bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal constants in the exceptional case of Sobolev inequalities on Riemannian manifolds
Authors: Faget Zoé 
Published: January 2008

Let

(
M
,
g
)

(M,g)

be a Riemannian compact

n
n

-manifold. We know that for any

ε
>
0

\varepsilon >0

, there exists

C
ε

>
0

C_\varepsilon >0

such that for any

u
∈

H
1
n

(
M
)

u\in H_1^n(M)

,

∫
M

e
u

d
v

g

≤

C
ε

exp
⁡
[
(

μ
n

+
ε
)

∫
M

|

∇
u

|

n

d
v

g

+

1

v
o
l

(
M
)

∫
M

u

d
v

g

]

\int _Me^u\mathrm {dv}_g\le C_\varepsilon \exp [(\mu _n+\varepsilon )\int _M|\nabla u|^n\mathrm {dv}_g+\frac {1}{\mathrm {vol}(M)}\int _Mu\mathrm {dv}_g]

,

μ
n

\mu _n

being the smallest constant possible such that the inequality remains true for any

u
∈

H
1
n

(
M
)

u\in H_1^n(M)

. We call

μ
n

\mu _n

the “first best constant”. We prove in this paper that it is possible to choose

ε
=
0

\varepsilon =0

and keep

C
ε

C_\varepsilon

a finite constant. In other words we prove the existence of a “second best constant” in the exceptional case of Sobolev inequalities on compact Riemannian manifolds.
Finiteness of cousin cohomologies
Authors: Kawasaki Takesi 
Published: January 2008

The notion of the Cousin complex of a module was given by Sharp in 1969. It wasn’t known whether its cohomologies are finitely generated until recently. In 2001, Dibaei and Tousi showed that the Cousin cohomologies of a finitely generated

A
A

-module

M
M

are finitely generated if the base ring

A
A

is local, has a dualizing complex,

M
M

satisfies Serre’s

(

S
2

)

(S_2)

-condition and is equidimensional. In the present article, the author improves their result. He shows that the Cousin cohomologies of

M
M

are finitely generated if

A
A

is universally catenary, all the formal fibers of all the localizations of

A
A

are Cohen-Macaulay, the Cohen-Macaulay locus of each finitely generated

A
A

-algebra is open and all the localizations of

M
M

are equidimensional. As a consequence of this, he gives a necessary and sufficient condition for a Noetherian ring to have an arithmetic Macaulayfication.
GenomeVx: simple web-based creation of editable circular chromosome maps
Authors: Conant Gavin C. , Wolfe Kenneth H. 
Published: January 2008

Abstract
We describe GenomeVx, a web-based tool for making editable, publication-quality, maps of mitochondrial and chloroplast genomes and of large plasmids. These maps show the location of genes and chromosomal features as well as a position scale. The program takes as input either raw feature positions or GenBank records. In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator.
Availability: GenomeVx is available at http://wolfe.gen.tcd.ie/GenomeVx
Contact: conantg@tcd.ie
Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data
Authors: Fröhlich Holger , Fellmann Mark , Sültmann Holger , Poustka Annemarie , Beissbarth Tim 
Published: January 2008

AbstractMotivation: Targeted interventions using RNA interference in combination with the measurement of secondary effects with DNA microarrays can be used to computationally reverse engineer features of upstream non-transcriptional signaling cascades based on the nested structure of effects.Results: We extend previous work by Markowetz et al., who proposed a statistical framework to score different network hypotheses. Our extensions go in several directions: we show how prior assumptions on the network structure can be incorporated into the scoring scheme by defining appropriate prior distributions on the network structure as well as on hyperparameters. An approach called module networks is introduced to scale up the original approach, which is limited to around 5 genes, to infer large-scale networks of more than 30 genes. Instead of the data discretization step needed in the original framework, we propose the usage of a beta-uniform mixture distribution on the P-value profile, resulting from differential gene expression calculation, to quantify effects. Extensive simulations on artificial data and application of our module network approach to infer the signaling network between 13 genes in the ER-α pathway in human MCF-7 breast cancer cells show that our approach gives sensible results. Using a bootstrapping and a jackknife approach, this reconstruction is found to be statistically stable.Availability: The proposed method is available within the Bioconductor R-package nem.Contact: h.froehlich@dkfz-heidelberg.de
Jane: suggesting journals, finding experts
Authors: Schuemie Martijn J. , Kors Jan A. 
Published: January 2008

Abstract
Summary: With an exponentially growing number of articles being published every year, scientists can use some help in determining which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work.
Jane (Journal/Author Name Estimator) is a freely available web-based application that, on the basis of a sample text (e.g. the title and abstract of a manuscript), can suggest journals and experts who have published similar articles.
Availability: http://biosemantics.org/jane
Contact: m.schuemie@erasmusmc.nl
Compressed indexing and local alignment of DNA
Authors: Lam T. W. , Sung W. K. , Tam S. L. , Wong C. K. , Yiu S. M. 
Published: January 2008

Abstract
Motivation: Recent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing very long strings such as the human genome in the main memory. For example, a BWT index for the human genome (with about 3 billion characters) occupies just around 1 G bytes. However, these indexes are designed for exact pattern matching, which is too stringent for biological applications. The demand is often on finding local alignments (pairs of similar substrings with gaps allowed). Without indexing, one can use dynamic programming to find all the local alignments between a text T and a pattern P in O(|T||P|) time, but this would be too slow when the text is of genome scale (e.g. aligning a gene with the human genome would take tens to hundreds of hours). In practice, biologists use heuristic-based software such as BLAST, which is very efficient but does not guarantee to find all local alignments.
Results: In this article, we show how to build a software called BWT-SW that exploits a BWT index of a text T to speed up the dynamic programming for finding all local alignments. Experiments reveal that BWT-SW is very efficient (e.g. aligning a pattern of length 3 000 with the human genome takes less than a minute). We have also analyzed BWT-SW mathematically for a simpler similarity model (with gaps disallowed), and we show that the expected running time is O(|T|0.628|P|) for random strings. As far as we know, BWT-SW is the first practical tool that can find all local alignments. Yet BWT-SW is not meant to be a replacement of BLAST, as BLAST is still several times faster than BWT-SW for long patterns and BLAST is indeed accurate enough in most cases (we have used BWT-SW to check against the accuracy of BLAST and found that only rarely BLAST would miss some significant alignments).
Availability: www.cs.hku.hk/~ckwong3/bwtsw
Contact: twlam@cs.hku.hk
Pathways of Fluid Drainage from the Brain ‐ Morphological Aspects and Immunological Significance in Rat and Man
Authors: Weller Roy O. , Kida Shinya , Zhang En‐Tan 
Published: January 2008

There is firm physiological evidence for the lymphatic drainage of interstitial fluid and cerebrospinal fluid from the brains of rats, rabbits and cats. The object of this review, is to describe firstly the morphological aspects of lymphatic drainage pathways from the rat brain and secondly, to explore through scanning and transmission electron microscope techniques, the possibility of similar lymphatic drainage pathways in man.Interstitial and oedema fluid spreads diffusely through the white matter in the rat and appears to drain into the ventricular cerebrospinal fluid. In grey matter, however, tracers pass along perivascular spaces to the surface of the brain and into the cerebrospinal fluid. Paravascular compartments in the subarachnoid space follow the course of major arterial branches to the circle of Willis and thence along the ethmoidal arteries to the cribriform plate of the ethmoid bone. Particulate tracers, such as Indian ink, enter channels in the arachnoid beneath the olfactory bulbs and connect directly with nasal lymphatics through channels which pass through holes in the cribriform plate. Proteins and other solutes may also drain along other cranial nerves. Thus, there is a bulk flow pathway for interstitial and cerebrospinal fluid from the rat brain into cervical lymphatics.In man, it is probable that diffuse interstitial drainage of fluid from the white matter occurs in a similar way to that in the rat. Furthermore, the anatomical pathways exist by which bulk drainage of fluid could occur along perivascular spaces from the grey matter into perivascular spaces of the leptomeningeal arteries and thence into the cerebrospinal fluid (CSF). Compartmentalisation of the subarachnoid space may allow directional flow of CSF to occur. Thus, although the vast bulk of CSF in man drains through arachnoid villi and granulations, anatomical pathways exist by which selective flow for lymphatic drainage of brain interstitial fluid and inflammatory cells could occur. Physiological evidence for traffic along such pathways in man, however, is still sparse. It seems probable that any lymphatic drainage of CSF in man is overshadowed by the high volume passage of CSF through the arachnoid granulations and villi.
October 1996 — Rapidly Progressive Weakness
Authors: Galloway Gloria , Giuliani Michael J. , Lacomis David 
Published: January 2008

Case AbstractOne week after a flu‐like illness, a 51‐year‐old woman developed rapidly progressive weakness. Within three weeks, she required mechanical ventilation. A neurological exam revealed severe motor involvement with normal sensory findings confirmed by nerve conduction studies. Five days after intubation a catastrophic brain hemorrhage occurred. Autopsy showed severe loss of axons in the motor roots with periaxonal macrophages and no lymphocytes. These findings are typical of acute motor axonal neuropathy, which is rare in the United States.
Fungal Infections
Authors: Chimelli Leila , Mahler‐Araújo Maria Betania 
Published: January 2008

Fungal infections have increased in frequency in the last decades because of the growing number of immunocompromised patients who survive longer periods of time than in the past, the widespread use of immunosuppressive drugs, a large aging population with increased numbers of malignancies, and the spread of AIDS. Although fungi are present everywhere, some mycoses predominate in the tropics, not only in view of warm temperature and humid climate, which favor their growth, but also because of inadequate hygienic and working conditions brought about by poverty.Mycotic diseases in the brain are usually secondary to infections elsewhere in the body, usually the lungs, less often from other extracranial sites, and in the vast majority of the cases spread via blood circulation. Only occasionally they result from direct exensions from infections of the sinuses or bone, and less frequently from prosthetic heart valves. Candida may be endogenous in origin, inhabiting the digestive tract. Most fungi cause basal meningitis or intraparenchymal abscesses. Direct extension from the cribriform plate cause necro‐bemorrhagic lesions in the base of the frontal lobe.Although fungi are common in our environment, few are pathogenic. In this paper mycotic infections are divided into opportunistic and pathogenic; although most of the latter have also been described in immunosuppressed patients, some of those caused by opportunistic organisms, have also occurred in the absence of predisposing factors.
Bacterial Infections
Authors: Gray Françoise 
Published: January 2008

The organisms that produce bacterial infections of the nervous system in tropical regions are similar to those existing in the rest of the world. However, because of poor socio‐economic conditions in the former areas, preventing the implementation of appropriate prophylactic and therapeutic measures, the incidence and course of these diseases may vary.In this paper the neuropathological appearances of the main bacterial diseases are reviewed and the main differences between those occurring in developed and developing countries emphasized.Despite great efforts by governments and communities, tuberculosis still remains a scourge in many countries and leprosy has not been eradicated from earth. Earlier optimism that antibiotics could finally put an end to syphilis have been dashed and the disease still persists. Moreover, the explosion of AIDS not only has produced a recrudescence of many of these diseases, but has also changed their clinical and pathological presentation.
September 1996 — New Onset Hemiparesis
Authors: Hamilton Ronald L. 
Published: January 2008

Case AbstractA 44 year old woman developed left hemiparesis. CT scan showed a contrast enhancing lesion in the right periventricular area. A stereotactic biopsy was performed. The initial impression was that of an astrocytic neoplasm, however the presence of perivascular lymphocytes and numerous foamy macrophages led to consultation. Special studies demonstrated demyelination and lymphocytic infiltrate with relative axonal preservation consistent with multiple sclerosis. Additional history from the patient revealed a flu‐like illness one week prior to the hemiparesis and a history of transitory visual problems, possibly early manifestations of her multiple sclerosis.
Mutations Associated with Failure of Raltegravir Treatment Affect Integrase Sensitivity to the Inhibitor In Vitro
Authors: Malet Isabelle , Delelis Olivier , Valantin Marc-Antoine , Montes Brigitte , Soulie Cathia , Wirden Marc , Tchertanov Luba , Peytavin Gilles , Reynes Jacques , Mouscadet Jean-François , Katlama Christine , Calvez Vincent , Marcelin Anne-Geneviève 
Published: January 2008

ABSTRACT
Raltegravir (MK-0518) is a potent inhibitor of human immunodeficiency virus (HIV) integrase and is clinically effective against viruses resistant to other classes of antiretroviral agents. However, it can select mutations in the HIV integrase gene. Nine heavily pretreated patients who received salvage therapy including raltegravir and who subsequently developed virological failure under raltegravir therapy were studied. For each patient, the sequences of the integrase-coding region were determined and compared to that at the beginning of the treatment. Four different mutation profiles were identified in these nine patients: E92Q, G140S Q148H, N155H, and E157Q mutations. For four patients, each harboring a different profile, the wild-type and mutated integrases were produced, purified, and assayed in vitro. All the mutations identified altered the activities of integrase protein: both 3′ processing and strand transfer activities were moderately affected in the E92Q mutant; strand transfer was markedly impaired in the N155H mutant; both activities were strongly impaired in the G140S Q148H mutant; and the E157Q mutant was almost completely inactive. The sensitivities of wild-type and mutant integrases to raltegravir were compared. The E92Q and G140S Q148H profiles were each associated with a 7- to 8-fold decrease in sensitivity, and the N155H mutant was more than 14-fold less sensitive to raltegravir. At least four genetic profiles (E92Q, G140S Q148H, N155H, and E157Q) can be associated with in vivo treatment failure and resistance to raltegravir. These mutations led to strong impairment of enzymes in vitro in the absence of raltegravir: strand transfer activity was affected, and in some cases 3′ processing was also impaired.
Genetic Structures at the Origin of Acquisition of the β-Lactamase
bla
KPC
Gene
Authors: Naas Thierry , Cuzon Gaelle , Villegas Maria-Virginia , Lartigue Marie-Frédérique , Quinn John P. , Nordmann Patrice 
Published: January 2008

ABSTRACT

Genetic structures surrounding the carbapenem-hydrolyzing Ambler class A
bla
KPC
gene were characterized in several KPC-positive
Klebsiella pneumoniae
and
Pseudomonas aeruginosa
strains isolated from the United States, Colombia, and Greece. The
bla
KPC
genes were associated in all cases with transposon-related structures. In the
K. pneumoniae
YC isolate from the United States, the β-lactamase
bla
KPC-2
gene was located on a novel Tn
3
-based transposon, Tn
4401
. Tn
4401
was 10 kb in size, was delimited by two 39-bp imperfect inverted repeat sequences, and harbored, in addition to the β-lactamase
bla
KPC-2
gene, a transposase gene, a resolvase gene, and two novel insertion sequences, IS
Kpn6
and IS
Kpn7
. Tn
4401
has been identified in all isolates. However, two isoforms of this transposon were found: Tn
4401
a was found in
K. pneumoniae
YC and
K. pneumoniae
GR from the United States and Greece, respectively, and differed by a 100-bp deletion, located just upstream of the
bla
KPC-2
gene, compared to the sequence of Tn
4401
b, which was found in the Colombian isolates. In all isolates tested, Tn
4401
was flanked by a 5-bp target site duplication, the signature of a recent transposition event, and was inserted in different open reading frames located on plasmids that varied in size and nature. Tn
4401
is likely at the origin of carbapenem-hydrolyzing β-lactamase KPC mobilization to plasmids and its further insertion into various-sized plasmids identified in nonclonally related
K. pneumoniae
and
P. aeruginosa
isolates.
Comparison of Lipid Amphotericin B Preparations in Treating Murine Zygomycosis
Authors: Ibrahim Ashraf S. , Gebremariam Teclegiorgis , Husseiny Mohamed I. , Stevens David A. , Fu Yue , Edwards John E. , Spellberg Brad 
Published: January 2008

ABSTRACT
We compared the efficacies of liposomal amphotericin B (LAmB) and an amphotericin B lipid complex (ABLC) in diabetic ketoacidotic (DKA) or neutropenic mice with disseminated zygomycosis. ABLC was as effective as LAmB in neutropenic but not DKA mice. Low-dose ABLC was less effective than LAmB at reducing brain fungal burdens in both models.
Antibiotic Susceptibility of Invasive
Haemophilus influenzae
Strains in Canada
Authors: Sill Michelle L. , Tsang Raymond S. W. 
Published: January 2008

ABSTRACT

Canadian invasive
Haemophilus influenzae
isolates from 1990 to 2006 were examined for antibiotic susceptibility: 42 strains (17.8%) were resistant to ampicillin by β-lactamase production, 5.5% were β-lactamase negative ampicillin intermediate, and 2.5% were intermediate to only the 2-μg ampicillin disk. An increase in β-lactamase-negative ampicillin-intermediate strains has been found.
Larger Vancomycin Doses (at Least Four Grams per Day) Are Associated with an Increased Incidence of Nephrotoxicity
Authors: Lodise Thomas P. , Lomaestro Ben , Graves Jeffrey , Drusano G. L. 
Published: January 2008

ABSTRACT

Recent guidelines recommend vancomycin trough concentrations between 15 and 20 mg/liter. In response, some clinicians increased vancomycin dosing to ≥4 g/day. Scant data are available regarding toxicities associated with higher vancomycin doses. The purpose of this study was to examine vancomycin-associated nephrotoxicity at ≥4 g/day. To accomplish the study objective, a cohort study among a random selection of patients receiving vancomycin or linezolid between 2005 and 2006 was performed. Patients were included if they (i) were ≥18 years of age, (ii) were nonneutropenic, (iii) were on therapy for >48 h, (iv) had baseline serum creatinine levels of <2.0 mg/dl, (v) did not suffer from cystic fibrosis, and (vi) had no intravenous contrast dye within the previous 7 days. For drug exposure, three treatment strata were created: standard vancomycin dose (<4 g/day), high vancomycin dose (≥4 g/day), and linezolid. Nephrotoxicity was defined as a serum creatinine increase of 0.5 mg/dl or 50%, whichever was greater, after therapy initiation. Stratified Kaplan-Meier analysis and Cox modeling were used to compare times to nephrotoxicity across groups. During the study, 246 patients on vancomycin (26 patients taking ≥4 g/day and 220 patients taking <4 g/day) and 45 patients on linezolid met the criteria. A significant difference in nephrotoxicity between patients receiving ≥4 g vancomycin/day, those receiving <4 g vancomycin/day, and those receiving linezolid was noted (34.6%, 10.9%, and 6.7%, respectively;
P
= 0.001), and Kaplan-Meier analysis identified significant differences in time to nephrotoxicity for the high-vancomycin-dose cohort compared to those for groups taking the standard dose and linezolid. In the Cox model, patients taking ≥4 g vancomycin/day, a total body weight of ≥101.4 kg, estimated creatinine clearance of ≤86.6 ml/min, and intensive care unit residence were independently associated with time to nephrotoxicity. The data suggest that higher-dose vancomycin regimens are associated with a higher likelihood of vancomycin-related nephrotoxicity.
Lactobacillus rhamnosus
Strain GG Prevents Enterohemorrhagic
Escherichia coli
O157:H7-Induced Changes in Epithelial Barrier Function
Authors: Johnson-Henry K. C. , Donato K. A. , Shen-Tu G. , Gordanpour M. , Sherman P. M. 
Published: January 2008

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 intimately attaches to intestinal epithelial monolayers and produces attaching and effacing (A/E) lesions. In addition, EHEC infection causes disruptions of intercellular tight junctions, leading to clinical sequelae that include acute diarrhea, hemorrhagic colitis, and the hemolytic-uremic syndrome. Current therapy remains supportive since antibiotic therapy increases the risk of systemic complications. This study focused on the potential therapeutic effect of an alternative form of therapy, probiotic
Lactobacillus rhamnosus
strain GG, to attenuate EHEC-induced changes in paracellular permeability in polarized MDCK-I and T84 epithelial cell monolayers. Changes in epithelial cell morphology, electrical resistance, dextran permeability, and distribution and expression of claudin-1 and ZO-1 were assessed using phase-contrast, immunofluorescence, and transmission electron microscopy and macromolecular flux. This study demonstrated that pretreatment of polarized MDCK-I and T84 cells with the probiotic
L. rhamnosus
GG reduced morphological changes and diminished the number of A/E lesions induced in response to EHEC O157:H7 infection. With probiotic pretreatment there was corresponding attenuation of the EHEC-induced drop in electrical resistance and the increase in barrier permeability assays. In addition,
L. rhamnosus
GG protected epithelial monolayers against EHEC-induced redistribution of the claudin-1 and ZO-1 tight junction proteins. In contrast to the effects seen with the live probiotic, heat-inactivated
L. rhamnosus
GG had no effect on EHEC binding and A/E lesion formation or on disruption of the barrier function. Collectively, these findings provide in vitro evidence that treatment with the probiotic
L. rhamnosus
strain GG could prove to be an effective management treatment for preventing injury of the epithelial cell barrier induced by A/E bacterial enteropathogens.