bluuebunny/crossref_metadata_2025 huggingface dataset:
Prolonged Residence Time of a Noncovalent Molecular Adapter, β-Cyclodextrin, within the Lumen of Mutant α-Hemolysin Pores
Authors: Gu Li-Qun , Cheley Stephen , Bayley Hagan
Published: July 2002

Noncovalent molecular adapters, such as cyclodextrins, act as binding sites for channel blockers when lodged in the lumen of the α-hemolysin (αHL) pore, thereby offering a basis for the detection of a variety of organic molecules with αHL as a sensor element. β-Cyclodextrin (βCD) resides in the wild-type αHL pore for several hundred microseconds. The residence time can be extended to several milliseconds by the manipulation of pH and transmembrane potential. Here, we describe mutant homoheptameric αHL pores that are capable of accommodating βCD for tens of seconds. The mutants were obtained by site-directed mutagenesis at position 113, which is a residue that lies near a constriction in the lumen of the transmembrane β barrel, and fall into two classes. Members of the tight-binding class, M113D, M113N, M113V, M113H, M113F and M113Y, bind βCD ∼104-fold more avidly than the remaining αHL pores, including WT-αHL. The lower Kd values of these mutants are dominated by reduced values of koff. The major effect of the mutations is most likely a remodeling of the binding site for βCD in the vicinity of position 113. In addition, there is a smaller voltage-sensitive component of the binding, which is also affected by the residue at 113 and may result from transport of the neutral βCD molecule by electroosmotic flow. The mutant pores for which the dwell time of βCD is prolonged can serve as improved components for stochastic sensors.
A Dynamic Attribute Satiation Model of Variety-Seeking Behavior
Authors: McAlister Leigh
Published: July 2002

This paper presents a model of individual consumer choice for separate choice occasions. Contrary to the notion that each choice is essentially independent of its predecessors, dependence is proposed as the key to variety-seeking behavior. As an individual's consumption history evolves, the pattern of attribute accumulations changes, leading to preference for items rich in different attributes at different points in time. The model is operationalized using soft drink consumption diaries, and predicts choices better than a model that ignores choice dependence.
Tate cohomology lowers chromatic Bousfield classes
Authors: Hovey Mark , Sadofsky Hal
Published: July 2002

Let

G
G

be a finite group. We use recent results of J. P. C. Greenlees and H. Sadofsky to show that the Tate homology of

E
(
n
)

E(n)

local spectra with respect to

G
G

produces

E
(
n
−
1
)

E(n-1)

local spectra. We also show that the Bousfield class of the Tate homology of

L

n

X

L_{n}X

(for

X
X

finite) is the same as that of

L

n
−
1

X

L_{n-1}X

. To be precise, recall that Tate homology is a functor from

G
G

-spectra to

G
G

-spectra. To produce a functor

P

G

P_{G}

from spectra to spectra, we look at a spectrum as a naive

G
G

-spectrum on which

G
G

acts trivially, apply Tate homology, and take

G
G

-fixed points. This composite is the functor we shall actually study, and we’ll prove that
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="mathematical left-angle upper P Subscript upper G Baseline left-parenthesis upper L Subscript n Baseline upper X right-parenthesis mathematical right-angle equals mathematical left-angle upper L Subscript n minus 1 Baseline upper X mathematical right-angle">

⟨

P

G

(

L

n

X
)
⟩
=
⟨

L

n
−
1

X
⟩

\langle P_{G}(L_{n}X) \rangle = \langle L_{n-1}X \rangle

when

X
X

is finite. When

G
=

Σ

p

G = \Sigma _{p}

, the symmetric group on

p
p

letters, this is related to a conjecture of Hopkins and Mahowald (usually framed in terms of Mahowald’s functor

R

P

−
∞

(
−
)

{\mathbf R}P_{-\infty }(-)

).
Homotopy coherent category theory
Authors: Cordier Jean-Marc , Porter Timothy
Published: July 2002

This article is an introduction to the categorical theory of homotopy coherence. It is based on the construction of the homotopy coherent analogues of end and coend, extending ideas of Meyer and others. The paper aims to develop homotopy coherent analogues of many of the results of elementary category theory, in particular it handles a homotopy coherent form of the Yoneda lemma and of Kan extensions. This latter area is linked with the theory of generalised derived functors.
The trace of jet space 𝐽^{𝑘}Λ^{𝜔} to an arbitrary closed subset of ℝⁿ
Authors: Brudnyi Yuri , Shvartsman Pavel
Published: July 2002

The classical Whitney extension theorem describes the trace

J
k

|

X

J^k|_X

of the space of

k
k

-jets generated by functions from

C
k

(

R

n

)

C^k(\mathbb R^n)

to an arbitrary closed subset

X
⊂

R

n

X\subset \mathbb R^n

. It establishes existence of a bounded linear extension operator as well. In this paper we investigate a similar problem for the space

C
k

Λ

C^k\Lambda

of functions whose higher derivatives satisfy the Zygmund condition with majorant

ω
\omega

. The main result states that the vector function

f
→

=
(

f
α

:
X
→

R

)

|

α

|

≤
k

\vec f=(f_\alpha \colon X\to \mathbb R)_{|\alpha |\le k}

belongs to the corresponding trace space if the trace

f
→

|

Y

\vec f|_Y

to every subset

Y
⊂
X

Y\subset X

of cardinality

3
⋅

2
ℓ

3\cdot 2^\ell

, where

ℓ
=
(

n
+
k
−
1
k
+
1

)

\ell =(\begin {smallmatrix}n+k-1 k+1\end {smallmatrix})

, can be extended to a function

f
Y

∈

C
k

Λ

f_Y\in C^k\Lambda

and

sup
Y

|

f
Y

|

C
k

Λ
ω

>
∞

\sup _Y|f_Y|_{C^k\Lambda ^\omega }>\infty

. The number

3
⋅

2
l

3\cdot 2^l

generally speaking cannot be reduced. The Whitney theorem can be reformulated in this way as well, but with a two-pointed subset

Y
⊂
X

Y\subset X

. The approach is based on the theory of local polynomial approximations and a result on Lipschitz selections of multivalued mappings.
Gorenstein space with nonzero evaluation map
Authors: Gammelin H.
Published: July 2002

Let

(
A
,
d
)

(A,d)

be a differential graded algebra of finite type, if

H
∗

(
A
)

H^*(A)

is a Gorenstein graded algebra, then so is

A
A

. The purpose of this paper is to prove the converse under some mild hypotheses. We deduce a new characterization of Poincaré duality spaces as well as spaces with a nonzero evaluation map.
On the optimal local regularity for the Yang-Mills equations in ℝ⁴⁺¹
Authors: Klainerman Sergiu , Tataru Daniel
Published: July 2002

The aim of the paper is to develop the Fourier Analysis techniques needed in the study of optimal well-posedness and global regularity properties of the Yang-Mills equations in Minkowski space-time

R

n
+
1

\mathbb {R}^{n+1}

, for the case of the critical dimension

n
=
4

n=4

. We introduce new functional spaces and prove new bilinear estimates for solutions of the homogeneous wave equation, which can be viewed as generalizations of the well-known Strichartz-Pecher inequalities.
Finite quaternionic matrix groups
Authors: Nebe Gabriele
Published: July 2002

Let

D

\mathcal {D}

be a definite quaternion algebra such that its center has degree

d
d

over

Q

\mathbb {Q}

. A subgroup

G
G

of

G

L
n

(

D

)

GL_n(\mathcal {D})

is absolutely irreducible if the

Q

\mathbb {Q}

-algebra spanned by the matrices in

G
G

is

D

n
×
n

\mathcal {D}^{n\times n}

. The finite absolutely irreducible subgroups of

G

L
n

(

D

)

GL_n(\mathcal {D})

are classified for

n
d
≤
10

nd \leq 10

by constructing representatives of the conjugacy classes of the maximal finite ones. Methods to construct the groups and to deal with the quaternion algebras are developed. The investigation of the invariant rational lattices yields quaternionic structures for many interesting lattices.
Cytoplasmic Localization and Evolutionary Conservation of MEI-218, a Protein Required for Meiotic Crossing-over inDrosophila
Authors: Manheim Elizabeth A. , Jang Janet K. , Dominic Danielle , McKim Kim S.
Published: July 2002

During Drosophila oogenesis, the oocyte is formed within a 16-cell cyst immediately after four incomplete cell divisions. One of the primary events in oocyte development is meiotic recombination. Here, we report the intracellular localization of the MEI-218 protein that is specifically required for meiotic crossing-over. To understand the role of mei-218 in meiosis and to study the regulation of genes required for meiotic recombination, we characterized the expression pattern of its RNA and protein. Furthermore, we cloned and sequenced mei-218from two other Drosophila species. Themei-218 RNA and protein have a similar expression pattern, appearing first in early meiotic prophase and then rapidly disappearing as prophase is completed. This pattern corresponds to a specific appearance of the mei-218 gene product in the region of the ovary where meiotic prophase occurs. Althoughmei-218 is required for 95% of all crossovers, the protein is found exclusively in the cytoplasm. Based on these results, we suggest that mei-218 does not have a direct role in recombination but rather regulates other factors required for the production of crossovers. We propose that mei-218 is a molecular link between oocyte differentiation and meiosis.
Calign: aligning sequences with restricted affine gap penalties.
Authors: Chao K M
Published: July 2002

MOTIVATION: Given a genomic DNA sequence, it is still an open problem to determine its coding regions, i.e. the region consisting of exons and introns. The comparison of cDNA and genomic DNA helps the understanding of coding regions. For such an application, it might be adequate to use the restricted affine gap penalties which penalize long gaps with a constant penalty. RESULTS: Several techniques developed for solving the approximate string-matching problem are employed to yield efficient algorithms for computing the optimal alignment with restricted affine gap penalties. In particular, efficient algorithms can be derived based on the suffix automaton with failure transitions and on the diagonalwise monotonicity of the cost tables. We have implemented the above methods in C on Sun workstations running SunOS Unix. Preliminary experiments show that these approaches are very promising for aligning a cDNA sequence with a genomic DNA sequence. AVAILABILITY: Calign is available free of charge by anonymous ftp at: iubio.bio. indiana.edu, directory: molbio/align, files: calign.driver.c calign. c. Another URL reference for the files is http://iubio.bio.indiana.edu/soft/molbio/align/+ ++calign.c.
The Predictive Toxicology Challenge 2000–2001
Authors: Helma C. , King R. D. , Kramer S. , Srinivasan A.
Published: July 2002

Summary: We initiated the Predictive Toxicology Challenge (PTC) to stimulate the development of advanced SAR techniques for predictive toxicology models. The goal of this challenge is to predict the rodent carcinogenicity of new compounds based on the experimental results of the US National Toxicology Program (NTP). Submissions will be evaluated on quantitative and qualitative scales to select the most predictive models and those with the highest toxicological relevance.

Availability: http://www.informatik.uni-freiburg.de/~ml/ptc/

Contact: helma@informatik.uni-freiburg.de

* To whom correspondence should be addressed.
Linear modes of gene expression determined by independent
component analysis
Authors: Liebermeister Wolfram
Published: July 2002

Motivation: The expression of genes is controlled by specific combinations of cellular variables. We applied Independent Component Analysis (ICA) to gene expression data, deriving a linear model based on hidden variables, which we term ‘expression modes’. The expression of each gene is a linear function of the expression modes, where, according to the ICA model, the linear influences of different modes show a minimal statistical dependence, and their distributions deviate sharply from the normal distribution.

Results: Studying cell cycle-related gene expression in yeast, we found that the dominant expression modes could be related to distinct biological functions, such as phases of the cell cycle or the mating response. Analysis of human lymphocytes revealed modes that were related to characteristic differences between cell types. With both data sets, the linear influences of the dominant modes showed distributions with large tails, indicating the existence of specifically up- and downregulated target genes. The expression modes and their influences can be used to visualize the samples and genes in low-dimensional spaces. A projection to expression modes helps to highlight particular biological functions, to reduce noise, and to compress the data in a biologically sensible way.

Availability: The FastICA algorithm (Hyvärinen, IEEE Trans. Neural Netw. , 10, 626–634, 1999) is freely available at http://www.cis.hut.fi/projects/ica/fastica/. Additional matlab scripts and detailed results can be downloaded from http://www.molgen.mpg.de/research/lehrach/projects/genica/

Contact: wolfram.liebermeister@rz.hu-berlin.de
Compensation for nucleotide bias in a genome by representation
as a discrete channel with noise
Authors: Schreiber Mark , Brown Chris
Published: July 2002

Motivation: Calculation of the information content of motifsin genomes highly biased in nucleotide composition is likely to lead to overestimates of the amount of useful informationin the motif. Calculating relative information can compensate for biases, however the resulting information content is the amount seen by an observer and not by a macromolecule binding to the motif. The latter is needed to calculate the discriminatory power of the motif and to compare motifs between species.

Results: By treating a biased genome as a discrete channel with noise, in accordance with Shannon Information Theory, we were able to remove both ‘Distortion’ and ‘Noise’ from the motif and recover a more instructive biological ‘signal.’ A Java application, LogoPaint, was developed to remove nucleotide bias distortion and triplet frequency noise from motifs, calculate information content and present the motif as a logo. We demonstrate how this technique can ‘unmask’ motifs in the translation initiation regions of bacteria that are obscured by strong sequence biases.

Availability: LogoPaint is available to all users from the authors as an executable JAR file. Source code is available by arrangement.

Contact: chris.brown@stonebow.otago.ac.nz

* To whom correspondence should be addressed.
ADVERTISING RESTRICTIONS, COMPETITION, AND ALCOHOL CONSUMPTION
Authors: Tremblay Victor J. , Okuyama Kumiko
Published: July 2002

Distilled spirits producers recently voted to eliminate their voluntary ban on broadcast advertising. The ban received public support because of the high social cost associated with alcohol consumption and the belief that advertising promotes alcohol consumption and abuse. In spite of this belief, the empirical evidence indicates that advertising has no significant effect on the market demand for distilled spirits. This evidence has led many policy economists to conclude that eliminating the ban will have no effect on alcohol consumption. The purpose of this research is to show that this conclusion is incorrect because it ignores the fact that advertising restrictions may affect industry competition as well as market demand.
Spontaneous insertion and partitioning of alkaline phosphatase into model lipid rafts
Authors: Milhiet Pierre‐Emmanuel , Giocondi Marie‐Cécile , Baghdadi Omid , Ronzon Frédéric , Roux Bernard , Le Grimellec Christian
Published: July 2002

Several cell surface eukaryotic proteins have a glycosylphosphatidylinositol (GPI) modification at the C‐terminal end that serves as an anchor to the plasma membrane and could be responsible for the presence of GPI proteins in rafts, a type of functionally important membrane microdomain enriched in sphingolipids and cholesterol. In order to understand better how GPI proteins partition into rafts, the insertion of the GPI‐anchored alkaline phosphatase (AP) was studied in real‐time using atomic force microscopy. Supported phospholipid bilayers made of a mixture of sphingomyelin–dioleoylphosphatidylcholine containing cholesterol (Chl+) or not (Chl−) were used to mimic the fluid‐ordered lipid phase separation in biological membranes. Spontaneous insertion of AP through its GPI anchor was observed inside both Chl+ and Chl− lipid ordered domains, but AP insertion was markedly increased by the presence of cholesterol.
Merging mitochondria matters
Authors: Westermann Benedikt
Published: July 2002

Fusion is essential for mitochondrial function in a great variety of eukaryotic cell types. Yeast cells defective in mitohondrial fusion are respiration‐deficient, human cells use complementation of fused mitochondria as a defence against the accumulation of oxidative damage during cellular aging and fusion is required to build an intracellular mitochondrial continuum that allows the dissipation of energy in the cell. Moreover, developmental processes such as spermatogenesis in Drosophila require regulated mitochondrial fusion. Some of the molecular mediators of mitochondrial membrane fusion have been identified in recent years. An evolutionarily conserved large GTPase in the outer membrane is essential for mitochondrial fusion, and genetic screens in yeast are revealing an increasing number of additional important genes. Mechanistic studies have provided the first insights into how the problem of faithfully fusing a double membrane‐bounded organelle in a coordinated manner is solved.
A multicentre randomized controlled trial of oral misoprostol and i.m. syntometrine in the management of the third stage of labour
Authors: Ng P.S. , Chan A.S.M. , Sin W.K. , Tang L.C.H. , Cheung K.B. , Yuen P.M.
Published: July 2002

Postpartum haemorrhage accounts for nearly 28% of maternal mortality in developing countries. Syntometrine is an effective and commonly used oxytocic in preventing postpartum haemorrhage, but it requires a controlled storage environment and i.m. administration. Misoprostol is an orally active uterotonic agent. A total of 2058 patients having a singleton pregnancy, low risk for postpartum haemorrhage and vaginal delivery were randomized to receive either 1 ml syntometrine or 600 μg misoprostol for the management of the third stage of labour. There were no significant differences between the two groups in the mean blood loss, the incidence of postpartum haemorrhage and the fall in haemoglobin concentration. The need for additional oxytocic injection was significantly higher in the misoprostol group [relative risk (RR) 1.62, 95% confidence interval (CI) 1.34–1.96], but that of manual removal of placenta was reduced (RR 0.29, 95% CI 0.09–0.87). Shivering and transient pyrexia were more common in the misoprostol group. Oral misoprostol might be used in the management of the third stage, especially in situations where the use of syntometrine is contraindicated and facilities for storage and parenteral administration of oxytocics are limited.
Increased circulating lipid peroxides in severe preeclampsia activate NF‐κΒ and upregulate ICAM‐1 in vascular endothelial cells
Authors: Takacs P. , Kauma S. W. , Sholley M. M. , Walsh S. W. , Dinsmoor M. J. , Green K.
Published: July 2002

Preeclampsia is a systemic disease of pregnancy characterized by maternal hypertension, proteinuria, and edema. These clinical pathological findings may be attributed to abnormalities in vascular endothelial activation secondary to increased oxidative stress. To test the hypothesis that increased circulating lipid peroxides in preeclamptic women activate vascular endothelial cells, we determined NF‐κΒ transcriptional activity and ICAM‐1 expression in human umbilical vein endothelial cells (HUVEC) cultured with plasma from women with severe preeclampsia (preeclamptic plasma, N = 12) or plasma from normal pregnancies (normal plasma, N = 12). Preeclamptic women had increased circulating lipid peroxides compared with normal pregnant women, as demonstrated by a 4.5‐fold higher concentration of plasma malondialdehyde (P<0.001). By using a NF‐κΒ luciferase reporter construct transfected into HUVEC, preeclamptic plasma was found to up‐regulate HUVEC NF‐κΒ activity by 2.5‐fold when compared with normal plasma (P<0.001). Inhibition of lipid peroxides with both vitamin E and N‐acetyl‐cysteine significantly reduced NF‐κΒ activation in response to preeclamptic‐plasma by 77% (P<0.005) and 76% (P<0.01), respectively. Flow cytometric analysis revealed that preeclamptic‐plasma also up‐regulated HUVEC ICAM‐1 expression by 30% (P<0.001) compared with normal‐plasma, while both vitamin E (P<0.005) and N‐acetyl‐cysteine (P<0.0001) significantly inhibited this effect. In summary, elevated plasma levels of lipid peroxides in preeclampsia are associated with increased NF‐κΒ activation and ICAM‐1 expression on HUVEC, which can be inhibited by vitamin E and N‐acetyl‐cysteine.
Predicting protein decomposition: the case of aspartic–acid racemization kinetics
Authors: Collins M. J. , Waite E. R. , van Duin A. C. T.
Published: July 2002

The increase in proportion of the non–biological (D–) isomer of aspartic–acid (Asp) relative to the L–isomer has been widely used in archaeology and geochemistry as a tool for dating. The method has proved controversial, particularly when used for bones. The non–linear kinetics of Asp racemization have prompted a number of suggestions as to the underlying mechanism(s) and have led to the use of mathematical transformations which linearize the increase in D–Asp with respect to time. Using one example, a suggestion that the initial rapid phase of Asp racemization is due to a contribution from asparagine (Asn), we demonstrate how a simple model of the degradation and racemization of Asn can be used to predict the observed kinetics. A more complex model of peptide bound Asx (Asn + Asp) racemization, which occurs via the formation of a cyclic succinimide (Asu), can be used to correctly predict Asx racemization kinetics in proteins at high temperatures (95–140°C). The model fails to predict racemization kinetics in dentine collagen at 37°C. The reason for this is that Asu formation is highly conformation dependent and is predicted to occur extremely slowly in triple helical collagen. As conformation strongly influences the rate of Asu formation and hence Asx racemization, the use of extrapolation from high temperatures to estimate racemization kinetics of Asx in proteins below their denaturation temperature is called into question.

In the case of archaeological bone, we argue that the D:L ratio of Asx reflects the proportion of non–helical to helical collagen, overlain by the effects of leaching of more soluble (and conformationally unconstrained) peptides. Thus, racemization kinetics in bone are potentially unpredictable, and the proposed use of Asx racemization to estimate the extent of DNA depurination in archaeological bones is challenged.
A new theory of cytotoxic T–lymphocyte memory: implications for HIV treatment
Authors: Wodarz Dominik , Page Karen M. , Arnaout Ramy A. , Thomsen Allan R. , Lifson Jeffrey D. , Nowak Martin A.
Published: July 2002

We use simple mathematical models to examine the dynamics of primary and secondary cytotoxic T–lymphocyte (CTL) responses to viral infections. In particular, we are interested in conditions required to resolve the infection and to protect the host upon secondary challenge. While protection against reinfection is only effective in a restricted set of circumstances, we find that resolution of the primary infection requires persistence of CTL precursors (CTLp), as well as a fast rate of activation of the CTLp. Since these are commonly the defining characteristics of CTL memory, we propose that CTL memory may have evolved in order to clear the virus during primary challenge. W e show experimental data from lymphocytic choriomeningitis virus infection in mice, supporting our theory on CTL memory. We adapt our models to HIV and find that immune impairment during the primary phase of the infection may result in the failure to establish CTL memory which in turn leads to viral persistence. Based on our models we suggest conceptual treatment regimes which ensure establishment of CTL memory. This would allow the immune response to control HIV in the long term in the absence of continued therapy.
Three–dimensional analysis of object properties during active electrolocation in mormyrid weakly electric fishes (Gnathonemus petersii)
Authors: Emde Gerhard von der , Schwarz Stephan
Published: July 2002

Weakly electric fishes are nocturnal and orientate in the absence of vision by using their electrical sense. This enables them not only to navigate but also to perceive and recognize objects in complete darkness. They create an electric field around their bodies by producing electric signals with specialized electric organs. Objects within this field alter the electric current at electroreceptor organs, which are distributed over almost the entire body surface. During active electrolocation, fishes detect, localize and analyse objects by monitoring their self–produced electric signals. We investigated the ability of the mormyridGnathonemus petersiito perceive objects three–dimensionally in space. Within a range of about 12cm,G.petersiican perceive the distance of objects. Depth perception is independent of object size, shape and material. The mechanism for distance determination through electrolocation involves calculating the ratio between two parameters (maximal slope and maximal amplitude) of the electrical image which each object projects onto the fish's skin. During active electrolocation, electric fishes cannot only locate objects in space but in addition can determine the three–dimensional shape of an object. Up to certain limits, objects are spontaneously categorized according to their shapes, but not according to their sizes or the materials of which they are made.
Episodic memory and autonoetic consciousness: a first–person approach
Authors: Gardiner John M.
Published: July 2002

Episodic memory is identified with autonoetic consciousness, which gives rise to remembering in the sense of self–recollection in the mental re–enactment of previous events at which one was present. Autonoetic consciousness is distinguished from noetic consciousness, which gives rise to awareness of the past that is limited to feelings of familiarity or knowing. Noetic consciousness is identified not with episodic but with semantic memory, which involves general knowledge. A recently developed approach to episodic memory makes use of ‘first–person’ reports of remembering and knowing. Studies using this approach have revealed many independent variables that selectively affect remembering and others that selectively affect knowing. These studies can also be interpreted in terms of distinctiveness and fluency of processing. Remembering and knowing do not correspond with degrees of confidence in memory. Nor does remembering always control the memory response. There is evidence that remembering is selectively impaired in various populations, including not only amnesic patients and older adults but also adults with Asperger's syndrome. This first–person approach to episodic memory represents one way in which that most elusive aspect of consciousness, its subjectivity, can be investigated scientifically. The two kinds of conscious experiences can be manipulated experimentally in ways that are systematic, replicable and intelligible theoretically.
The loop domain of heat shock transcription factor 1 dictates DNA-binding specificity and responses to heat stress
Authors: Ahn Sang-Gun , Liu Phillip C.C. , Klyachko Katya , Morimoto Richard I. , Thiele Dennis J.
Published: July 2002

Eukaryotic heat shock transcription factors (HSF) regulate an evolutionarily conserved stress-response pathway essential for survival against a variety of environmental and developmental stresses. Although the highly similar HSF family members have distinct roles in responding to stress and activating target gene expression, the mechanisms that govern these roles are unknown. Here we identify a loop within the HSF1 DNA-binding domain that dictates HSF isoform specific DNA binding in vitro and preferential target gene activation by HSF family members in both a yeast transcription assay and in mammalian cells. These characteristics of the HSF1 loop region are transposable to HSF2 and sufficient to confer DNA-binding specificity, heat shock inducibleHSP gene expression and protection from heat-induced apoptosis in vivo. In addition, the loop suppresses formation of the HSF1 trimer under basal conditions and is required for heat-inducible trimerization in a purified system in vitro, suggesting that this domain is a critical part of the HSF1 heat-stress-sensing mechanism. We propose that this domain defines a signature for HSF1 that constitutes an important determinant for how cells utilize a family of transcription factors to respond to distinct stresses.
IRE1-mediated unconventional mRNA splicing and S2P-mediated ATF6 cleavage merge to regulate XBP1 in signaling the unfolded protein response
Authors: Lee Kyungho , Tirasophon Witoon , Shen Xiaohua , Michalak Marek , Prywes Ron , Okada Tetsuya , Yoshida Hiderou , Mori Kazutoshi , Kaufman Randal J.
Published: July 2002

All eukaryotic cells respond to the accumulation of unfolded proteins in the endoplasmic reticulum (ER) by signaling an adaptive pathway termed the unfolded protein response (UPR). In yeast, a type-I ER transmembrane protein kinase, Ire1p, is the proximal sensor of unfolded proteins in the ER lumen that initiates an unconventional splicing reaction onHAC1mRNA. Hac1p is a transcription factor required for induction of UPR genes. In higher eukaryotic cells, the UPR also induces site-2 protease (S2P)-mediated cleavage of ER-localized ATF6 to generate an N-terminal fragment that activates transcription of UPR genes. To elucidate the requirements for IRE1α and ATF6 for signaling the mammalian UPR, we identified a UPR reporter gene that was defective for induction inIRE1α-null mouse embryonic fibroblasts and S2P-deficient Chinese hamster ovary (CHO) cells. We show that the endoribonuclease activity of IRE1α is required to spliceXBP1(X-boxbindingprotein) mRNA to generate a new C terminus, thereby converting it into a potent UPR transcriptional activator. IRE1α was not required for ATF6 cleavage, nuclear translocation, or transcriptional activation. However, ATF6 cleavage was required for IRE1α-dependent induction of UPR transcription. We propose that nuclear-localized IRE1α and cytoplasmic-localized ATF6 signaling pathways merge through regulation of XBP1 activity to induce downstream gene expression. Whereas ATF6 increases the amount ofXBP1mRNA, IRE1α removes an unconventional 26-nucleotide intron that increases XBP1 transactivation potential. Both processing of ATF6 and IRE1α-mediated splicing ofXBP1mRNA are required for full activation of the UPR.
A Novel Active L1 Retrotransposon Subfamily in the Mouse
Authors: Goodier John L. , Ostertag Eric M. , Du Kevin , Kazazian Haig H.
Published: July 2002

Unlike human L1 retrotransposons, the 5′ UTR of mouse L1 elements contains tandem repeats of ∼200 bp in length called monomers. Multiple L1 subfamilies exist in the mouse which are distinguished by their monomer sequences. We previously described a young subfamily, called the TF subfamily, which contains ∼1800 active elements among its 3000 full-length members. Here we characterize a novel subfamily of mouse L1 elements, GF, which has unique monomer sequence and unusual patterns of monomer organization. A majority of these GF elements also have a unique length polymorphism in ORF1. Polymorphism analysis of GF elements in various mouse subspecies and laboratory strains revealed that, like TF, the GF subfamily is young and expanding. About 1500 full-length GF elements exist in the diploid mouse genome and, based on the results of a cell culture assay, ∼400 GF elements are potentially capable of retrotransposition. We also tested 14 A-type subfamily elements in the assay and estimate that about 900 active A elements may be present in the mouse genome. Thus, it is now known that there are three large active subfamilies of mouse L1s; TF, A, and GF, and that in total ∼3000 full-length elements are potentially capable of active retrotransposition. This number is in great excess to the number of L1 elements thought to be active in the human genome.
Comparative Sequence Analysis of the Imprinted Dlk1–Gtl2 Locus in Three Mammalian Species Reveals Highly Conserved Genomic Elements and Refines Comparison with the Igf2–H19 Region
Authors: Paulsen Martina , Takada Shuji , Youngson Neil A. , Benchaib Mehdi , Charlier Carole , Segers Karin , Georges Michel , Ferguson-Smith Anne C.
Published: July 2002

The Dlk1–Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potential to contribute to our understanding of common features involved in imprinting control. We have sequenced this conserved region in the mouse and sheep and included the human sequence in a three species comparison. This analysis resulted in a precise conservation map and identification of highly conserved sequence elements, some of which we have shown previously to be differentially methylated in the mouse. Additionally, this analysis facilitated identification of a CpG-rich tandem repeat array located ∼13–15 kb upstream of Gtl2. Furthermore, we have identified a third imprinted transcript that overlaps with the last Dlk1 exon in the mouse. This transcript lacks a conserved open reading frame and is probably generated by cleavage of extendedDlk1 transcripts. Because Dlk1 and Gtl2share many of the imprinting properties of the well-characterizedIgf2–H19 domain, it has been proposed that the two regions may be regulated in the same way. Comparative genomic examination of the two domains indicates that although there are similarities, other features are very different, including the location of conserved CTCF-binding sites, and the level of conservation at regulatory regions.

[The sequence data described in this paper have been submitted to the GenBank data library under accession no. AJ320506.]
High-Throughput Gene Mapping in Caenorhabditis elegans
Authors: Swan Kathryn A. , Curtis Damian E. , McKusick Kathleen B. , Voinov Alexander V. , Mapa Felipa A. , Cancilla Michael R.
Published: July 2002

Positional cloning of mutations in model genetic systems is a powerful method for the identification of targets of medical and agricultural importance. To facilitate the high-throughput mapping of mutations in Caenorhabditis elegans, we have identified a further 9602 putative new single nucleotide polymorphisms (SNPs) between two C. elegans strains, Bristol N2 and the Hawaiian mapping strain CB4856, by sequencing inserts from a CB4856 genomic DNA library and using an informatics pipeline to compare sequences with the canonical N2 genomic sequence. When combined with data from other laboratories, our marker set of 17,189 SNPs provides even coverage of the complete worm genome. To date, we have confirmed >1099 evenly spaced SNPs (one every 91 ± 56 kb) across the six chromosomes and validated the utility of our SNP marker set and new fluorescence polarization-based genotyping methods for systematic and high-throughput identification of genes in C. elegans by cloning several proprietary genes. We illustrate our approach by recombination mapping and confirmation of the mutation in the cloned gene, dpy-18.

[The sequence data described in this paper have been submitted to the NCBI dbSNP data library under accession nos. 4388625–4389689 and GenBank dbSTS under accession nos. 973810–974874. The following individuals and institutions kindly provided reagents, samples, or unpublished information as indicated in the paper: The C. elegans Sequencing Consortium and TheCaenorhabditis Genetics Center.]
Engineering a Reduced Escherichia coli Genome
Authors: Kolisnychenko Vitaliy , Plunkett Guy , Herring Christopher D. , Fehér Tamás , Pósfai János , Blattner Frederick R. , Pósfai György
Published: July 2002

Our goal is to construct an improved Escherichia coli to serve both as a better model organism and as a more useful technological tool for genome science. We developed techniques for precise genomic surgery and applied them to deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions to the genome. They are loaded with cryptic prophages, transposons, damaged genes, and genes of unknown function. Our method leaves no scars or markers behind and can be applied sequentially. Twelve K-islands were successfully deleted, resulting in an 8.1% reduced genome size, a 9.3% reduction of gene count, and elimination of 24 of the 44 transposable elements ofE. coli. These are particularly detrimental because they can mutagenize the genome or transpose into clones being propagated for sequencing, as happened in 18 places of the draft human genome sequence. We found no change in the growth rate on minimal medium, confirming the nonessential nature of these islands. This demonstration of feasibility opens the way for constructing a maximally reduced strain, which will provide a clean background for functional genomics studies, a more efficient background for use in biotechnology applications, and a unique tool for studies of genome stability and evolution.

[Sequence data described in this paper have been submitted to the DNA Data Bank of Japan, European Molecular Biology Laboratory, and GenBank databases under accession nos. AF402780,AF402779, and AF406953, respectively.]
Improved detection of homologous membrane proteins by inclusion of information from topology predictions
Authors: Hedman Maria , Deloof Hans , Von Heijne Gunnar , Elofsson Arne
Published: July 2002

A total of 20%–25% of the proteins in a typical genome are helical membrane proteins. The transmembrane regions of these proteins have markedly different properties when compared with globular proteins. This presents a problem when homology search algorithms optimized for globular proteins are applied to membrane proteins. Here we present modifications of the standard Smith‐Waterman and profile search algorithms that significantly improve the detection of related membrane proteins. The improvement is based on the inclusion of information about predicted transmembrane segments in the alignment algorithm. This is done by simply increasing the alignment score if two residues predicted to belong to transmembrane segments are aligned with each other. Benchmarking over a test set of G‐protein‐coupled receptor sequences shows that the number of false positives is significantly reduced in this way, both when closely related and distantly related proteins are searched for.
Artifact analysis of approximate helical cone‐beam CT reconstruction algorithms
Authors: Köhler Th. , Proksa R. , Bontus C. , Grass M. , Timmer J.
Published: July 2002

In this paper, four approximate cone‐beam CT reconstruction algorithms are compared: Advanced single slice rebinning (ASSR) as a representative of algorithms employing a two dimensional approximation, PI, PI‐SLANT, and 3‐PI which all use a proper three dimensional back‐projection. A detailed analysis of the image artifacts produced by these techniques shows that aliasing in the z‐direction is the predominant source of artifacts for a 16‐row scanner with 1.25 mm nominal slice thickness. For a detector with isotropic resolution of 0.5 mm, we found that ASSR and PI produce different kinds of artifacts which are almost at the same level, while PI‐SLANT produces none of these artifacts. It is shown that the use of redundant data in the 3‐PI method suppresses aliasing artifacts efficiently for both scanners.
Parameter optimization of a computer‐aided diagnosis scheme for the segmentation of microcalcification clusters in mammograms
Authors: Gavrielides Marios A. , Lo Joseph Y. , Floyd Carey E.
Published: July 2002

Our purpose in this study is to develop a parameter optimization technique for the segmentation of suspicious microcalcification clusters in digitized mammograms. In previous work, a computer‐aided diagnosis (CAD) scheme was developed that used local histogram analysis of overlapping subimages and a fuzzy rule‐based classifier to segment individual microcalcifications, and clustering analysis for reducing the number of false positive clusters. The performance of this previous CAD scheme depended on a large number of parameters such as the intervals used to calculate fuzzy membership values and on the combination of membership values used by each decision rule. These parameters were optimized empirically based on the performance of the algorithm on the training set. In order to overcome the limitations of manual training and rule generation, the segmentation algorithm was modified in order to incorporate automatic parameter optimization. For the segmentation of individual microcalcifications, the new algorithm used a neural network with fuzzy‐scaled inputs. The fuzzy‐scaled inputs were created by processing the histogram features with a family of membership functions, the parameters of which were automatically extracted from the distribution of the feature values. The neural network was trained to classify feature vectors as either positive or negative. Individual microcalcifications were segmented from positive subimages. After clustering, another neural network was trained to eliminate false positive clusters. A database of 98 images provided training and testing sets to optimize the parameters and evaluate the CAD scheme, respectively. The performance of the algorithm was evaluated with a FROC analysis. At a sensitivity rate of 93.2%, there was an average of 0.8 false positive clusters per image. The results are very comparable with those taken using our previously published rule‐based method. However, the new algorithm is more suited to generalize its performance on a larger population, depends on two monotonic outputs making its evaluation much easier and can be trained in an automatic way making practical its application on a large database.
Automated segmentation of anatomic regions in chest radiographs using an adaptive‐sized hybrid neural network
Authors: Tsujii Osamu , Freedman Matthew T. , Mun Seong K.
Published: July 2002

The purposes of this research are to investigate the effectiveness of our novel image features for segmentation of anatomic regions such as the lungs and the mediastinum in chest radiographs and to develop an automatic computerized method for image processing. A total of 85 screening chest radiographs from Johns Hopkins University Hospital were digitized to 2 K by 2.5 K pixels with 12 bit gray scale. To reduce the amount of information, the images were smoothed and subsampled to 256 by 310 pixels with 8 bit. The determination approach consists of classifying each pixel into two anatomic classes (lung and others) on the basis of several image features: (1) relative pixel address based on lung edges extracted through image processing using profile, (2) density normalized from lungs and mediastinum density, and (3) histogram equalized entropy. The combinations of image features were evaluated using an adaptive‐sized hybrid neural network consisting of an input, a hidden, and an output layer. Fourteen images were used for the training of the neural network and the remaining 71 images for testing. Using four features of relative address normalized density, and histogram equalized entropy, the neural networks classified lungs at 92% accuracy against test images following the same rules as for the training images.
A method for incorporating organ motion due to breathing into 3D dose calculations
Authors: Lujan Anthony E. , Larsen Edward W. , Balter James M. , Ten Haken Randall K.
Published: July 2002

A method is proposed that incorporates the effects of intratreatment organ motion due to breathing on the dose calculations for the treatment of liver disease. Our method is based on the convolution of a static dose distribution with a probability distribution function (PDF) which describes the nature of the motion. The organ motion due to breathing is assumed here to be one‐dimensional (in the superior–inferior direction), and is modeled using a periodic but asymmetric function (more time spent at exhale versus inhale). The dose distribution calculated using convolution‐based methods is compared to the static dose distribution using dose difference displays and the effective volume of the uninvolved liver, as per a liver dose escalation protocol in use at our institution. The convolution‐based calculation is also compared to direct simulations that model individual fractions of a treatment. Analysis shows that incorporation of the organ motion could lead to changes in the dose prescribed for a treatment based on the of the uninvolved liver. Comparison of convolution‐based calculations and direct simulation of various worst‐case scenarios indicates that a single convolution‐based calculation is sufficient to predict the dose distribution for the example treatment plan given.
Segmentation of suspicious clustered microcalcifications in mammograms
Authors: Gavrielides Marios A. , Lo Joseph Y. , Vargas‐Voracek Rene , Floyd Carey E.
Published: July 2002

We have developed a multistage computer‐aided diagnosis (CAD) scheme for the automated segmentation of suspicious microcalcification clusters in digital mammograms. The scheme consisted of three main processing steps. First, the breast region was segmented and its high‐frequency content was enhanced using unsharp masking. In the second step, individual microcalcifications were segmented using local histogram analysis on overlapping subimages. For this step, eight histogram features were extracted for each subimage and were used as input to a fuzzy rule‐based classifier that identified subimages containing microcalcifications and assigned the appropriate thresholds to segment any microcalcifications within them. The final step clustered the segmented microcalcifications and extracted the following features for each cluster: the number of microcalcifications, the average distance between microcalcifications, and the average number of times pixels in the cluster were segmented in the second step. Fuzzy logic rules incorporating the cluster features were designed to remove nonsuspicious clusters, defined as those with typically benign characteristics. A database of 98 images, with 48 images containing one or more microcalcification clusters, provided training and testing sets to optimize the parameters and evaluate the CAD scheme, respectively. The results showed a true positive rate of 93.2% and an average of 0.73 false positive clusters per image. A comparison of our results with other reported segmentation results on the same database showed comparable sensitivity and at the same time an improved false positive rate. The performance of the CAD scheme is encouraging for its use as an automatic tool for efficient and accurate diagnosis of breast cancer.
A laboratory-based nonlinear dynamics course for science and engineering students
Authors: Sungar N. , Sharpe J. P. , Moelter M. J. , Fleishon N. , Morrison K. , McDill J. , Schoonover R.
Published: July 2002

We describe the implementation of a new laboratory-based interdisciplinary undergraduate course on nonlinear dynamical systems. Geometrical methods and data visualization techniques are especially emphasized. A novel feature of the course is a required laboratory where the students analyze the behavior of a number of dynamical systems. Most of the laboratory experiments can be economically implemented using equipment available in many introductory physics microcomputer-based laboratories.