bluuebunny/crossref_metadata_2025 huggingface dataset:
Homogeneity and the disjoint arcs property
Authors: Krupski Paweł
Published: July 2002

Some previous results of the author towards a classification of homogeneous metric continua are improved. The disjoint arcs property is fully revealed in this context. In particular, closednn-manifolds,n=1,2n=1,2, are characterized as those homogeneous continua which do not have the disjoint arcs property.
On the Schwarz symmetry principle in a model case
Authors: Merker Joël , Meylan Francine
Published: July 2002

In this article, we prove that smooth CR diffeomorphisms between two real analytic holomorphically nondegenerate hypersurfaces, one of which is rigid and polynomial, extend to be locally biholomorphic. It turns out that the result can be generalized to not totally degenerate mappings, in the sense of Baouendi and Rothschild.
Recurrent critical points and typical limit sets of rational maps
Authors: Blokh Alexander , Mayer John , Oversteegen Lex
Published: July 2002

We consider a rational map

f
:

C

^

→

C

^

f:\widehat {\mathbb {C}}\to \widehat {\mathbb {C}}

of the Riemann sphere with normalized Lebesgue measure

μ
\mu

and show that if there is a subset of the Julia set

J
(
f
)

J(f)

of positive

μ
\mu

-measure whose points have limit sets not contained in the union of the limit sets of recurrent critical points, then

ω
(
x
)
=

C

^

=
J
(
f
)

\omega (x)=\widehat {\mathbb {C}}=J(f)

for

μ
\mu

-a.e. point

x
x

and

f
f

is conservative, ergodic and exact.
The structure of some virtually free pro-𝑝 groups
Authors: Scheiderer Claus
Published: July 2002

We prove two conjectures on pro-

p
p

groups made by Herfort, Ribes and Zalesskii. The first says that a finitely generated pro-

p
p

group which has an open free pro-

p
p

subgroup of index

p
p

is a free pro-

p
p

product

H
0

∗
(

S
1

×

H
1

)
∗
⋯
∗
(

S
m

×

H
m

)

H_0*(S_1\times H_1)*\cdots *(S_m\times H_m)

, where the

H
i

H_i

are free pro-

p
p

of finite rank and the

S
i

S_i

are cyclic of order

p
p

. The second says that if

F
F

is a free pro-

p
p

group of finite rank and

S
S

is a finite

p
p

-group of automorphisms of

F
F

, then

Fix
⁡
(
S
)

\operatorname {Fix}(S)

is a free factor of

F
F

. The proofs use cohomology, and in particular a “Brown theorem” for profinite groups.
Pi-envelopes of Lie superalgebras
Authors: Bahturin Yuri , Montgomery Susan
Published: July 2002

In this paper we find necessary and sufficient conditions on a finite-dimensional Lie superalgebra under which any associative PI-envelope of

L
L

is finite-dimensional. We also extend M. Scheunert’s result which enables one to pass from color Lie superalgebras to the ordinary ones, to the case of gradings by an arbitrary abelian group.
Integration and homogeneous functions
Authors: Lasserre Jean
Published: July 2002

We show that integrating a (positively) homogeneous function

f
f

on a compact domain

Ω
⊂

R
n

\Omega \subset R^n

reduces to integrating a related function on the boundary

∂

Ω

\partial {\Omega }

. The formula simplifies when the boundary

∂

Ω

\partial {\Omega }

is determined by homogeneous functions. Similar results are also presented for integration of exponentials and logarithms of homogeneous functions.
A characterization of the Clifford torus
Authors: Cheng Qing-Ming , Ishikawa Susumu
Published: July 2002

In this paper, we prove that an

n
n

-dimensional closed minimal hypersurface

M
M

with Ricci curvature

R
i
c
(
M
)
≥

n
2

Ric(M) \geq \dfrac {n}{2}

of a unit sphere

S

n
+
1

(
1
)

S^{n+1}(1)

is isometric to a Clifford torus if

n
≤
S
≤
n
+

14
(
n
+
4
)

9
n
+
30

n\leq S\leq n+\frac {14(n+4)}{9n+30}

, where

S
S

is the squared norm of the second fundamental form of

M
M

.
Bimodules over nest algebras and Deddens’ theorem
Authors: Todorov I.
Published: July 2002

We generalize Deddens’ theorem for nest algebras in the case of w*-closed nest algebras bimodules. For each such bimodule, we introduce a norm closed sub-bimodule of it, which corresponds to the radical of a nest algebra and describe it in a number of ways, generalizing known facts about nest algebras.
The sixth, eighth, ninth, and tenth powers of Ramanujan’s theta function
Authors: Ahlgren Scott
Published: July 2002

In his Lost Notebook, Ramanujan claimed that the “circular” summation of the

n
n

-th powers of the symmetric theta function

f
(
a
,
b
)

f(a,b)

satisfies a factorization of the form

f
(
a
,
b
)

F

n

(
a
b
)

f(a,b)F_{n}(ab)

. Moreover, Ramanujan recorded identities expressing

F

2

(
q
)

F_{2}(q)

,

F

3

(
q
)

F_{3}(q)

,

F

4

(
q
)

F_{4}(q)

,

F

5

(
q
)

F_{5}(q)

, and

F

7

(
q
)

F_{7}(q)

in terms of his theta functions

φ
(
q
)

\varphi (q)

,

ψ
(
q
)

\psi (q)

, and

f
(
−
q
)

f(-q)

. Ramanujan’s claims were proved by Rangachari, and later (via elementary methods) by Son. In this paper we obtain similar identities for

F

6

(
q
)

F_{6}(q)

,

F

8

(
q
)

F_{8}(q)

,

F

9

(
q
)

F_{9}(q)

, and

F

10

(
q
)

F_{10}(q)

.
On the Well-Posedness of the Kirchhoff String
Authors: Arosio Alberto , Panizzi Stefano
Published: July 2002

Let us consider the Cauchy problem for the quasilinear hyperbolic integro-differential equation
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartLayout 1st Row 1st Column u Subscript t t Baseline minus m left-parenthesis integral Underscript Subscript partial-differential normal upper Omega Baseline Endscripts StartAbsoluteValue nabla Subscript x Baseline u EndAbsoluteValue squared d x right-parenthesis delta Subscript x Baseline u equals f left-parenthesis x comma t right-parenthesis 2nd Column a m p semicolon 3rd Column a m p semicolon 4th Column a m p semicolon left-parenthesis x element-of normal upper Omega comma t greater-than 0 right-parenthesis comma 2nd Row 1st Column u left-parenthesis dot comma t right-parenthesis Subscript vertical-bar partial-differential normal upper Omega Baseline equals 0 2nd Column a m p semicolon 3rd Column a m p semicolon 4th Column a m p semicolon left-parenthesis t greater-than-or-equal-to 0 right-parenthesis comma EndLayout">

u

t
t

−
m

(

∫

∂

Ω

|

∇

x

u

|

2

d
x
)

δ

x

u
=
f
(
x
,
t
)

a
m
p
;

a
m
p
;

a
m
p
;
(
x
∈

Ω
,
t
>
0
)
,

u
(
⋅
,
t

)

|

∂
Ω

=
0

a
m
p
;

a
m
p
;

a
m
p
;
(
t
≥
0
)
,

\begin{align*} u_{tt} - m \left (\int _{_{\partial {\Omega }}} |\nabla _{x}u|^{2} \, dx \right ) \delta _{x}u= f(x,t) &&& (x\in \, \Omega , t > 0),\\ u(\cdot ,t)_{|\partial \Omega } =0 &&& (t\geq 0), \end{align*}

where

Ω
\Omega

is an open subset of

R

n

\mathbb {R}^{n}

and

m
m

is a positive function of one real variable which is continuously differentiable. We prove the well-posedness in the Hadamard sense (existence, uniqueness and continuous dependence of the local solution upon the initial data) in Sobolev spaces of low order.
One and two dimensional Cantor-Lebesgue type theorems
Authors: Ash J. , Wang Gang
Published: July 2002

Let

φ
(
n
)

\varphi (n)

be any function which grows more slowly than exponentially in

n
,

n,

i.e.,

lim sup

n
→
∞

φ
(
n

)

1

/

n

≤
1.

\limsup _{n\rightarrow \infty }\varphi (n)^{1/n}\leq 1.

There is a double trigonometric series whose coefficients grow like

φ
(
n
)
,

\varphi (n),

and which is everywhere convergent in the square, restricted rectangular, and one-way iterative senses. Given any preassigned rate, there is a one dimensional trigonometric series whose coefficients grow at that rate, but which has an everywhere convergent partial sum subsequence. There is a one dimensional trigonometric series whose coefficients grow like

φ
(
n
)
,

\varphi (n),

and which has the everywhere convergent partial sum subsequence

S

2
j

.

S_{2^j}.

For any

p
>
1
,

p>1,

there is a one dimensional trigonometric series whose coefficients grow like

φ
(

n

p
−
1

p

)
,

\varphi (n^{\frac {p-1}p}),

and which has the everywhere convergent partial sum subsequence

S

[

j
p

]

.

S_{[j^p]}.

All these examples exhibit, in a sense, the worst possible behavior. If

m
j

m_j

is increasing and has arbitrarily large gaps, there is a one dimensional trigonometric series with unbounded coefficients which has the everywhere convergent partial sum subsequence

S

m
j

.

S_{m_j}.
Rings with FZP
Authors: Fuchs P. , Maxson C. , Pilz G.
Published: July 2002

In this paper we investigate the problem of characterizing those rings 

R
R

such that every nonzero polynomial with coefficients from 

R
R

has a finite number of zeros in 

R
R

. Particular attention is directed to the class of skew polynomial domains.
Essentially Normal Operator + Compact Operator = Strongly Irreducible Operator
Authors: Jiang Chunlan , Sun Shunhua , Wang Zongyao
Published: July 2002

It is shown that given an essentially normal operator

T
T

with connected spectrum, there exists a compact operator

K
K

such that

T
+
K

T+K

is strongly irreducible.
On the Denjoy rank, the Kechris-Woodin rank and the Zalcwasser rank
Authors: Ki Haseo
Published: July 2002

We show that the Denjoy rank and the Zalcwasser rank are incomparable. We construct for any countable ordinal

α
\alpha

differentiable functions

f
f

and

g
g

such that the Zalcwasser rank and the Kechris-Woodin rank of

f
f

are

α
+
1

\alpha +1

but the Denjoy rank of

f
f

is 2 and the Denjoy rank and the Kechris-Woodin rank of

g
g

are

α
+
1

\alpha +1

but the Zalcwasser rank of

g
g

is 1. We then derive a theorem that shows the surprising behavior of the Denjoy rank, the Kechris-Woodin rank and the Zalcwasser rank.
Cohomological construction of quantized universal enveloping algebras
Authors: Donin Joseph , Shnider Steven
Published: July 2002

Given an associative algebra

A
A

and the category

C

\mathcal C

of its finite dimensional modules, additional structures on the algebra

A
A

induce corresponding ones on the category

C

\mathcal C

. Thus, the structure of a rigid quasi-tensor (braided monoidal) category on

R
e

p

A

Rep_{A}

is induced by an algebra homomorphism

A
→
A
⊗
A

A\to A\otimes A

(comultiplication), coassociative up to conjugation by

Φ
∈

A

⊗
3

\Phi \in A^{\otimes 3}

(associativity constraint) and cocommutative up to conjugation by

R

∈

A

⊗
2

\mathcal R \in A^{\otimes 2}

(commutativity constraint), together with an antiautomorphism (antipode)

S
S

of

A
A

satisfying the compatibility conditions. A morphism of quasi-tensor structures is given by an element

F
∈

A

⊗
2

F\in A^{\otimes 2}

with suitable induced actions on

Φ
\Phi

,

R

\mathcal R

and

S
S

. Drinfeld defined such a structure on

A
=
U
(

G

)
[
[
h
]
]

A=U(\mathcal G )[[h]]

for any semisimple Lie algebra

G

\mathcal {G}

with the usual comultiplication and antipode but nontrivial

R

\mathcal R

and

Φ
\Phi

, and proved that the corresponding quasi-tensor category is isomomorphic to the category of representations of the Drinfeld-Jimbo (DJ) quantum universal enveloping algebra (QUE),

U

h

(

G

)

U_{h}(\mathcal G )

. In the paper we give a direct cohomological construction of the

F
F

which reduces

Φ
\Phi

to the trivial associativity constraint, without any assumption on the prior existence of a strictly coassociative QUE. Thus we get a new approach to the DJ quantization. We prove that

F
F

can be chosen to satisfy some additional invariance conditions under (anti)automorphisms of

U
(

G

)
[
[
h
]
]

U(\mathcal G )[[h]]

, in particular,

F
F

gives an isomorphism of rigid quasi-tensor categories. Moreover, we prove that for pure imaginary values of the deformation parameter, the elements

F
F

,

R
R

and

Φ
\Phi

can be chosen to be formal unitary operators on the second and third tensor powers of the regular representation of the Lie group associated to

G

\mathcal G

with

Φ
\Phi

depending only on even powers of the deformation parameter. In addition, we consider some extra properties of these elements and give their interpretation in terms of additional structures on the relevant categories.
Intersection Lawson homology
Authors: Gajer Pawel
Published: July 2002

The aim of this paper is to construct and describe basic properties of a theory that unifies Lawson homology and intersection homology. It is shown that this theory has a localization sequence, is functorial, satisfies a property analogous to the Lawson Suspension Theorem, and is equipped with an operation analogous to the Friedlander-Mazur

s

\mathbf s

-operation.
Singular set of some Kähler orbifolds
Authors: Jeffres Thalia
Published: July 2002

We consider some examples of orbifolds with positive first Chern class. Applying a result of Ding and Tian, we show that the singularities must be very mild if the orbifold admits a Kähler-Einstein metric.
Structural properties of universal minimal dynamical systems for discrete semigroups
Authors: Balcar Bohuslav , Franek Frantisek
Published: July 2002

We show that for a discrete semigroup

S
S

there exists a uniquely determined complete Boolean algebra

B
(
S
)

B(S)

- the algebra of clopen subsets of

M
(
S
)

M(S)

.

M
(
S
)

M(S)

is the phase space of the universal minimal dynamical system for

S
S

and it is an extremally disconnected compact Hausdorff space. We deal with this connection of semigroups and complete Boolean algebras focusing on structural properties of these algebras. We show that

B
(
S
)

B(S)

is either atomic or atomless; that

B
(
S
)

B(S)

is weakly homogenous provided

S
S

has a minimal left ideal; and that for countable semigroups

B
(
S
)

B(S)

is semi-Cohen. We also present a class of what we call group-like semigroups that includes commutative semigroups, inverse semigroups, and right groups. The group reflection

G
(
S
)

G(S)

of a group-like semigroup

S
S

can be constructed via universal minimal dynamical system for

S
S

and, moreover,

B
(
S
)

B(S)

and

B
(
G
(
S
)
)

B(G(S))

are the same.
A fixed point index for generalized inward mappings of condensing type
Authors: Lan Kunquan , Webb Jeffrey
Published: July 2002

A fixed point index is defined for mappings defined on a cone

K
K

which do not necessarily take their values in

K
K

but satisfy a weak type of boundary condition called generalized inward. This class strictly includes the well-known weakly inward class. New results for existence of multiple fixed points are established.
On Vassiliev knot invariants induced from finite type 3-manifold invariants
Authors: Greenwood Matt , Lin Xiao-Song
Published: July 2002

We prove that the knot invariant induced by a

Z

\mathbb {Z}

-homology 3-sphere invariant of order

≤
k

\leq k

in Ohtsuki’s sense, where

k
≥
4

k\geq 4

, is of order

≤
k
−
2

\leq k-2

. The method developed in our computation shows that there is no

Z

\mathbb {Z}

-homology 3-sphere invariant of order 5.
Vaught’s conjecture and the Glimm-Effros property for Polish transformation groups
Authors: Hjorth Greg , Solecki Slawomir
Published: July 2002

We extend the original Glimm-Effros theorem for locally compact groups to a class of Polish groups including the nilpotent ones and those with an invariant metric. For this class we thereby obtain the topological Vaught conjecture.
Spherical functions and conformal densities on spherically symmetric 𝐶𝐴𝑇(-1)-spaces
Authors: Coornaert Michel , Papadopoulos Athanase
Published: July 2002

Let

X
X

be a

C
A
T
(
−
1
)

CAT(-1)

-space which is spherically symmetric around some point

x

0

∈
X

x_{0}\in X

and whose boundary has finite positive

s
−

s-

dimensional Hausdorff measure. Let

μ
=
(

μ

x

)

x
∈
X

\mu =(\mu _{x})_{x\in X}

be a conformal density of dimension

d
>
s

/

2

d>s/2

on

∂
X

\partial X

. We prove that

μ

x

0

\mu _{x_{0}}

is a weak limit of measures supported on spheres centered at

x

0

x_{0}

. These measures are expressed in terms of the total mass function of

μ
\mu

and of the

d
−

d-

dimensional spherical function on

X
X

. In particular, this result proves that

μ
\mu

is entirely determined by its dimension and its total mass function. The results of this paper apply in particular for symmetric spaces of rank one and semi-homogeneous trees.
Compressions of resolvents and maximal radius of regularity
Authors: Badea C. , Mbekhta M.
Published: July 2002

Suppose that

λ
−
T

\lambda - T

is left invertible in

L
(
H
)

L(H)

for all

λ
∈
Ω

\lambda \in \Omega

, where

Ω
\Omega

is an open subset of the complex plane. Then an operator-valued function

L
(
λ
)

L(\lambda )

is a left resolvent of

T
T

in

Ω
\Omega

if and only if

T
T

has an extension

T
~

\tilde {T}

, the resolvent of which is a dilation of

L
(
λ
)

L(\lambda )

of a particular form. Generalized resolvents exist on every open set

U
U

, with

U
¯

\overline {U}

included in the regular domain of

T
T

. This implies a formula for the maximal radius of regularity of

T
T

in terms of the spectral radius of its generalized inverses. A solution to an open problem raised by J. Zemánek is obtained.
The octonions
Authors: Baez John
Published: July 2002

The octonions are the largest of the four normed division algebras. While somewhat neglected due to their nonassociativity, they stand at the crossroads of many interesting fields of mathematics. Here we describe them and their relation to Clifford algebras and spinors, Bott periodicity, projective and Lorentzian geometry, Jordan algebras, and the exceptional Lie groups. We also touch upon their applications in quantum logic, special relativity and supersymmetry.
Analytic and geometric background of recurrence and non-explosion of the Brownian motion on Riemannian manifolds
Authors: Grigor’yan Alexander
Published: July 2002

We provide an overview of such properties of the Brownian motion on complete non-compact Riemannian manifolds as recurrence and non-explosion. It is shown that both properties have various analytic characterizations, in terms of the heat kernel, Green function, Liouville properties, etc. On the other hand, we consider a number of geometric conditions such as the volume growth, isoperimetric inequalities, curvature bounds, etc., which are related to recurrence and non-explosion.
Well-posedness in Sobolev spaces of the full water wave problem in 3-D
Authors: Wu Sijue
Published: July 2002

We consider the motion of the interface of a 3-D inviscid, incompressible, irrotational water wave, with air region above water region and surface tension zero. We prove that the motion of the interface of the water wave is not subject to Taylor instability, as long as the interface separates the whole 3-D space into two simply connected

C

2

C^{2}

regions. We prove further the existence and uniqueness of solutions of the full 3-D water wave problem, locally in time, for any initial interface that separates the whole 3-D space into two simply connected regions.
Crofton formulas in projective Finsler spaces
Authors: Álvarez Paiva J. , Fernandes E.
Published: July 2002

We extend the classical Crofton formulas in Euclidean integral geometry to Finsler metrics on

R

n

\mathbb {R}^n

whose geodesics are straight lines.
Kazhdan-Lusztig polynomials and a combinatoric for tilting modules
Authors: Soergel Wolfgang
Published: July 2002

This article gives a self-contained treatment of the theory of Kazhdan-Lusztig polynomials with special emphasis on affine reflection groups. There are only a few new results but several new proofs. We close with a conjectural character formula for tilting modules, which formed the starting point of these investigations.
Wound Closure in the Lamellipodia of Single Cells: Mediation by Actin Polymerization in the Absence of an Actomyosin Purse String
Authors: Henson John H. , Nazarian Ronniel , Schulberg Katrina L. , Trabosh Valerie A. , Kolnik Sarah E. , Burns Andrew R. , McPartland Kenneth J.
Published: July 2002

The actomyosin purse string is an evolutionarily conserved contractile structure that is involved in cytokinesis, morphogenesis, and wound healing. Recent studies suggested that an actomyosin purse string is crucial for the closure of wounds in single cells. In the present study, morphological and pharmacological methods were used to investigate the role of this structure in the closure of wounds in the peripheral cytoplasm of sea urchin coelomocytes. These discoidal shaped cells underwent a dramatic form of actin-based centripetal/retrograde flow and occasionally opened and closed spontaneous wounds in their lamellipodia. Fluorescent phalloidin staining indicated that a well defined fringe of actin filaments assembles from the margin of these holes, and drug studies with cytochalasin D and latrunculin A indicated that actin polymerization is required for wound closure. Additional evidence that actin polymerization is involved in wound closure was provided by the localization of components of the Arp2/3 complex to the wound margin. Significantly, myosin II immunolocalization demonstrated that it is not associated with wound margins despite being present in the perinuclear region. Pharmacological evidence for the lack of myosin II involvement in wound closure comes from experiments in which a microneedle was used to produce wounds in cells in which actomyosin contraction was inhibited by treatment with kinase inhibitors. Wounds produced in kinase inhibitor-treated cells closed in a manner similar to that seen with control cells. Taken together, our results suggest that an actomyosin purse string mechanism is not responsible for the closure of lamellar wounds in coelomocytes. We hypothesize that the wounds heal by means of a combination of the force produced by actin polymerization alone and centripetal flow. Interestingly, these cells did assemble an actomyosin structure around the margin of phagosome-like membrane invaginations, indicating that myosin is not simply excluded from the periphery by some general mechanism. The results indicate that the actomyosin purse string is not the only mechanism that can mediate wound closure in single cells.
The Outer Dynein Arm-Docking Complex: Composition and Characterization of a Subunit (Oda1) Necessary for Outer Arm Assembly
Authors: Takada Saeko , Wilkerson Curtis G. , Wakabayashi Ken-ichi , Kamiya Ritsu , Witman George B.
Published: July 2002

To learn more about how dyneins are targeted to specific sites in the flagellum, we have investigated a factor necessary for binding of outer arm dynein to the axonemal microtubules ofChlamydomonas. This factor, termed the outer dynein arm-docking complex (ODA-DC), previously was shown to be missing from axonemes of the outer dynein armless mutants oda1 and oda3. We have now partially purified the ODA-DC, determined that it contains equimolar amounts ofMr∼105,000 and ∼70,000 proteins plus a third protein of Mr∼25,000, and found that it is associated with the isolated outer arm in a 1:1 molar ratio. We have cloned a full-length cDNA encoding theMr∼70,000 protein; the sequence predicts a 62.5-kDa protein with potential homologs in higher ciliated organisms, including humans. Sequencing of corresponding cDNA from strain oda1 revealed it has a mutation resulting in a stop codon just downstream of the initiator ATG; thus, it is unable to make the full-length Mr∼70,000 protein. These results demonstrate that the ODA1 gene encodes the Mr∼70,000 protein, and that the protein is essential for assembly of the ODA-DC and the outer dynein arm onto the doublet microtubule.
The Yeast Synaptojanin-like Proteins Control the Cellular Distribution of Phosphatidylinositol (4,5)-Bisphosphate
Authors: Stefan Christopher J. , Audhya Anjon , Emr Scott D.
Published: July 2002

Phosphoinositides (PI) are synthesized and turned over by specific kinases, phosphatases, and lipases that ensure the proper localization of discrete PI isoforms at distinct membranes. We analyzed the role of the yeast synaptojanin-like proteins using a strain that expressed only a temperature-conditional allele of SJL2. Our analysis demonstrated that inactivation of the yeast synaptojanins leads to increased cellular levels of phosphatidylinositol (3,5)-bisphosphate and phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2), accompanied by defects in actin organization, endocytosis, and clathrin-mediated sorting between the Golgi and endosomes. The phenotypes observed in synaptojanin-deficient cells correlated with accumulation of PtdIns(4,5)P2, because these effects were rescued by mutations in MSS4or a mutant form of Sjl2p that harbors only PI 5-phosphatase activity. We utilized green fluorescent protein-pleckstrin homology domain chimeras (termed FLAREs for fluorescent lipid-associated reporters) with distinct PI-binding specificities to visualize pools of PtdIns(4,5)P2and phosphatidylinositol 4-phosphate in yeast. PtdIns(4,5)P2localized to the plasma membrane in a manner dependent on Mss4p activity. On inactivation of the yeast synaptojanins, PtdIns(4,5)P2accumulated in intracellular compartments, as well as the cell surface. In contrast, phosphatidylinositol 4-phosphate generated by Pik1p localized in intracellular compartments. Taken together, our results demonstrate that the yeast synaptojanins control the localization of PtdIns(4,5)P2in vivo and provide further evidence for the compartmentalization of different PI species.
Human Chromosomes 9, 12, and 15 Contain the Nucleation Sites of Stress-Induced Nuclear Bodies
Authors: Denegri Marco , Moralli Daniela , Rocchi Mariano , Biggiogera Marco , Raimondi Elena , Cobianchi Fabio , De Carli Luigi , Riva Silvano , Biamonti Giuseppe
Published: July 2002

We previously reported the identification of a novel nuclear compartment detectable in heat-shocked HeLa cells that we termed stress-induced Src-activated during mitosis nuclear body (SNB). This structure is the recruitment center for heat shock factor 1 and for a number of RNA processing factors, among a subset of Serine-Arginine splicing factors. In this article, we show that stress-induced SNBs are detectable in human but not in hamster cells. By means of hamster>human cell hybrids, we have identified three human chromosomes (9, 12, and 15) that are individually able to direct the formation of stress bodies in hamster cells. Similarly to stress-induced SNB, these bodies are sites of accumulation of hnRNP A1-interacting protein and heat shock factor 1, are usually associated to nucleoli, and consist of clusters of perichromatin granules. We show that the p13-q13 region of human chromosome 9 is sufficient to direct the formation of stress bodies in hamster>human cell hybrids. Fluorescence in situ hybridization experiments demonstrate that the pericentromeric heterochromatic q12 band of chromosome 9 and the centromeric regions of chromosomes 12 and 15 colocalize with stress-induced SNBs in human cells. Our data indicate that human chromosomes 9, 12, and 15 contain the nucleation sites of stress bodies in heat-shocked HeLa cells.
SplitsTree: analyzing and visualizing evolutionary data.
Authors: Huson D H
Published: July 2002

MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.
MView: a web-compatible database search or multiple alignment viewer.
Authors: Brown N P , Leroy C , Sander C
Published: July 2002

SUMMARY: MView is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. AVAILABILITY: Free from http://www.sander.ebi.ac.uk/mview/ subject to copyright restrictions. CONTACT: brown@ebi.ac.uk
MODELTEST: testing the model of DNA substitution.
Authors: Posada D , Crandall K A
Published: July 2002

SUMMARY: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
ESPript: analysis of multiple sequence alignments in PostScript.
Authors: Gouet P , Courcelle E , Stuart D I , M√©toz F
Published: July 2002

MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information. RESULTS: ESPript can be run via a command file or a friendly html-based user interface. The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences. It offers a palette of markers to highlight important regions in the alignment. ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program. AVAILABILITY: ESPript can be accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file is held in the directory pub/ESPript.
Artemis: sequence visualization and annotation
Authors: Rutherford Kim , Parkhill Julian , Crook James , Horsnell Terry , Rice Peter , Rajandream Marie-Adèle , Barrell Bart
Published: July 2002

Summary: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation. Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format.

Availability: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis

Contact: kmr@sanger.ac.uk
CONSEL: for assessing the confidence of phylogenetic tree
selection
Authors: Shimodaira Hidetoshi , Hasegawa Masami
Published: July 2002

Summary: CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees. The main thrust of the program is to calculate the p-value of the Approximately Unbiased (AU) test using the multi-scale bootstrap technique. This p-value is less biased than the other conventional p-values such as the Bootstrap Probability (BP), the Kishino–Hasegawa (KH) test, the Shimodaira–Hasegawa (SH) test, and the Weighted Shimodaira–Hasegawa (WSH) test. CONSEL calculates all these p-values from the output of the phylogeny program packages such as Molphy, PAML, and PAUP*. Furthermore, CONSEL is applicable to a wide class of problems where the BPs are available.

Availability: The programs are written in C language. The source code for Unix and the executable binary for DOS are found at http://www.ism.ac.jp/~shimo/

Contact: shimo@ism.ac.jp
Analysis of genomic sequences by Chaos Game Representation
Authors: Almeida Jonas S. , Carriço João
   A. , Maretzek António , Noble Peter A. , Fletcher Madilyn
Published: July 2002

Motivation: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find the coordinates for their position in a continuous space. This distribution of positions has two properties: it is unique, and the source sequence can be recovered from the coordinates such that distance between positions measures similarity between the corresponding sequences. The possibility of using the latter property to identify succession schemes have been entirely overlooked in previous studies which raises the possibility that CGR may be upgraded from a mere representation technique to a sequence modeling tool.

Results: The distribution of positions in the CGR plane were shown to be a generalization of Markov chain probability tables that accommodates non-integer orders. Therefore, Markov models are particular cases of CGR models rather than the reverse, as currently accepted. In addition, the CGR generalization has both practical (computational efficiency) and fundamental (scale independence) advantages. These results are illustrated by using Escherichia coli K-12 as a test data-set, in particular, the genes thrA , thrB and thrC of the threonine operon.

Availability: A web page interface has been created where analyses of arbitrary sequences by CGR can be performed on-line (http://www.itqb.unl.pt:1111/biomat/resources/resources.htm). The test data-set used in this report is also included.

Contact: almeidaj@musc.edu; mfletcher@biol.sc.edu
Evaluation of methods for the prediction of membrane spanning
regions
Authors: Möller Steffen , Croning Michael D. R. , Apweiler Rolf
Published: July 2002

Motivation: A variety of tools are available to predict the topology of transmembrane proteins. To date no independent evaluation of the performance of these tools has been published. A better understanding of the strengths and weaknesses of the different tools would guide both the biologist and the bioinformatician to make better predictions of membrane protein topology.

Results: Here we present an evaluation of the performance of the currently best known and most widely used methods for the prediction of transmembrane regions in proteins. Our results show that TMHMM is currently the best performing transmembrane prediction program.

Contact: moeller@ebi.ac.uk; croning@ebi.ac.uk; apweiler@ebi.ac.uk
Support vector machine approach for protein subcellular
localization prediction
Authors: Hua Sujun , Sun Zhirong
Published: July 2002

Motivation: Subcellular localization is a key functional characteristic of proteins. A fully automatic and reliable prediction system for protein subcellular localization is needed, especially for the analysis of large-scale genome sequences.

Results: In this paper, Support Vector Machine has been introduced to predict the subcellular localization of proteins from their amino acid compositions. The total prediction accuracies reach 91.4% for three subcellular locations in prokaryotic organisms and 79.4% for four locations in eukaryotic organisms. Predictions by our approach are robust to errors in the protein N-terminal sequences. This new approach provides superior prediction performance compared with existing algorithms based on amino acid composition and can be a complementary method to other existing methods based on sorting signals.

Availability: A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.

Contact: sunzhr@mail.tsinghua.edu.cn; huasj00@mails.tsinghua.edu.cn

Supplementary information: Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.

* To whom correspondence should be addressed.
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster
Authors: Grant J. D. , Dunbrack R. L. , Manion F. J. , Ochs M. F.
Published: July 2002

Summary: BeoBLAST is an integrated software package that handles user requests and distributes BLAST and PSI-BLAST searches to nodes of a Beowulf cluster, thus providing a simple way to implement a scalable BLAST system on top of relatively inexpensive computer clusters. Additionally, BeoBLAST offers a number of novel search features through it's web interface, including the ability to perform simultaneous searches of multiple databases with multiple queries, and the ability to start a search using the PSSM generated from a previous PSI-BLAST search on a different database. The underlying system can also handle automated querying for high throughput work.

Availability: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/

Contact: jd_grant@fccc.edurl_dunbrack@fccc.edufj_manion@fccc.edum_ochs@fccc.edu

* To whom correspondence should be addressed.
Computers and Productivity: are Aggregation Effects Important?
Authors: McGuckin Robert H. , Stiroh Kevin J.
Published: July 2002

This article examines the empirical implications of aggregation bias when measuring the productive impact of computers. To isolate “aggregation in variables” and “aggregation in relations” problems, we compare production function estimates across specifications, econometric estimators, and data levels. The results show both sources of bias are important, especially when moving from sectors to the economy level, and when the elasticity of all types of noncomputer capital are restricted to be equal. The elasticity of computers is surprisingly stable between industry and sector regressions and does not appear biased by incorporating a restrictive measure of non‐computer capital. The data consistently show that computers have a large impact on output.
Estrogen receptors: orchestrators of pleiotropic cellular responses
Authors: Moggs Jonathan G , Orphanides George
Published: July 2002

Estrogen receptors (ERs) orchestrate both transcriptional and non‐genomic functions in response to estrogens, xenoestrogens and signals emanating from growth factor signalling pathways. The pleiotropic and tissue‐specific effects of estrogens are likely to be mediated by the differential expression of distinct estrogen receptor subtypes (ERα and ERβ) and their coregulators. The recent analysis of transcription complexes associated with estrogen‐responsive promoters has revealed unexpected levels of complexity in the dynamics of ER‐mediated transcription. Furthermore, a small fraction of ERs also appears to directly interact with components of the cytosolic signalling machinery. Analysis of the interrelationship between these distinct modes of ER action is likely to reveal novel aspects of estrogen signalling that will impact on nuclear receptor biology and human health.
CHIP is a chaperone‐dependent E3 ligase that ubiquitylates unfolded protein
Authors: Murata Shigeo , Minami Yasufumi , Minami Michiko , Chiba Tomoki , Tanaka Keiji
Published: July 2002

The ubiquitin–proteasome system catalyses the immediate destruction of misfolded or impaired proteins generated in cells, but how this proteolytic machinery recognizes abnormality of cellular proteins for selective elimination remains elusive. Here, we report that the C‐terminus of Hsc70‐interacting protein (CHIP) with a U‐box domain is an E3 ubiquitin‐ligase collaborating with molecular chaperones Hsp90 and Hsc70. Thermally denatured firefly luciferase was multiubiquitylated by CHIP in the presence of E1 and E2 (Ubc4 or UbcH5c) in vitro, only when the unfolded substrate was captured by Hsp90 or Hsc70 and Hsp40. No ubiquitylating activity was detected in CHIP lacking the U‐box region. CHIP efficiently ubiquitylated denatured luciferase trapped by the C‐terminal region of Hsp90, which contains a CHIP binding site. CHIP also showed self‐ubiquitylating activity independent of target ubiquitylation. Our results indicate that CHIP can be regarded as ‘a quality‐control E3’ that selectively ubiquitylates unfolded protein(s) by collaborating with molecular chaperones.
Prosaposin treatment induces PC12 entry in the S phase of the cell cycle and prevents apoptosis: activation of ERKs and sphingosine kinase
Authors: MISASI ROBERTA , SORICE MAURIZIO , MARZIO LUISA DI , CAMPANA W. MARIE , MOLINARI SABRINA , CIFONE MARIA GRAZIA , PAVAN ANTONIO , PONTIERI GIUSEPPE M. , O’BRIEN JOHN S.
Published: July 2002

We report that prosaposin treatment induced extracellular signal‐regulated kinases (ERKs) and sphingosine kinase activity, increased DNA synthesis, and prevented cell apoptosis. Prosaposin treatment induced pheochromocytoma cells (PC12) to enter the S phase of the cell cycle;this effect was inhibited by the MEK inhibitor PD98059, indicating that prosaposin‐induced ERK phosphorylation is required for stimulation of DNA synthesis. The prosaposin effect was also inhibited by pertussis toxin, indicating that the prosaposin receptor is a G‐protein‐coupled receptor. Prosaposin rescued PC12 cells from apoptosis induced by staurosporine or ceramide. Sphingosine kinase activity was increased by prosaposin treatment. We propose that this effect is a mechanism underlying the proliferative and anti‐apoptotic functions of prosaposin. Prosaposin appears to be a key regulatory factor in the ceramide‐S‐1‐P rheostat, which regulates cell fate.—Misasi, R., Sorice, M., Di Marzio, L., Campana, W. M., Molinari, S., Cifone, M. G., Pavan, A., Pontieri, G. M., O'Brien, J. S. Prosaposin treatment induces PC12 entry in the S phase of the cell cycle and prevents apoptosis: activation of ERKs and sphingosine kinase. FASEB J. 15, 467‐474 (2001)
Modelling global terrestrial vegetation–climate interaction
Authors: Claussen Martin , Brovkin Victor , Ganopolski Andrey , Kubatzki Claudia , Petoukhov Vladimir
Published: July 2002

By coupling an atmospheric general circulation model asynchronously with an equilibrium vegetation model, manifold equilibrium solutions of the atmosphere–biosphere system have been explored. It is found that under present–day conditions of the Earth's orbital parameters and sea–surface temperatures, two stable equilibria of vegetation patterns are possible: one corresponding to present–day sparse vegetation in the Sahel, the second solution yielding savannah which extends far into the south–western part of the Sahara. A similar picture is obtained for conditions during the last glacial maximum (21 000 years before present (BP)). For the mid–Holocene (6000 years BP), however, the model finds only one solution: the green Sahara. We suggest that this intransitive behaviour of the atmosphere–biosphere is related to a westward shift of the Hadley–Walker circulation. A conceptual model of atmosphere–vegetation dynamics is used to interpret the bifurcation as well as its change in terms of stability theory.
Fish otoliths: do sizes correlate with taxonomic group, habitat and/or luminescence?
Authors: Paxton John R.
Published: July 2002

Otoliths are dense structures in the ears of fishes that function in hearing and gravity perception. Otolith (sagitta) diameters, as percentages of standard length (% SL), are calculated for 247 marine fish species in 147 families and compared by taxonomic group (usually order), habitat and presence or absence of luminescence. Otolith sizes range from 0.4–31.4 mm and 0.08–11.2% SL. The eel and spiny eel orders Anguilliformes and Notacanthiformes have small to very small otoliths, as do the triggerfish order Tetraodontiformes, pipefish order Gasterosteiformes, billfish suborder Scombroidei and many of the dragonfish order Stomiiformes. The soldierfish order Beryciformes has moderate to very large otoliths. The perch order Perciformes has a wide range of otolith sizes but most have small to moderate otoliths 2–5% SL. Only 16 out of the 247 species have the relatively largest otoliths, over 7% SL. Seven out of these 16 species are also luminous from a variety of habitats. Luminous species have slightly to much larger otoliths than non–luminous species in the same family. Both beryciforms and luminous fishes live in low–light environments, where acute colour vision is probably impossible. Most fishes of the epipelagic surface waters have very small otoliths, perhaps due to background noise and/or excessive movement of heavy otoliths in rough seas. Bathypelagic species usually have small otoliths and regressed or absent swimbladders. Other habitats have species with a range of otolith sizes. While the relationship between hearing ability and otolith length is unknown, at least some groups with modified swim–bladders have larger otoliths, which may be associated with more acute hearing.
The Ligand Gated Ion Channel database: an example of a sequence database in neuroscience
Authors: Novére Nicolas Le , Changeux Jean-Pierre
Published: July 2002

Multiple comparisons of receptor sequences, or receptor subunit sequences, has proved to be an invaluable tool in modern pharmacological investigations. Although of outstanding importance, general sequence databases suffer from several imperfections due to their size and their non–specificity. Room therefore exists for expert–maintained databases of restricted focus, where knowledge of the research field helps to filter the huge amount of data generated. Accordingly, neuroscientists have designed databases covering several types of proteins, in particular receptors for neurotransmitters.

Ligand–gated ion channels are oligomeric transmembrane proteins involved in the fast response to neurotransmitters. All these receptors are formed by the assembly of homologous subunits, and an unexpected wealth of genes coding for these subunits has been revealed during the last two decades. The Ligand Gated Ion Channel database (LGICdb) has been developed to handle this growing body of information. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences.
Novel Protein Domains and Repeats in Drosophila melanogaster: Insights into Structure, Function, and Evolution
Authors: Ponting Chris P. , Mott Richard , Bork Peer , Copley Richard R.
Published: July 2002

Sequence database searching methods such asBLAST, are invaluable for predicting molecular function on the basis of sequence similarities among single regions of proteins. Searches of whole databases however, are not optimized to detect multiple homologous regions within a single polypeptide. Here we have used the prospero algorithm to perform self-comparisons of all predicted Drosophila melanogaster gene products. Predicted repeats, and their homologs from all species, were analyzed further to detect hitherto unappreciated evolutionary relationships. Results included the identification of novel tandem repeats in the human X-linked retinitis pigmentosa type-2 gene product, repeated segments in cystinosin, associated with a defect in cystine transport, and ‘nested’ homologous domains in dysferlin, whose gene is mutated in limb girdle muscular dystrophy. Novel signaling domain families were found that may regulate the microtubule-based cytoskeleton and ubiquitin-mediated proteolysis, respectively. Two families of glycosyl hydrolases were shown to contain internal repetitions that hint at their evolution via a piecemeal, modular approach. In addition, three examples of fruit fly genes were detected with tandem exons that appear to have arisen via internal duplication. These findings demonstrate how completely sequenced genomes can be exploited to further understand the relationships between molecular structure, function, and evolution.