bluuebunny/crossref_metadata_2025_split huggingface dataset:
EXPERIMENTAL LIVER NECROSIS; III. NITROGENOUS METABOLISMS
Authors: Pearce Richard M. , Jackson Holmes C. 
Published: June 2004

1. In focal and diffuse necroses of the liver due to hæmotoxic sera there occurs an increased elimination of total nitrogen with a corresponding augmented output of urea. The ammonia excretion becomes slightly diminished at first, but later rises somewhat above normal. The undetermined nitrogen is markedly increased.
2. In diffuse degeneration with no necrosis on the other hand only a slightly increased output of total nitrogen is evident. A rearrangement of the urea-ammonia proportion occurs in that the ammonia excretion is augmented while the urea elimination is correspondingly diminished. The undetermined nitrogen rises but little.
3. In control experiments with normal serum no effect is produced.
4. These results would appear to indicate that in lesions characterized by uniform degeneration of the liver parenchyma, in contradistinction to necrosis, there occurs no increased nitrogen elimination but merely a disturbance of the urea-forming function of the cell without the appearance in the urine of products of autolysis. On the other hand in necrosis, of even considerable extent, the total-nitrogen is greatly augmented, as is also the rest-nitrogen; while the production of urea, on account of the persistence of normally functioning liver cells, remains relatively unchanged.
This "factor of safety"32 possessed by the liver is, we think, one of the most important results brought out in this investigation and must be given great weight in any consideration of the chemistry of hepatic disturbances.
BIOLOGICAL RELATIONSHIPS OF DIPLOCOCCUS INTRACELLULARIS AND GONOCOCCUS
Authors: Wollstein Martha 
Published: June 2004

The most marked differences, exclusive of pathogenic effects in man, between gonococcus and Diplococcus intracellulans are cultural ones, and consist chiefly in abundance of growth and choice of medium.
Relatively larger doses of gonococci than of diplococci are required to kill young guinea-pigs, but the lesions are very similar in the two cases, and both organisms lose pathogenic power rapidly when cultivated artificially.
Agglutinins, aggressins, protective power, and the amboceptors developed in the serum of immunized animals seem to be largely common to both diplococcus and gonococcus.
Neither other Gram negative cocci nor Streptococcus pyogenes have any receptors in common with intracellularis and gonococcus.
Grekos’ S function has a linear growth
Authors: Cassaigne Julien , Plagne Alain 
Published: June 2004

An exact additive asymptotic basis is a set of nonnegative integers such that there exists an integer

h
h

with the property that any sufficiently large integer can be written as a sum of exactly

h
h

elements of

A

\mathcal {A}

. The minimal such

h
h

is the exact order of

A

\mathcal {A}

(denoted by

ord

∗

(

A

)

\mbox {ord}^{\ast } ( \mathcal {A} )

). Given any exact additive asymptotic basis

A

\mathcal {A}

, we define

A

∗

\mathcal {A}^{\ast }

to be the subset of

A

\mathcal {A}

composed with the elements

a
∈

A

a \in \mathcal {A}

such that

A

∖
{
a
}

\mathcal {A} \setminus \{ a \}

is still an exact additive asymptotic basis. It is known that

A

∖

A

∗

\mathcal {A} \setminus \mathcal {A}^{\ast }

is finite. In this framework, a central quantity introduced by Grekos is the function

S
(
h
)

S(h)

defined as the following maximum (taken over all bases

A

\mathcal {A}

of exact order

h
h

):
\[

S
(
h
)
=

max

A

lim sup

a
∈

A

∗

ord

∗

(

A

∖
{
a
}
)
.

S (h) = \max _{\mathcal {A}} \qquad \limsup _{a \in \mathcal {A}^{\ast }} \qquad \mbox {ord}^{\ast } ( \mathcal {A} \setminus \{ a \}).

\]
In this paper, we introduce a new and simple method for the study of this function. We obtain a new estimate from above for

S
S

which improves drastically and in any case on all previously known estimates. Our estimate, namely

S
(
h
)
≤
2
h

S(h) \leq 2h

, cannot be too far from the truth since

S
S

verifies

S
(
h
)
≥
h
+
1

S(h) \geq h+1

. However, it is certainly not always optimal since

S
(
2
)
=
3

S(2)=3

. Our last result shows that

S
(
h
)

S (h)

is in fact a strictly increasing sequence.
A new proof for Rockafellar’s characterization of maximal monotone operators
Authors: Simons S. , Zălinescu C. 
Published: June 2004

We provide a new and short proof for Rockafellar’s characterization of maximal monotone operators in reflexive Banach spaces based on S. Fitzpatrick’s function and a technique used by R. S. Burachik and B. F. Svaiter for proving their result on the representation of a maximal monotone operator by convex functions.
On extension of isometries between unit spheres of 𝐴𝐿_{𝑝}-spaces (0<𝑝<∞)
Authors: Jian Wang 
Published: June 2004

In this paper, we study the extension of isometries between unit spheres of atomicALpAL_p-spaces(0>p>∞, p≠2)(0>p>\infty ,\ p\neq 2). We find a condition under which an isometryTTbetween unit spheres can be linearly isometrically extended. Moreover, we prove that every onto isometry between unit spheres of atomicALpAL_p-spaces(0>p>∞, p≠2)(0>p>\infty ,\ p\neq 2)can be linearly isometrically extended to the whole space.
Biologically valid linear factor models of gene expression
Authors: Girolami Mark , Breitling Rainer 
Published: June 2004

Abstract
Motivation: The identification of physiological processes underlying and generating the expression pattern observed in microarray experiments is a major challenge. Principal component analysis (PCA) is a linear multivariate statistical method that is regularly employed for that purpose as it provides a reduced-dimensional representation for subsequent study of possible biological processes responding to the particular experimental conditions. Making explicit the data assumptions underlying PCA highlights their lack of biological validity thus making biological interpretation of the principal components problematic. A microarray data representation which enables clear biological interpretation is a desirable analysis tool.
Results: We address this issue by employing the probabilistic interpretation of PCA and proposing alternative linear factor models which are based on refined biological assumptions. A practical study on two well-understood microarray datasets highlights the weakness of PCA and the greater biological interpretability of the linear models we have developed.
Availability: The model estimation routines are currently implemented as Matlab routines and these, as well as data and results reported, are available from the following URL: http://www.dcs.gla.ac.uk/~girolami/lfm/index.html
Breakpoint identification and smoothing of array comparative genomic hybridization data
Authors: Jong Kees , Marchiori Elena , Meijer Gerrit , Vaart A. v. d. , Ylstra Bauke 
Published: June 2004

Abstract
Summary: We describe a tool, called aCGH-Smooth, for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is written in visual C++, has a user-friendly interface including a visualization of the results and user-defined parameters adapting the performance of data smoothing and breakpoint recognition. aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data.
Availability: aCGH-Smooth is free for researchers at academic and non-profit institutions at http://www.few.vu.nl/~vumarray/
CTRD: a fast applet for computing signed translocation distance between genomes
Authors: Feng WangSen , Wang Lusheng , Zhu Daming 
Published: June 2004

Abstract
Summary: CTRD is a software for computing translocation distance between genomes. It takes two genomes as its input and tests whether one genome can be transformed into the other. If possible, it computes the translocation distance between two genomes, and gives the translocation operation serial. We adopt the fastest known O(n2log n) algorithm.
Our contributions include (1) give a necessary and sufficient condition to ensure that one genome can be transformed into the other for translocation operations, and (2) develop a software using the fastest known O(n2log n) algorithm.
Availability: Free from http://www.cs.cityu.edu.hk/~lwang/software/Translocation/ subject to copyright restrictions.
QuickJoin—fast neighbour-joining tree reconstruction
Authors: Mailund Thomas , Pedersen Christian N. S. 
Published: June 2004

Abstract
Summary: We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm—while still constructing the same tree as the original neighbour-joining algorithm—making it possible to construct trees for 8000 species in &lt;10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree neighbour-joining implementation.
Availability: The source code for QuickJoin is available from http://www.birc.dk/Software/QuickJoin under the GNU Public License (GPL).
SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays
Authors: Niu Tianhua , Hu Zhenjun 
Published: June 2004

Abstract
Summary: Simple, low-cost and accurate genotyping methods for single nucleotide polymorphisms (SNPs) are in high demand in the post-genome-sequencing era. We present a graphical tool called SNPicker, implemented in Java, which significantly facilitates the design of mutagenic endonuclease restriction assays. SNPicker uses the online NEB REBASE to automatically scan for all possible designs of mutagenic primers that can facilitate the picking of mismatched PCR primers to artificially introduce or abolish a restriction site at the target SNP site. We successfully applied SNPicker in designing endonuclease restriction assays for 14 SNPs for the MTHFR gene, the Coagulation Factor II gene and the Coagulation Factor V gene. The SNP assays designed using SNPicker were cross-validated using the MassARRAY technology.
Availability: SNPicker, as a software tool in the Web-based SeqVISTA Suite, is freely available at http://zlab.bu.edu/SeqVISTA/. A tutorial for SNPicker is available at http://zlab.bu.edu/SeqVISTA/manual/SNPicker.htm
BioSilico: an integrated metabolic database system
Authors: Hou Bo Kyeng , Kim Jin Sik , Jun Ji Hoon , Lee Dong-Yup , Kim Yong Wook , Chae Sujin , Roh Mira , In Yong-Ho , Lee Sang Yup 
Published: June 2004

Abstract
Summary: BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways. Heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc are integrated in a systematic way, thereby allowing users to efficiently retrieve the relevant information on enzymes, biochemical compounds and reactions. In addition, it provides well-designed view pages for more detailed summary information. BioSilico is developed as an extensible system with a robust systematic architecture.
Availability: BioSilico database system is accessible at http://biosilico.kaist.ac.kr
Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
Authors: Sætrom Pål 
Published: June 2004

Abstract
Motivation: Both small interfering RNAs (siRNAs) and antisense oligonucleotides can selectively block gene expression. Although the two methods rely on different cellular mechanisms, these methods share the common property that not all oligonucleotides (oligos) are equally effective. That is, if mRNA target sites are picked at random, many of the antisense or siRNA oligos will not be effective. Algorithms that can reliably predict the efficacy of candidate oligos can greatly reduce the cost of knockdown experiments, but previous attempts to predict the efficacy of antisense oligos have had limited success. Machine learning has not previously been used to predict siRNA efficacy.
Results: We develop a genetic programming based prediction system that shows promising results on both antisense and siRNA efficacy prediction. We train and evaluate our system on a previously published database of antisense efficacies and our own database of siRNA efficacies collected from the literature. The best models gave an overall correlation between predicted and observed efficacy of 0.46 on both antisense and siRNA data. As a comparison, the best correlations of support vector machine classifiers trained on the same data were 0.40 and 0.30, respectively.
Availability: The prediction system uses proprietary hardware and is available for both commercial and strategic academic collaborations. The siRNA database is available upon request.
‘Nectosome’: a novel cytoplasmic vesicle containing nectin in the egg of the sea urchin, Temnopleurus hardwickii
Authors: Kato Koichi H. , Abe Tetsuya , Nakashima Seiko , Matranga Valeria , Zito Francesca , Yokota Yukio 
Published: June 2004

Localization of an extracellular matrix protein, Th‐nectin, in the eggs and embryos of the sea urchin Temnopleurus hardwickii was examined by both immunofluorescence and immunoelectron microscopy. The protein is associated with a tubular structure packaged in rod‐shaped vesicles that were designated as ‘nectosomes’. In unfertilized eggs, nectosomes are distributed uniformly throughout the cytoplasm, but after fertilization, they gradually translocate to the cortical zone where they are arranged perpendicular to the plasma membrane. The migration of the nectosomes was strongly inhibited by cytochalasin B, which suggested that microfilaments play an important role in this process. Immunocytochemical and immunoblotting analyses both ascertained that nectin is secreted into the hyaline layer. Some nectosomes remain in the apical cytoplasm of dermal cells until the gastrula stage. Ultrastructural examination revealed that the accumulation of nectosomes in the oocyte cytoplasm begins quite early in oogenesis, concomitant with the accumulation of cortical vesicles.
Regulation of the Ysa Type III Secretion System ofYersinia enterocoliticaby YsaE/SycB and YsrS/YsrR
Authors: Walker Kimberly A. , Miller Virginia L. 
Published: June 2004

ABSTRACTYersinia enterocoliticabiovar 1B contains two type III secretion systems (TTSSs), the plasmid-encoded Ysc-Yop system and the chromosomally encoded Ysa-Ysp system. Proteins secreted from the Ysa TTSS (Ysps) have only been detected in vitro when cells are cultured at 26°C in a high-NaCl medium. However, the exact role of the Ysa TTSS is unclear. Thus, investigations into the regulation of this system may help elucidate the role of the Ysps during the life cycle ofY. enterocolitica. Here we present evidence that the AraC-like regulator YsaE acts together with the chaperone SycB to regulate transcription of thesycByspBCDAoperon, a phenomenon similar to that seen in the closely relatedSalmonellaSPI-1 andShigella flexneriMxi-Spa-Ipa TTSSs. Deletion of eithersycBorysaEresults in a twofold reduction in the activity of asycB-lacZfusion compared to the wild type. In a reconstitutedEscherichia colisystem, transcription ofsycBwas activated sixfold only when both YsaE and SycB were present, demonstrating that they are necessary for activation.ysrRandysrSare located near theysagenes and encode a putative two-component regulatory system. Mutations in either gene indicated that both YsrR and YsrS were required for secretion of Ysps. In addition, transcription fromsycB-lacZandysaE-lacZfusions was decreased 6.5- and 25-fold, respectively, in theysrSmutant compared to the wild type. Furthermore, in the absence of NaCl, the activity ofysaE-lacZwas reduced 25-fold in the wild-type and ΔysrSstrains, indicating that YsrS is probably required for the salt-dependent expression of theysalocus. These results suggest that the putative two-component system YsrRS may be a key element in the regulatory cascade for the Ysa TTSS.
Free and Hemophore-Bound Heme Acquisitions through the Outer Membrane Receptor HasR Have Different Requirements for the TonB-ExbB-ExbD Complex
Authors: Létoffé Sylvie , Delepelaire Philippe , Wandersman Cécile 
Published: June 2004

ABSTRACTMany gram-negative bacteria have specific outer membrane receptors for free heme, hemoproteins, and hemophores. Heme is a major iron source and is taken up intact, whereas hemoproteins and hemophores are not transported: the iron-containing molecule has to be stripped off at the cell surface, with only the heme moiety being taken up. TheSerratia marcescenshemophore-specific outer membrane receptor HasR can transport either heme itself or heme bound to the hemophore HasA. This second mechanism is much more efficient and requires a higher TonB-ExbB-ExbD (TonB complex) concentration than does free or hemoglobin-bound heme uptake. This requirement for more of the TonB complex is associated with a higher energy requirement. Indeed, the sensitivity of heme-hemophore uptake to the protonophore carbonyl cyanidem-chlorophenyl hydrazone is higher than that of heme uptake from hemoglobin. We show that a higher TonB complex concentration is required for hemophore dissociation from the receptor. This dissociation is concomitant with heme uptake. We propose that increasing the TonB complex concentration drives more energy to the outer membrane receptor and speeds up the release of empty hemophores, which, if they remained on receptors, would inhibit heme transport.
The
fabM
Gene Product of
Streptococcus mutans
Is Responsible for the Synthesis of Monounsaturated Fatty Acids and Is Necessary for Survival at Low pH
Authors: Fozo Elizabeth M. , Quivey Robert G. 
Published: June 2004

ABSTRACT

Previously, it has been demonstrated that the membrane fatty acid composition of
Streptococcus mutans
is affected by growth pH (E. M. Fozo and R. G. Quivey, Jr., Appl. Environ. Microbiol.
70:
929-936, 2004; R. G. Quivey, Jr., R. Faustoferri, K. Monahan, and R. Marquis, FEMS Microbiol. Lett.
189:
89-92, 2000). Specifically, the proportion of monounsaturated fatty acids increases when the organism is grown in acidic environments; if the shift to increased monounsaturated fatty acids is blocked by the addition of a fatty acid biosynthesis inhibitor, the organism is rendered more acid sensitive (E. M. Fozo and R. G. Quivey, Jr., Appl. Environ. Microbiol.
70:
929-936, 2004). Recently, work with
Streptococcus pneumoniae
has identified a novel enzyme, FabM, responsible for the production of monounsaturated fatty acids (H. Marrakchi, K. H. Choi, and C. O. Rock, J. Biol. Chem.
277:
44809-44816, 2002). Using the published
S. pneumoniae
sequence, a putative FabM was identified in the
S. mutans
strain UA159. We generated a
fabM
strain that does not produce unsaturated fatty acids as determined by gas chromatography of fatty acid methyl esters. The mutant strain was extremely sensitive to low pH in comparison to the wild type; however, the acid-sensitive phenotype was relieved by growth in the presence of long-chain monounsaturated fatty acids or through genetic complementation. The strain exhibited reduced glycolytic capability and altered glucose-PTS activity. In addition, the altered membrane composition was more impermeable to protons and did not maintain a normal ΔpH. The results suggest that altered membrane composition can significantly affect the acid survival capabilities, as well as several enzymatic activities, of
S. mutans
.
Extracellular Proteolytic Activity Plays a Central Role in Swarming Motility inBacillus subtilis
Authors: Bindel Connelly Mariah , Young Glenn M. , Sloma Alan 
Published: June 2004

ABSTRACTNatural isolates ofBacillus subtilisexhibit a robust multicellular behavior known as swarming. A form of motility, swarming is characterized by a rapid, coordinated progression of a bacterial population across a surface. As a collective bacterial process, swarming is often associated with biofilm formation and has been linked to virulence factor expression in pathogenic bacteria. While the swarming phenotype has been well documented forBacillusspecies, an understanding of the molecular mechanisms responsible remains largely isolated to gram-negative bacteria. To better understand how swarming is controlled in members of the genusBacillus, we investigated the effect of a series of gene deletions on swarm motility. Our analysis revealed that a strain deficient for the production of surfactin and extracellular proteolytic activity did not swarm or form biofilm. While it is known that surfactin, a lipoprotein surfactant, functions in swarming motility by reducing surface tension, this is the first report demonstrating that general extracellular protease activity also has an important function. These results not only help to define the factors involved in eliciting swarm migration but support the idea that swarming and biofilm formation may have overlapping control mechanisms.
Altering the Substrate Specificity of Polyhydroxyalkanoate Synthase 1 Derived from
Pseudomonas putida
GPo1 by Localized Semirandom Mutagenesis
Authors: Sheu Der-Shyan , Lee Chia-Yin 
Published: June 2004

ABSTRACT

The substrate specificity of polyhydroxyalkanoate (PHA) synthase 1 (PhaC1

Pp

, class II) from
Pseudomonas putida
GPo1 (formerly known as
Pseudomonas oleovorans
GPo1) was successfully altered by localized semirandom mutagenesis. The enzyme evolution system introduces multiple point mutations, designed on the basis of the conserved regions of the PHA synthase family, by using PCR-based gene fragmentation with degenerate primers and a reassembly PCR. According to the opaqueness of the colony, indicating the accumulation of large amounts of PHA granules in the cells, 13 PHA-accumulating candidates were screened from a mutant library, with
Pseudomonas putida
GPp104 PHA
−
as the host. The in vivo substrate specificity of five candidates, L1-6, D7-47, PS-A2, PS-C2, and PS-E1, was evaluated by the heterologous expression in
Ralstonia eutropha
PHB
−
4 supplemented with octanoate. Notably, the amount of 3-hydroxybutyrate (short-chain-length [SCL] 3-hydroxyalkanoate [3-HA] unit) was drastically increased in recombinants that expressed evolved mutant enzymes L1-6, PS-A2, PS-C2, and PS-E1 (up to 60, 36, 50, and 49 mol%, respectively), relative to the amount in the wild type (12 mol%). Evolved enzyme PS-E1, in which 14 amino acids had been changed and which was heterologously expressed in
R. eutropha
PHB
−
4, not only exhibited broad substrate specificity (49 mol% SCL 3-HA and 51 mol% medium-chain-length [MCL] 3-HA) but also conferred the highest PHA production (45% dry weight) among the candidates. The 3-HA and MCL 3-HA units of the PHA produced by
R. eutropha
PHB
−
4/pPS-E1 were randomly copolymerized in a single polymer chain, as analytically confirmed by acetone fractionation and the
13
C nuclear magnetic resonance spectrum.