bluuebunny/crossref_metadata_2025 huggingface dataset:
Shewanella
secretes flavins that mediate extracellular electron transfer
Authors: Marsili Enrico , Baron Daniel B. , Shikhare Indraneel D. , Coursolle Dan , Gralnick Jeffrey A. , Bond Daniel R.
Published: March 2008

Bacteria able to transfer electrons to metals are key agents in biogeochemical metal cycling, subsurface bioremediation, and corrosion processes. More recently, these bacteria have gained attention as the transfer of electrons from the cell surface to conductive materials can be used in multiple applications. In this work, we adapted electrochemical techniques to probe intact biofilms of
Shewanella oneidensis
MR-1 and
Shewanella sp.
MR-4 grown by using a poised electrode as an electron acceptor. This approach detected redox-active molecules within biofilms, which were involved in electron transfer to the electrode. A combination of methods identified a mixture of riboflavin and riboflavin-5′-phosphate in supernatants from biofilm reactors, with riboflavin representing the dominant component during sustained incubations (>72 h). Removal of riboflavin from biofilms reduced the rate of electron transfer to electrodes by >70%, consistent with a role as a soluble redox shuttle carrying electrons from the cell surface to external acceptors. Differential pulse voltammetry and cyclic voltammetry revealed a layer of flavins adsorbed to electrodes, even after soluble components were removed, especially in older biofilms. Riboflavin adsorbed quickly to other surfaces of geochemical interest, such as Fe(III) and Mn(IV) oxy(hydr)oxides. This
in situ
demonstration of flavin production, and sequestration at surfaces, requires the paradigm of soluble redox shuttles in geochemistry to be adjusted to include binding and modification of surfaces. Moreover, the known ability of isoalloxazine rings to act as metal chelators, along with their electron shuttling capacity, suggests that extracellular respiration of minerals by
Shewanella
is more complex than originally conceived.
A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies
Authors: Frey Gary , Peng Hanqin , Rits-Volloch Sophia , Morelli Marco , Cheng Yifan , Chen Bing
Published: March 2008

Most antibodies induced by HIV-1 are ineffective at preventing initiation or spread of infection because they are either nonneutralizing or narrowly isolate-specific. Rare, “broadly neutralizing” antibodies have been detected that recognize relatively conserved regions on the envelope glycoprotein. Using stringently characterized, homogeneous preparations of trimeric HIV-1 envelope protein in relevant conformations, we have analyzed the molecular mechanism of neutralization by two of these antibodies, 2F5 and 4E10. We find that their epitopes, in the membrane-proximal segment of the envelope protein ectodomain, are exposed only on a form designed to mimic an intermediate state during viral entry. These results help explain the rarity of 2F5- and 4E10-like antibody responses and suggest a strategy for eliciting them.
Nucleoprotein structure of the CD4 locus: Implications for the mechanisms underlying CD4 regulation during T cell development
Authors: Yu Ming , Wan Mimi , Zhang Jianmin , Wu Jie , Khatri Rohini , Chi Tian
Published: March 2008

The CD4 gene is regulated in a stage-specific manner during T cell development, being repressed in CD4
−
CD8
−
double-negative (DN) and CD8 cells, but expressed in CD4
+
CD8
+
double-positive (DP) and CD4 cells. Furthermore, the expression/repression pattern is reversible in developing (DN and DP) thymocytes, but irreversible in mature (CD4 and CD8) T cells. Here, we explored the molecular mechanisms underlying this complex mode of regulation by examining the nucleoprotein structure of the CD4 locus throughout T cell development and in DN cells lacking the CD4 silencer. In DN cells, the CD4 enhancer is preloaded with multiple transcription activators, but p300 recruitment is impaired by the silencer that is associated with the repressor Runx1. DP cells achieve high-level CD4 expression via a combination of CD4 derepression and true activation, but Runx1 remains bound to the silencer that retains an open chromatin configuration. In CD4 cells, Runx1 dissociates from the silencer that has become less accessible, and CD4 transcription appears to be achieved via a mechanism distinct from that operating in DP cells. In CD8 cells, the CD4 promoter becomes incorporated into heterochromatin-like structure. Our data shed light on the molecular basis of CD4 regulation and provide a conceptual framework for understanding how the same regulatory elements can mediate both reversible and irreversible CD4 regulation.
Copying behind during Dictation
Authors: Poulton E. C.
Published: March 2008

Simple prose was presented in groups of one, three, or six words, with silent intervals between groups. The overall rate of presentation was equated for these three conditions at about twice as fast as the subjects could print in capital letters. They were instructed to continue printing until they could not remember what came next, and then to start again at once with the next word which they heard. The same passages were presented three times.

On the first presentation an error-free ear-hand span of 14 words was found. This is within the range of the extreme spans reported by Bryan and Harter, and is larger than the spans reported for other receptors and effectors. Presenting six words at a time gave only slightly larger spans than presenting fewer words more frequently. The subjects tended to give up at positions related to punctuation, presumably because they stored the material according to its syntax and meaning. The small size of the differences found between the three methods of presentation was partly attributed to this.
Miscellanea: Apparatus for Continuous Recording of the Visual Threshold by the Method of “Closed Loop Control”
Authors: Dixon N. F.
Published: March 2008

An apparatus is described for the continuous recording of visual thresholds and the integration of visual thresholds over any given time period. The apparatus provides for the simultaneous but independent stimulation of the two eyes where either or both of the respective stimulus intensities may be under the control of the subject.
Somaesthetic Alternation, Discrimination and Orientation after Frontal and Parietal Lesions in Monkeys
Authors: Ettlinger George , Wegener Jonathan
Published: March 2008

Eight naïve monkeys were trained on non-visual tests of alternation and discrimination. These animals were also taught to perform a test of orientation with or without visual control. Four animals then received bilateral frontal excisions and three (of four) animals survived bilateral removal of the posterior parietal region. Following surgery, all frontal operates were found to be severely impaired on the somaesthetic alternation test. The parietal operates, on the other hand, were unimpaired on this test though all gave evidence of defective orientation in space. Some implications of the results are discussed.
On the Reduction of Choice Reaction Times with Practice
Authors: Mowbray G. H. , Rhoades M. V.
Published: March 2008

Information theory concepts have been discussed in relation to data from choice reaction time experiments. Specifically, it has been stated that choice reaction time is proportional to the logarithm of the number of randomly appearing alternative stimuli. It is suggested that the reported increase in choice reaction times with an increased number of alternatives is the result of insufficient practice. Data are provided to show that, with sufficient practice, this increase does not occur between two and four choices.
Attention in Dichotic Listening: Affective Cues and the Influence of Instructions
Authors: Moray Neville
Published: March 2008

In shadowing one of two simultaneous messages presented dichotically, subjects are unable to report any of the content of the rejected message. Even if the rejected message consists of a short list of simple words repeated many times, a recognition test fails to reveal any trace of the list. If numbers are interpolated in prose passages presented for dichotic shadowing, no more are recalled from the rejected messages if the instructions are specifically to remember numbers than if the instructions are general: a specific set for numbers will not break through the attentional barrier set up in this task. The only stimulus so far found that will break through this barrier is the subject's own name. It is probably only material “important” to the subject that will break through the barrier.
Shorter Articles and Notes: Reaction Times to Auditory and Visual Stimulation in Schizophrenic and Normal Subjects
Authors: Venables P. H. , O'connor N.
Published: March 2008

An experiment carried out to determine the relation between auditory and visual reaction times suggested that when the general level of response is slow visual RTs are faster than auditory, and that the reverse is the case when the level of response is fast. Thus most normal subjects have an auditory RT faster than visual, and most schizophrenics the reverse. However, the difference between auditory and visual RTs does not appear to depend directly on schizophrenic pathology except in so far as this is a factor in the general slowness of reaction time.
Central Intermittency: Some Further Observations
Authors: Elithorn Alick
Published: March 2008

When the human subject is asked to respond to two stimuli separated by a very short time interval the response to the second stimulus may be relatively delayed. The present experiment is designed to test the hypothesis that the elements of the delay attributable to the sensory and motor components of the stimulus-response situation may be subserved by relatively independent neural mechanisms. The results obtained are compatible with this hypothesis and are briefly discussed.
Ensemble Size and Selective Response Times with a Constant Signal Rate
Authors: Brebner John , Gordon Ian
Published: March 2008

Using a selective response task in which subjects were required to respond only to one of a number of alternative digits, although signal rate was held constant, the latency of selective responses was found to lengthen as the number of alternatives increased. This finding does not support the inference drawn from the work of Mowbray (1960) that, with signal rate held constant, there should be no significant lengthening of reaction times as the ensemble of digits increases.
The Visual Discrimination of Shape by Octopus: The Effects of Stimulus Size
Authors: Sutherland N. S. , Carr A. E.
Published: March 2008

Octopuses were trained in a successive situation to discriminate between vertical and horizontal rectangles: Group S was trained with rectangles of side length 5 × 1 cm., Group M with 10 × 2 cm. rectangles, and Group L with 20 × 4 cm. rectangles. The larger the shapes used, the more readily were they discriminated, both in terms of speed of learning and of the asymptote of performance. After training, each group was given transfer tests with the two pairs of rectangles not used in training and with two further pairs of 2.5 × 0.5 cm. and 40 × 8 cm. The results can be summarized in three generalizations: (1) When the size of a shape is changed, performance is worse than on the original training shape. (2) The bigger the change in proportionate size, the less transfer is shown. (3) For corresponding changes of proportionate size, there is better transfer to larger shapes than to smaller. These generalizations are supported by data from earlier experiments on the question of transfer to different sized shapes: some of these data were reworked and are presented in detail here. The theoretical implications of the results are discussed.
Overtraining and Transfer within and between Dimensions in the Rat
Authors: Mackintosh N. J.
Published: March 2008

Although reversal learning in the rat is normally assisted by overtraining, it seems that transfer to a new discrimination in a different stimulus dimension is not. This effect is confirmed in the present experiment, even though the stimuli of the second problem had been present (and necessarily attended to) in the first problem. This result is taken to show that the effects of overtraining cannot be accounted for by supposing that it strengthens an overt orienting response of the animal. A second group of rats was run to show that transfer to a second discrimination problem within the same dimension as the first is facilitated by overtraining. The important variable, therefore, that determines the direction of the effect of overtraining on transfer between problems, is the relationship between the stimulus dimensions concerned.
Noise and the Shifting of Attention
Authors: Samuel W. M. S.
Published: March 2008

An experiment was carried out to test the hypothesis that performance on a task which involves a shift of attention between spatially separated sources would be lower under noise conditions than one which involved no such shift. The results indicated that the hypothesis was not proved; rather they showed that the subject's performance on the shift of attention task was better under noise than under quiet. An attempt is made to put forward possible reasons for this occurrence.
Stimulus Set and Response Set: The Alternation of Attention
Authors: Broadbent D. E. , Gregory Margaret
Published: March 2008

Recently Gray and Wedderburn showed that if a meaningful phrase of three words was presented together with three digits, in such a way that each ear received some items of each of the two types of material, it was no harder to recall the items grouped by type than it was to recall them grouped by ear. This finding is repeated and confirmed in several forms, culminating in the use of three letters of the alphabet and three digits as the six items presented. It is also shown, however, that even when all material is presented to one ear, it is harder to recall a list made up of alternate items of two classes than it is to recall the same items arranged as two successive sub-lists. Thus Gray and Wedderburn's result does not appear to reveal a situation in which alternation of attention between the ears is especially easy, but rather one in which continued attention to one ear is especially difficult because it requires alternation between classes of item.

A further series of experiments showed that a reduction in the presentation rate of stimuli produced a much greater improvement in performance when the items were of two alternated classes than when the classes were left separate. Equally, a slow presentation rate is more helpful when alternation between ears is required than when each ear is to be dealt with separately. These results support the idea that attention takes time to shift; but require a separate kind of attention, to a class of item rather than to a source of stimulation.
Binocular Masking Induced by a Moving Object
Authors: Grindley G. C. , Townsend Valerie
Published: March 2008

Movement in a part of either of two binocular fields can, under some conditions, produce temporary obliteration of the corresponding part of the other field. This paper is a mainly qualitative study of this rather surprising phenomenon. The effect is found to increase from the fovea to the periphery, to be greatest at a velocity of about 20° visual angle per sec. and to vary with the orientation of the fixation point in the visual field. Some further lines of research designed to elucidate the relation of the effect described here to certain other visual phenomena are suggested.
Incidental Cue Learning in Rats
Authors: Mackintosh N. J.
Published: March 2008

Continuity theories of discrimination learning appear to say that animals learn equally about all cues impinging upon their receptors; noncontinuity theories that they learn about only one cue at a time. Experiment I showed that neither of these positions is correct: rats trained to attend to one cue learned less about a subsequently introduced incidental cue than rats given no such pretraining; but attention to one cue did not totally prevent learning about the other. A second experiment established that if rats are trained with one cue, and a second cue is then also made relevant, the amount learned about this second cue varies directly with (a) the abruptness with which it is introduced, and (b) the difficulty of the original discrimination.
Exposure Duration and Effective Figure-Ground Contrast
Authors: Kahneman Daniel
Published: March 2008

The pre-and post-exposure fields in the tachistoscopic presentation are assumed to reduce the apparent contrast of the figure by brightness summation. A matching procedure was used to measure this effect. Apparent contrast rises linearly with duration, but only in the upper range. Further observations confirm the suggestion that the pre-and post-exposure fields retard the formation of bounding contours with a further reduction of apparent contrast at short durations as a result. It is indicated that the contrast-matching method provides a short-cut technique for the measurement of the temporal range of brightness summation.
The Size-Constancy of Underwater Swimmers
Authors: Ross Helen E.
Published: March 2008

The size-constancy of divers was measured by requiring them to adjust the distance between two disks of unequal size so that they appeared phenomenally equal. In clear water divers showed greater constancy-ratios than on land. In murky water, where visibility was reduced by suspended particles, constancy-ratios were the same as, or less than, on land. It is suggested that these effects may be due to changes in apparent distance: in clear water objects appear nearer through refraction, but in murky water they appear further away because of the distance cues provided by the visibility gradient.

The orientation of the display, or of the diver's body, did not affect constancy under water, though it does on land. It is argued that the effect on land is due to visual and proprioceptive cues which are absent in the water.
Functional and genomic profiling of effector CD8 T cell subsets with distinct memory fates
Authors: Sarkar Surojit , Kalia Vandana , Haining W. Nicholas , Konieczny Bogumila T. , Subramaniam Shruti , Ahmed Rafi
Published: March 2008

An important question in memory development is understanding the differences between effector CD8 T cells that die versus effector cells that survive and give rise to memory cells. In this study, we provide a comprehensive phenotypic, functional, and genomic profiling of terminal effectors and memory precursors. Using killer cell lectin-like receptor G1 as a marker to distinguish these effector subsets, we found that despite their diverse cell fates, both subsets possessed remarkably similar gene expression profiles and functioned as equally potent killer cells. However, only the memory precursors were capable of making interleukin (IL) 2, thus defining a novel effector cell that was cytotoxic, expressed granzyme B, and produced inflammatory cytokines in addition to IL-2. This effector population then differentiated into long-lived protective memory T cells capable of self-renewal and rapid recall responses. Experiments to understand the signals that regulate the generation of terminal effectors versus memory precursors showed that cells that continued to receive antigenic stimulation during the later stages of infection were more likely to become terminal effectors. Importantly, curtailing antigenic stimulation toward the tail end of the acute infection enhanced the generation of memory cells. These studies support the decreasing potential model of memory differentiation and show that the duration of antigenic stimulation is a critical regulator of memory formation.
Inferior Clinical Outcome of the CD4+ Cell Count–Guided Antiretroviral Treatment Interruption Strategy in the SMART Study: Role of CD4+ Cell Counts and HIV RNA Levels during Follow-up
Authors:   The Strategies for Management of Antiretroviral Therapy (SMART) Study Group
Published: March 2008

Background and methodsThe SMART study compared 2 strategies for using antiretroviral therapy—drug conservation (DC) and viral suppression (VS)—in 5472 human immunodeficiency virus (HIV)–infected patients with CD4+ cell counts >350 cells/μL. Rates and predictors of opportunistic disease or death (OD/death) and the relative risk (RR) in DC versus VS groups according to the latest CD4+ cell count and HIV RNA level are reported

ResultsDuring a mean of 16 months of follow-up, DC patients spent more time with a latest CD4+ cell count <350 cells/μL (for DC vs. VS, 31% vs. 8%) and with a latest HIV RNA level >400 copies/mL (71% vs. 28%) and had a higher rate of OD/death (3.4 vs. 1.3/100 person-years) than VS patients. For periods of follow-up with a CD4+ cell count <350 cells/μL, rates of OD/death were increased but similar in the 2 groups (5.7 vs. 4.6/100 person-years), whereas the rates were higher in DC versus VS patients (2.3 vs. 1.0/100 person-years; RR, 2.3 [95% confidence interval, 1.5–3.4]) for periods with the latest CD4+ cell count ⩾350 cells/μL—an increase explained by the higher HIV RNA levels in the DC group

ConclusionsThe higher risk of OD/death in DC patients was associated with (1) spending more follow-up time with relative immunodeficiency and (2) living longer with uncontrolled HIV replication even at higher CD4+ cell counts. Ongoing HIV replication at a given CD4+ cell count places patients at an excess risk of OD/death

Trial registrationClinicalTrials.gov identifier: NCT00027352
Heat diffusivity model and temperature simulations in RFX-mod
Authors: Frassinetti L. , Alfier A. , Pasqualotto R. , Bonomo F. , Innocente P.
Published: March 2008

The core transport properties of reversed field pinch (RFP) plasmas in the standard regime are generally associated with a high level of magnetic chaos. Indeed, in the RFX-mod RFP device, the core temperature profile is often very flat, indicating that the heat diffusivity is very high. In contrast, the temperature edge profile has a steep gradient, indicating that the edge is characterized by low heat transport. These simple experimental evidences are the basis of a heat diffusivity model that is used as an input to a numerical code for plasma temperature simulation. The simulated temperature reproduces with good accuracy both the experimentalTetime evolution and its radial profiles in different plasma scenarios, showing that the model is useful for estimating the plasma heat diffusivity. This work suggests that the heat transport properties in the RFP plasma core are dominated by magnetic chaos in standard discharges and suggests a simple way to estimate electron heat diffusivity from density, input power and magnetic fluctuation measurements.
On the convergence in capacity on compact Kahler manifolds and its applications
Authors: Hiep Pham
Published: March 2008

The main aim of the present note is to study the convergence in

C

X
,
ω

C_{X,\omega }

on a compact Kahler mainfold

X
X

. The obtained results are used to study global extremal functions and describe the

ω
\omega

-pluripolar hull of an

ω
\omega

-pluripolar subset in

X
X

.
On Krein’s example
Authors: Kostrykin Vadim , Makarov Konstantin
Published: March 2008

In his 1953 paper [Matem. Sbornik 33 (1953), 597–626] Mark Krein presented an example of a symmetric rank one perturbation of a self-adjoint operator such that for all values of the spectral parameter in the interior of the spectrum, the difference of the corresponding spectral projections is not trace class. In the present note it is shown that in the case in question this difference has simple Lebesgue spectrum filling in the interval

[
−
1
,
1
]

[-1,1]

and, therefore, the pair of the spectral projections is generic in the sense of Halmos but not Fredholm.
Polynomials with roots in ℚ_{𝕡} for all 𝕡
Authors: Sonn Jack
Published: March 2008

Let

f
(
x
)

f(x)

be a monic polynomial in

Z

[
x
]

\mathbb {Z}[x]

with no rational roots but with roots in

Q

p

\mathbb {Q}_{p}

for all

p
p

, or equivalently, with roots mod

n
n

for all

n
n

. It is known that

f
(
x
)

f(x)

cannot be irreducible but can be a product of two or more irreducible polynomials, and that if

f
(
x
)

f(x)

is a product of

m
>
1

m>1

irreducible polynomials, then its Galois group must be a union of conjugates of

m
m

proper subgroups. We prove that for any

m
>
1

m>1

, every finite solvable group that is a union of conjugates of

m
m

proper subgroups (where all these conjugates have trivial intersection) occurs as the Galois group of such a polynomial, and that the same result (with

m
=
2

m=2

) holds for all Frobenius groups. It is also observed that every nonsolvable Frobenius group is realizable as the Galois group of a geometric, i.e. regular, extension of

Q

(
t
)

\mathbb {Q}(t)

.
Normalization of monomial ideals and Hilbert functions
Authors: Villarreal Rafael
Published: March 2008

We study the normalization of a monomial ideal, and show how to compute its Hilbert function (using Ehrhart polynomials) if the ideal is zero dimensional. A positive lower bound for the second coefficient of the Hilbert polynomial is shown.
On multipliers for Hardy-Sobolev spaces
Authors: Beatrous Frank , Burbea Jacob
Published: March 2008

It is shown that membership of holomorphic functions in Hardy-Sobolev spaces in the unit ball cannot be characterized by finiteness of any integral norm. In addition, sufficient conditions are given for a holomorphic function to be a pointwise multiplier of a Hardy-Sobolev space.
Functional relations and special values of Mordell-Tornheim triple zeta and 𝐿-functions
Authors: Matsumoto Kohji , Nakamura Takashi , Tsumura Hirofumi
Published: March 2008

In this paper, we prove the existence of meromorphic continuation of certain triple zeta-functions of Lerch’s type. Based on this result, we prove some functional relations for triple zeta and

L
L

-functions of the Mordell-Tornheim type. Using these functional relations, we prove new explicit evaluation formulas for special values of these functions. These can be regarded as triple analogues of known results for double zeta and

L
L

-functions.
Adjoints and formal adjoints of matrices of unbounded operators
Authors: Möller Manfred , Szafraniec Franciszek
Published: March 2008

In this paper we discuss diverse aspects of the mutual relationship between adjoints and formal adjoints of unbounded operators bearing a matrix structure. We emphasize the behaviour of row and column operators as they turn out to be the germs of an arbitrary matrix operator, providing most of the information about the latter as it is the troublemaker.
Radial limits of inner functions and Bloch spaces
Authors: Doubtsov Evgueni
Published: March 2008

Let

f
f

be an inner function in the unit ball

B
n

⊂

C

n

B_n \subset \mathbb {C}^n

,

n
≥
1

n\ge 1

. Assume that
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sup Underscript z element-of upper B Subscript n Baseline Endscripts StartFraction StartAbsoluteValue script upper R f left-parenthesis z right-parenthesis EndAbsoluteValue left-parenthesis 1 minus StartAbsoluteValue z EndAbsoluteValue squared right-parenthesis Superscript 1 plus beta Baseline Over left-parenthesis 1 minus StartAbsoluteValue f left-parenthesis z right-parenthesis EndAbsoluteValue squared right-parenthesis squared EndFraction greater-than normal infinity comma">

sup

z
∈

B
n

|

R

f
(
z
)

|

(
1
−

|

z

|

2

)

1
+
β

(
1
−

|

f
(
z
)

|

2

)

2

>
∞
,

\sup _{z\in B_n} \frac {|\mathcal {R} f(z)|(1-|z|^2)^{1+\beta }}{\left (1-|f(z)|^2 \right )^2} > \infty ,

\]
where

β
∈
(
0
,
1
)

\beta \in (0,1)

and

R

f

\mathcal {R} f

is the radial derivative. Then, for all

α
∈
∂

B
1

\alpha \in \partial B_1

, the set

{
ζ
∈
∂

B
n

:

f
∗

(
ζ
)
=
α
}

\{\zeta \in \partial B_n:\, f^*(\zeta ) =\alpha \}

has a non-zero real Hausdorff

t

2
n
−
1
−
β

t^{2n-1-\beta }

-content, and it has a non-zero complex Hausdorff

t

n
−
β

t^{n-\beta }

-content.
Semiregular automorphisms of cubic vertex transitive graphs
Authors: Li Cai
Published: March 2008

It is shown that for a connected cubic graph

Γ
\Gamma

, a vertex transitive group

G
≤

A
u
t

Γ

G\le {\sf {Aut}}\,{\Gamma }

contains a large semiregular subgroup. This confirms a conjecture of Cameron and Sheehan (2001).
Non-vanishing of the twisted cohomology on the complement of hypersurfaces
Authors: Kawahara Yukihito
Published: March 2008

Generically, the cohomology with coefficients in a local system of rank one on the complement in

P

n

\mathbb {P}^n

of the union of a finite number of hypersurfaces vanishes except in the highest dimension. We study the non-generic case, in which the cohomology in other dimensions does not vanish. When the hypersurfaces are hyperplanes, many examples of this kind are known. In this paper, we consider the case in which the hypersurfaces need not be hyperplanes. We prove that the hypersurfaces given by some particular linear systems have non-vanishing local system cohomologies.
Cohomology in one-dimensional substitution tiling spaces
Authors: Barge Marcy , Diamond Beverly
Published: March 2008

Anderson and Putnam showed that the cohomology of a substitution tiling space may be computed by collaring tiles to obtain a substitution which “forces its border.” One can then represent the tiling space as an inverse limit of an inflation and substitution map on a cellular complex formed from the collared tiles; the cohomology of the tiling space is computed as the direct limit of the homomorphism induced by inflation and substitution on the cohomology of the complex. For one-dimensional substitution tiling spaces, we describe a modification of the Anderson-Putnam complex on collared tiles that allows for easier computation and provides a means of identifying certain special features of the tiling space with particular elements of the cohomology.
Uniqueness of the solution of a partial differential equation problem with a non-constant coefficient
Authors: Lopes Ernesto , de Mattos José
Published: March 2008

We consider the problem

K
(
x
)

u

x
x

=

u

t

K(x)u_{xx}=u_{t}

,

0
>
x
>
1

0>x>1

,

t
≥
0

t\geq 0

, where

K
(
x
)

K(x)

is bounded below by a positive constant. The solution on the boundary

x
=
0

x=0

is a known function and

u

x

(
0
,
t
)
=
0

u_{x}(0,t)=0

. This is an ill-posed problem in the sense that a small disturbance on the boundary specification can produce a big change in its solution, if it exists. In a previous work, we used a Wavelet Galerkin Method with the Meyer Multiresolution Analysis to generate a sequence of well-posed approximating problems to it. In the present work, by assuming that

1

/

K
(
x
)

1/K(x)

is Lipschitz, we are able to prove that the existence of a solution

u
(
x
,
⋅
)
∈

H

1

(
R
)

u(x,\cdot )\in H^{1}(R)

, for this problem, implies its uniqueness.
Pointwise Hardy inequalities and uniformly fat sets
Authors: Lehrbäck Juha
Published: March 2008

We prove that it is equivalent for domain in

R

n

\mathbb {R}^n

to admit the pointwise

p
p

-Hardy inequality, have uniformly

p
p

-fat complement, or satisfy a uniform inner boundary density condition.
Strong periodicity of links and the coefficients of the Conway polynomial
Authors: Chbili Nafaa
Published: March 2008

Przytycki and Sokolov proved that a three-manifold admits a semi-free action of the finite cyclic group of order

p
p

with a circle as the set of fixed points if and only if

M
M

is obtained from the three-sphere by surgery along a strongly

p
p

-periodic link

L
L

. Moreover, if the quotient three-manifold is an integral homology sphere, then we may assume that

L
L

is orbitally separated. This paper studies the behavior of the coefficients of the Conway polynomial of such a link. Namely, we prove that if

L
L

is a strongly

p
p

-periodic orbitally separated link and

p
p

is an odd prime, then the coefficient

a

2
i

(
L
)

a_{2i}(L)

is congruent to zero modulo

p
p

for all

i
i

such that

2
i
>
p
−
1

2i>p-1

.
Equivariant Hopf bifurcation for neutral functional differential equations
Authors: Guo Shangjiang , Lamb Jeroen
Published: March 2008

In this paper we employ an equivariant Lyapunov-Schmidt procedure to give a clearer understanding of the one-to-one correspondence of the periodic solutions of a system of neutral functional differential equations with the zeros of the reduced bifurcation map, and then set up equivariant Hopf bifurcation theory. In the process we derive criteria for the existence and direction of branches of bifurcating periodic solutions in terms of the original system, avoiding the process of center manifold reduction.
Distribution of Farey fractions in residue classes and Lang–Trotter conjectures on average
Authors: Cojocaru Alina , Shparlinski Igor
Published: March 2008

We prove that the set of Farey fractions of order

T
T

, that is, the set

{
α

/

β
∈

Q

 
:
 
gcd
⁡
(
α
,
β
)
=
1
,
 
1
≤
α
,
β
≤
T
}

\{\alpha /\beta \in \mathbb {Q}\ : \ \operatorname {gcd}(\alpha , \beta ) = 1, \ 1 \le \alpha , \beta \le T\}

, is uniformly distributed in residue classes modulo a prime

p
p

provided

T
≥

p

1

/

2
+
ε

T \ge p^{1/2 +\varepsilon }

for any fixed

ε
>
0

\varepsilon >0

. We apply this to obtain upper bounds for the Lang–Trotter conjectures on Frobenius traces and Frobenius fields “on average” over a one-parametric family of elliptic curves.
Global conformal Assouad dimension in the Heisenberg group
Authors: Tyson Jeremy
Published: March 2008

We study global conformal Assouad dimension in the Heisenberg group

H

n

\mathbb {H}^n

. For each

α
∈
{
0
}
∪
[
1
,
2
n
+
2
]

\alpha \in \{0\}\cup [1,2n+2]

, there is a bounded set in

H

n

\mathbb {H}^n

with Assouad dimension

α
\alpha

whose Assouad dimension cannot be lowered by any quasiconformal map of

H

n

\mathbb {H}^n

. On the other hand, for any set

S
S

in

H

n

\mathbb {H}^n

with Assouad dimension strictly less than one, the infimum of the Assouad dimensions of sets

F
(
S
)

F(S)

, taken over all quasiconformal maps

F
F

of

H

n

\mathbb {H}^n

, equals zero. We also consider dilatation-dependent bounds for quasiconformal distortion of Assouad dimension. The proofs use recent advances in self-similar fractal geometry and tilings in

H

n

\mathbb {H}^n

and regularity of the Carnot–Carathéodory distance from smooth hypersurfaces.
The Integrin-coupled Signaling Adaptor p130Cas Suppresses Smad3 Function in Transforming Growth Factor-β Signaling
Authors: Kim Wook , Seok Kang Yong , Soo Kim Jin , Shin Nah-Young , Hanks Steven K. , Song Woo Keun
Published: March 2008

Reciprocal cooperative signaling by integrins and growth factor receptors at G1 phase during cell cycle progression is well documented. By contrast, little is known about the cross-talk between integrin and transforming growth factor (TGF)-β signaling. Here, we show that integrin signaling counteracts the inhibitory effects of TGF-β on cell growth and that this effect is mediated by p130Cas (Crk-associated substrate, 130 kDa). Adhesion to fibronectin or laminin reduces TGF-β–induced Smad3 phosphorylation and thus inhibits TGF-β–mediated growth arrest; loss of p130Cas abrogates these effects. Loss and gain of function studies demonstrated that, once tyrosine-phosphorylated via integrin signaling, p130Cas binds to Smad3 and reduces phosphorylation of Smad3. That in turn leads to inhibition of p15 and p21 expression and facilitation of cell cycle progression. Thus, p130Cas-mediated control of TGF-β/Smad signaling may provide an additional clue to the mechanism underlying resistance to TGF-β–induced growth inhibition.
The Atg16L Complex Specifies the Site of LC3 Lipidation for Membrane Biogenesis in Autophagy
Authors: Fujita Naonobu , Itoh Takashi , Omori Hiroko , Fukuda Mitsunori , Noda Takeshi , Yoshimori Tamotsu
Published: March 2008

Two ubiquitin-like molecules, Atg12 and LC3/Atg8, are involved in autophagosome biogenesis. Atg12 is conjugated to Atg5 and forms an ∼800-kDa protein complex with Atg16L (referred to as Atg16L complex). LC3/Atg8 is conjugated to phosphatidylethanolamine and is associated with autophagosome formation, perhaps by enabling membrane elongation. Although the Atg16L complex is required for efficient LC3 lipidation, its role is unknown. Here, we show that overexpression of Atg12 or Atg16L inhibits autophagosome formation. Mechanistically, the site of LC3 lipidation is determined by the membrane localization of the Atg16L complex as well as the interaction of Atg12 with Atg3, the E2 enzyme for the LC3 lipidation process. Forced localization of Atg16L to the plasma membrane enabled ectopic LC3 lipidation at that site. We propose that the Atg16L complex is a new type of E3-like enzyme that functions as a scaffold for LC3 lipidation by dynamically localizing to the putative source membranes for autophagosome formation.
Predicting proteolytic sites in extracellular proteins: only halfway there
Authors: Kliger Yossef , Gofer Eyal , Wool Assaf , Toporik Amir , Apatoff Avihay , Olshansky Moshe
Published: March 2008

Motivation: Many secretory proteins are synthesized as inactive precursors that must undergo post-translational proteolysis in order to mature and become active. In the current study, we address the challenge of sequence-based discovery of proteolytic sites in secreted proteins using machine learning.

Results: The results revealed that only half of the extracellular proteolytic sites are currently annotated, leaving over 3600 unannotated ones. Furthermore, we have found that only 6% of the unannotated sites are similar to known proteolytic sites, whereas the remaining 94% do not share significant similarity with any annotated proteolytic site. The computational challenges in these two cases are very different. While the precision in detecting the former group is close to perfect, only a mere 22% of the latter group were detected with a precision of 80%. The applicability of the classifier is demonstrated through members of the FGF family, in which we verified the conservation of physiologically-relevant proteolytic sites in homologous proteins.

Contact:  kliger@compugen.co.il; yossef.kliger@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Biology of the skates Bathyraja brachyurops and B. griseocauda in waters around the Falkland Islands, Southwest Atlantic
Authors: Arkhipkin Alexander I. , Baumgartner Nina , Brickle Paul , Laptikhovsky Vladimir V. , Pompert Joost H. W. , Shcherbich Zhanna N.
Published: March 2008

Arkhipkin, A. I., Baumgartner, N., Brickle, P., Laptikhovsky, V. V., Pompert, J. H. W., and Shcherbich, Z. N. 2008. Biology of the skates Bathyraja brachyurops and B. griseocauda in waters around the Falkland Islands, Southwest Atlantic. – ICES Journal of Marine Science, 65: 560–570. The distributions and length compositions of two large, abundant skates, broadnose skate Bathyraja brachyurops and grey-tail skate B. griseocauda, were studied using an extensive dataset (∼48 000 skates) collected from the commercial fishery and research cruises on the southeastern Patagonian Shelf around the Falkland Islands between 1992 and 2006. Bathyraja brachyurops mostly inhabit the shelf at depths shallower than 250 m, whereas B. griseocauda are found deeper (>250 m), off the shelf break and slope. Small individuals of both species are most segregated spatially. Growth increments on caudal thorns and vertebral centra revealed that B. brachyurops grow slower and have a shorter lifespan, attaining a maximum total length of 125 cm at 20 years, compared with B. griseocauda (∼150 cm at 28 years). Maturity is attained at 8–10 years for male and female B. brachyurops, and at 15 and 17 years for B. griseocauda, respectively. Spawning takes place on spatially segregated spawning grounds, B. brachyurops reproducing above the shelf break, and B. griseocauda just below the shelf break throughout the year, with a smaller proportion of females of both species laying eggs in winter.
Diversions of a radio telescope
Authors: Graham-Smith Sir Francis , Lovell Sir Bernard
Published: March 2008

The first use of the 250-foot radio telescope at Jodrell Bank, an instrument designed for academic research, was as a radar, when it obtained echoes from the rocket launcher of Sputnik 1 in October 1957. It was soon realized that this was the only radar system capable of detecting intercontinental missiles soon after their launch from within the USSR. The Air Ministry then organized the installation of a more powerful radar on the telescope. It has been revealed only recently that for several years Jodrell Bank played a role in defence during a critical period of the Cold War.
Expression of vasohibin as a novel endothelium‐derived angiogenesis inhibitor in endometrial cancer
Authors: Yoshinaga Kousuke , Ito Kiyoshi , Moriya Takuya , Nagase Satoru , Takano Tadao , Niikura Hitoshi , Yaegashi Nobuo , Sato Yasufumi
Published: March 2008

We have previously reported on vasohibin as a novel endothelium‐derived vascular endothelial growth factor (VEGF)–inducible inhibitor of angiogenesis. The aim of our present study was to define the role of vasohibin in endometrioid endometrial adenocarcinoma. We collected 78 sections of endometrial carcinoma for assessment using immunohistochemistry. Twenty‐seven were well differentiated (G1), 25 were moderately differentiated (G2), and 26 were poorly differentiated endometrioid adenocarcinomas (G3). We also included 12 sections of normal cyclic endometria, six of which were in the proliferative phase and six were in the secretory phase. We investigated the expression of vasohibin, and compared it to VEGF receptor‐2 (VEGFR‐2: KDR/flk‐1), CD34, Ki‐67, VEGF‐A, and D2‐40 (as a lymphatic vessel marker). We assessed the ratio of vasohibin‐ and VEGFR‐2‐positive vessels in the stroma of endometrial carcinoma. Immunohistochemical assessment was classified as negative or positive based on staining intensity. Vasohibin was selectively expressed on vascular endothelial cells in both cyclic endometria and endometrial carcinomas. Vasohibin was highly expressed in the normal functional endmetrium of the secretory phase, especially in the spiral artery, and was highly expressed in all grades of endometrioid adenocarcinomas. The stromal endothelial cells in G3 expressed vasohibin and VEGFR‐2 more frequently than these in G1. In endometrioid adenocarcinomas, there was a significant correlation between the expression percentage of vasohibin and that of VEGFR‐2 (P < 0.0001, r2 = 0.591). This is the first study to elucidate the correlation between expression of vasohibin in the stromal endothelial cells and that of VEGFR‐2 in human carcinomas. (Cancer Sci 2008; 99: 914–919)
Functional analysis of individual cells and microenvironment of breast cancer‐draining lymph nodes
Authors: Zurgil Naomi , Deutsch Assaf , Afrimzon Elena , Shafran Yana , Tirosh Reuven , Sandbank Judith , Pappo Itzhak , Deutsch Mordechai
Published: March 2008

The development of distant metastases is the major cause of death in breast cancer (BC). In many BC cases, metastases are present in patients with no metastasis‐positive lymph nodes (LN). Hence, there is a need to improve prognosis by a better prediction of the nodal status and tumor spread. The current study is designed to develop and utilize new functional characteristics of the cells and microenvironment of BC‐draining LN, which may help to improve the estimation of LN metastatic involvement. Innovative devices and methodologies were developed for collecting, transferring, and analyzing LN at an individual‐cell resolution. Using these devices, a suspension of living cells were prepared from the LN and processed for various assays, including immunophenotypic analysis, activation status, and invasion activity. The functional profile of tumor‐activated LN cells showed an increase in the intracellular enzymatic reaction rate, accompanied by a homogeneous distribution of transferrin receptor as well as by a significant increase in matrix metalloproteinase proteolytic activity. Moreover, the proportion of cells exhibiting such a profile was significantly higher in tumor‐containing LN than in tumor‐free LN. Thus, the live and postfixation features of LN cells and their microenvironment, correlated with the functional status of the LN, may serve to improve their predictive value in breast cancer examination. (Cancer Sci 2008; 99: 936–945)
Increased CD177 (PRV1) expression in thalassaemia and the underlying erythropoietic activity
Authors: Zoi Katerina , Terpos Evangelos , Zoi Christine , Loukopoulos Dimitris
Published: March 2008

CD177 (PRV1) expression is strongly related to polycythaemia vera (PV). Whilst studying CD177 expression in PV patients and controls, individuals with β‐thalassaemia minor were found to display an elevated expression of CD177. The study was expanded to include patients with thalassaemia intermedia, sickle cell/β‐thalassaemia and thalassaemia major. CD177 expression was increased in these thalassaemic groups and correlated with their erythropoietic activity, as assessed by the measurement of serum erythropoietin and soluble transferrin receptor levels. Within this context, elevated CD177 expression is not only a specific feature of PV but may be an indicator of increased erythropoietic activity in thalassaemia syndromes.
Chronic lymphocytic leukaemia CD20 expression is dependent on the genetic subtype: a study of quantitative flow cytometry and fluorescent in‐situ hybridization in 510 patients
Authors: Tam Constantine S. , Otero‐Palacios Joselle , Abruzzo Lynne V. , Jorgensen Jeffrey L. , Ferrajoli Alessandra , Wierda William G. , Lerner Susan , O’Brien Susan , Keating Michael J.
Published: March 2008

CD20 is an important therapeutic target in chronic lymphocytic leukaemia (CLL). In order to examine the relationship between CD20 expression and cytogenetic abnormalities, we correlated the fluorescent in‐situ hybridization (FISH) genetic subtype of 510 treatment‐naïve patients with CD20 expression as measured by quantitative flow cytometry. Patients were classified using the Dohner hierarchial classification. The median numbers of CD20 antigen sites by FISH subtypes were: 17p‐ (n = 26), 9341 per cell; 11q‐ (n = 42), 5886 per cell; +12 (n = 93), 23 603 per cell; negative FISH (n = 153), 8828 per cell; and 13q‐ (n = 196), 10 781 per cell. Compared to cases with negative FISH, 11q‐ cases had significantly lower CD20 expression (P = 0·001), and +12 cases had significantly higher CD20 expression (P < 0·001). The significance of trisomy 12 and high CD20 expression was maintained after multivariate analysis accounting for other disease characteristics. Fifty‐nine patients received the combination of rituximab and granulocyte‐macrophage colony‐stimulating factor as frontline therapy; responses were observed in 13 of 14 (93%) patients with +12, in two of four (50%) patients with 11q‐, and in 30 of 41 (73%) patients with negative FISH, 13q‐ or 17p‐ CLL. Leukemic CD20 expression differed significantly between FISH subtypes. Patients with trisomy 12 CLL showed strong leukemic cell CD20 expression and had a high rate of response to rituximab‐based therapy.
Magnetic resonance imaging for the detection of bone marrow involvement in malignant lymphoma
Authors: Kwee Thomas C. , Kwee Robert M. , Verdonck Leo F. , Bierings Marc B. , Nievelstein Rutger A. J.
Published: March 2008

This study systematically reviewed the published data regarding the sensitivity of magnetic resonance imaging (MRI) compared with bone marrow biopsy as reference standard for the detection of bone marrow involvement in patients with malignant lymphoma. A systematic search for relevant studies was performed of the PubMed/MEDLINE and Embase databases. Two reviewers independently assessed the methodological quality of each study and the sensitivity of the included studies was calculated. The 11 included studies had moderate methodological quality. Sensitivity of MRI for the detection of bone marrow involvement ranged from 50% to 100%, with a median of 100%. MRI is probably sufficiently sensitive to rule out bone marrow involvement in patients with malignant lymphoma. However, a well‐designed study with a large sample size is needed to confirm current results.