temperature. We propose that the multifactor complex is an important intermediate in translation initiation in vivo.
SAGA is an essential in vivo target of the yeast acidic activator Gal4p
Authors: Bhaumik Sukesh R. , Green Michael R.
Published: July 2002

Despite major advances in characterizing the eukaryotic transcriptional machinery, the function of promoter-specific transcriptional activators (activators) is still not understood. For example, in no case have the direct in vivo targets of a transcriptional activator been unambiguously identified, nor has it been resolved whether activators have a single essential target or multiple redundant targets. Here we address these issues for the prototype acidic activator yeast Gal4p. Gal4p binds to the upstream activating sequence (UAS) of GAL1 and several other GALgenes and stimulates transcription in the presence of galactose. Previous studies have shown that GAL1 transcription is dependent on the yeast SAGA (Spt/Ada/GCN5/acetyltransferase) complex. Using formaldehyde-based in vivo cross-linking, we show that the Gal4p activation domain recruits SAGA to the GAL1 UAS. If SAGA is not recruited to the UAS, the preinitiation complex (PIC) fails to assemble at the GAL1 core promoter, and transcription does not occur. SAGA, but not other transcription components, is also recruited by the Gal4p activation domain to a plasmid containing minimal Gal4p-binding sites. Recruitment of SAGA by Gal4p and stimulation of PIC assembly is dependent on several SAGA subunits but not the SAGA histone acetyl-transferase (HAT) GCN5. Based on these and other results, we conclude that SAGA is an essential target of Gal4p that, following recruitment to the UAS, facilitates PIC assembly and transcription.
Structure of the Highly Conserved HERC2 Gene and of Multiple Partially Duplicated Paralogs in Human
Authors: Ji Yonggang , Rebert Nancy A. , Joslin John M. , Higgins Michael J. , Schultz Roger A. , Nicholls Robert D.
Published: July 2002

Recombination between chromosome-specific low-copy repeats (duplicons) is an underlying mechanism for several genetic disorders. Recently, a chromosome 15 duplicon was discovered in the common breakpoint regions of Prader–Willi and Angelman syndrome deletions. We identified previously the large HERC2 transcript as an ancestral gene in this duplicon, with ∼11 HERC2-containing duplicons, and demonstrated that recessive mutations in mouseHerc2 lead to a developmental syndrome, juvenile development and fertility 2 (jdf2). We have now constructed and sequenced a genomic contig of HERC2, revealing a total of 93 exons spanning ∼250 kb and a CpG island promoter. A processed ribosomal protein L41 pseudogene occurs in intron 2 of HERC2, and putative VNTRs occur in intron 70 (28 copies, ∼76-bp repeat) and 3′ exon 40 through intron 40 (6 copies, ∼62-bp repeat). Sequence comparisons show that HERC2-containing duplicons have undergone several deletion, inversion, and dispersion events to form complex duplicons in 15q11, 15q13, and 16p11. To further understand the developmental role of HERC2, a highly conservedDrosophila ortholog was characterized, with 70% amino acid sequence identity to human HERC2 over the carboxy-terminal 743 residues. Combined, these studies provide significant insights into the structure of complex duplicons and into the evolutionary pathways of formation, dispersal, and genomic instability of duplicons. Our results establish that some genes not only have a protein coding function but can also play a structural role in the genome.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AF189221 (Drosophila HERC2 partial cDNA),AC004583 (human HERC2 exons 1–52, genomic);AF224242–AF224257 (human HERC2 exons 54–70, partial genomic sequences); AF225400–AF225409 (human HERC2 exons 71–93, partial genomic sequences). The exon-intron boundaries for exons 53–93 are derived from BACs R-142A11 and 263O22. Additional information is available as a supplementary table at www.genome.org.]
Two Rhamnogalacturonide Tetrasaccharides Isolated from Semi-Retted Flax Fibers Are Signaling Molecules in Rubus fruticosus L. Cells
Authors: Dinand E. , Excoffier G. , Lienart Y. , Vignon M. R.
Published: July 2002

Water extraction of semi-retted flax (Linum usitatissimum L.) fiber bundles yielded a mixture of pectic oligosaccharides and two acidic rhamnogalacturonide tetrasaccharides that were separated by size-exclusion chromatography. One- and two-dimensional nuclear magnetic resonance studies and fast atom bombardment-mass spectrometry experiments indicated that the two tetrasaccharides have a common primary structure, i.e. α--D-[delta]GalpA(1[->2)-α--L-Rhap(1->4)-α--D-GalpA-(1 ->2)-L-α-,β-Rha p, with a rhamnopyranose as terminal reducing end, and a 4-deoxy-β-L-threo-hex-4-eno-pyranosiduronic acid at the nonreducing end. However, the two tetrasaccharides differ by an acetyl group located at the O-3 position of the internal galacturonic acid residue. These two tetrasaccharides induce the activation of D-glycohydrolases of Rubus fructicosus L. cells or protoplasts within minutes.
Fluence and Wavelength Requirements for Arabidopsis CAB Gene Induction by Different Phytochromes
Authors: Hamazato F. , Shinomura T. , Hanzawa H. , Chory J. , Furuya M.
Published: July 2002

The roles of different phytochromes have been investigated in the photoinduction of several chlorophyll a/b-binding protein genes (CAB) of Arabidopsis thaliana. Etiolated seedlings of the wild type, a phytochrome A (PhyA) null mutant (phyA), a phytochrome B (PhyB) null mutant (phyB), and a phyA/phyB double mutant were exposed to monochromatic light to address the questions of the fluence and wavelength requirements for CAB induction by different phytochromes. In the wild type and the phyB mutant, PhyA photoirreversibly induced CAB expression upon irradiation with very-low-fluence light of 350 to 750 nm. In contrast, using the phyA mutant, PhyB photoreversibly induced CAB expression with low-fluence red light. The threshold fluences of red light for PhyA- and PhyB-specific induction were about 10 nmol m-2 and 10 [mu]mol m-2, respectively. In addition, CAB expression was photoreversibly induced with low-fluence red light in the phyA/phyB double mutant, revealing that another phytochrome(s) (PhyX) regulated CAB expression in a manner similar to PhyB. These data suggest that plants utilize different phytochromes to perceive light of varying wave-lengths and fluence, and begin to explain how plants respond so exquisitely to changing light in their environment.
Auxin Transport Is Required for Hypocotyl Elongation in Light-Grown but Not Dark-Grown Arabidopsis1
Authors: Jensen Philip J. , Hangarter Roger P. , Estelle Mark
Published: July 2002

Many auxin responses are dependent on redistribution and/or polar transport of indoleacetic acid. Polar transport of auxin can be inhibited through the application of phytotropins such as 1-naphthylphthalamic acid (NPA). WhenArabidopsis thaliana seedlings were grown in the light on medium containing 1.0 μm NPA, hypocotyl and root elongation and gravitropism were strongly inhibited. When grown in darkness, however, NPA disrupted the gravity response but did not affect elongation. The extent of inhibition of hypocotyl elongation by NPA increased in a fluence-rate-dependent manner to a maximum of about 75% inhibition at 50 μmol m−2 s−1 of white light. Plants grown under continuous blue or far-red light showed NPA-induced hypocotyl inhibition similar to that of white-light-grown plants. Plants grown under continuous red light showed less NPA-induced inhibition. Analysis of photoreceptor mutants indicates the involvement of phytochrome and cryptochrome in mediating this NPA response. Hypocotyls of some auxin-resistant mutants had decreased sensitivity to NPA in the light, but etiolated seedlings of these mutants were similar in length to the wild type. These results indicate that light has a significant effect on NPA-induced inhibition in Arabidopsis, and suggest that auxin has a more important role in elongation responses in light-grown than in dark-grown seedlings.
Formate Dehydrogenase, an Enzyme of Anaerobic Metabolism, Is Induced by Iron Deficiency in Barley Roots1
Authors: Suzuki Kazuya , Itai Reiko , Suzuki Koichiro , Nakanishi Hiromi , Nishizawa Naoko-Kishi , Yoshimura Etsuro , Mori Satoshi
Published: July 2002

To identify the proteins induced by Fe deficiency, we have compared the proteins of Fe-sufficient and Fe-deficient barley (Hordeum vulgare L.) roots by two-dimensional polyacrylamide gel electrophoresis. Peptide sequence analysis of induced proteins revealed that formate dehydrogenase (FDH), adenine phosphoribosyltransferase, and the Ids3gene product (for Fe deficiency-specific) increased in Fe-deficient roots. FDH enzyme activity was detected in Fe-deficient roots but not in Fe-sufficient roots. A cDNA encoding FDH (Fdh) was cloned and sequenced. Fdh expression was induced by Fe deficiency. Fdh was also expressed under anaerobic stress and its expression was more rapid than that induced by Fe deficiency. Thus, the expression of Fdh observed in Fe-deficient barley roots appeared to be a secondary effect caused by oxygen deficiency in Fe-deficient plants.
Isolation of the Ornithine-δ-Aminotransferase cDNA and Effect of Salt Stress on Its Expression inArabidopsis thaliana1
Authors: Roosens Nancy H.C.J. , Thu Tran T. , Iskandar Hayati M. , Jacobs Michel
Published: July 2002

To evaluate the relative importance of ornithine (Orn) as a precursor in proline (Pro) synthesis, we isolated and sequenced a cDNA encoding the Orn-δ-aminotransferase (δ-OAT) from Arabidopsis thaliana. The deduced amino acid sequence showed high homology with bacterial, yeast, mammalian, and plant sequences, and the N-terminal residues exhibited several common features with a mitochondrial transit peptide. Our results show that under both salt stress and normal conditions, δ-OAT activity and mRNA in young plantlets are slightly higher than in older plants. This appears to be related to the necessity to dispose of an easy recycling product, glutamate. Analysis of the expression of the gene revealed a close association with salt stress and Pro production. In young plantlets, free Pro content, Δ1-pyrroline-5-carboxylate synthase mRNA, δ-OAT activity, and δ-OAT mRNA were all increased by salt-stress treatment. These results suggest that for A. thaliana, the Orn pathway, together with the glutamate pathway, plays an important role in Pro accumulation during osmotic stress. Conversely, in 4-week-old A. thaliana plants, although free Pro level also increased under salt-stress conditions, the δ-OAT activity appeared to be unchanged and δ-OAT mRNA was not detectable. Δ1-pyrroline-5-carboxylate synthase mRNA was still induced at a similar level. Therefore, for the adult plants the free Pro increase seemed to be due to the activity of the enzymes of the glutamate pathway.
Potent Inhibition of Ribulose-Bisphosphate Carboxylase by an Oxidized Impurity in Ribulose-1,5-Bisphosphate1
Authors: Kane Heather J. , Wilkin Jean-Marc , Portis Archie R. , John Andrews T.
Published: July 2002

Oxidation of d-ribulose-1,5-bisphosphate (ribulose-P2) during synthesis and/or storage producesd-glycero-2,3-pentodiulose-1,5-bisphosphate (pentodiulose-P2), a potent slow, tight-binding inhibitor of spinach (Spinacia oleracea L.) ribulose-P2 carboxylase/oxygenase (Rubisco). Differing degrees of contamination with pentodiulose-P2 caused the decline in Rubisco activity seen during Rubisco assay time courses to vary between different preparations of ribulose-P2. With some ribulose-P2 preparations, this compound can be the dominant cause of the decline, far exceeding the significance of the catalytic by-product, d-xylulose-1,5-bisphosphate. Unlike xylulose-1,5-bisphosphate, pentodiulose-P2 did not appear to be a significant by-product of catalysis by wild-type Rubisco at saturating CO2 concentration. It was produced slowly during frozen storage of ribulose-P2, even at low pH, more rapidly in Rubisco assay buffers at room temperature, and particularly rapidly on deliberate oxidation of ribulose-P2with Cu2+. Its formation was prevented by the exclusion of transition metals and O2. Pentodiulose-P2 was unstable and decayed to a variety of other less-inhibitory compounds, particularly in the presence of some buffers. However, it formed a tight, stable complex with carbamylated spinach Rubisco, which could be isolated by gel filtration, presumably because its structure mimics that of the enediol intermediate of Rubisco catalysis. Rubisco catalyzes the cleavage of pentodiulose-P2 by H2O2, producing P-glycolate.
Developmental Expression and Substrate Specificities of Alfalfa Caffeic Acid 3-O-Methyltransferase and Caffeoyl Coenzyme A 3-O-Methyltransferase in Relation to Lignification1
Authors: Inoue Kentaro , Sewalt Vincent J.H. , Murray Ballance G. , Ni Weiting , Stürzer Cornelia , Dixon Richard A.
Published: July 2002

The biosynthesis of monolignols can potentially occur via two parallel pathways involving free acids or their coenzyme A (CoA) esters. Caffeic acid 3-O-methyltransferase (COMT) and caffeoyl CoA 3-O-methyltransferase (CCOMT) catalyze functionally identical reactions in these two pathways, resulting in the formation of mono- or dimethoxylated lignin precursors. The activities of the two enzymes increase from the first to the sixth internode in stems of alfalfa (Medicago sativa L.), preceding the deposition of lignin. Alfalfa CCOMT is highly similar at the amino acid sequence level to the CCOMT from parsley, although it contains a six-amino acid insertion near the N terminus. Transcripts encoding both COMT and CCOMT are primarily localized to vascular tissue in alfalfa stems. Alfalfa CCOMT expressed in Escherichia coli catalyzesO-methylation of caffeoyl and 5-hydroxyferuloyl CoA, with preference for caffeoyl CoA. It has low activity against the free acids. COMT expressed in E. coli is active against both caffeic and 5-hydroxyferulic acids, with preference for the latter compound. Surprisingly, very little extractableO-methyltransferase activity versus 5-hydroxyferuloyl CoA is present in alfalfa stem internodes, in which relativeO-methyltransferase activity against 5-hy-droxyferulic acid increases with increasing maturity, correlating with increased lignin methoxyl content.