bluuebunny/crossref_metadata_2025_split huggingface dataset:
Racial/Ethnic Preferences, Sex Preferences, and Perceived Discrimination Related to End‐of‐Life Care
Authors: Duffy Sonia A. , Jackson Frances C. , Schim Stephanie M. , Ronis David L. , Fowler Karen E. 
Published: November 2005

This study investigated racial/ethnic preferences, sex preferences, and perceived discrimination related to end‐of‐life care. Ten focus groups and a follow‐up survey were conducted to obtain in‐depth information on end‐of‐life preferences across five racial/ethnic groups in Michigan stratified by sex. There were 73 focus group participants, including Arab Muslims, Arab Christians, Hispanics, blacks, and whites. The mean age±standard deviation was 67±8.5 (range 50–83). A focus group screener was used to recruit participants. A moderator discussion guide was used to guide the focus groups. A take‐home questionnaire asked about demographic information and end‐of‐life issues.Arab Americans were in favor of making peace on earth and were against assisted suicide, extending life artificially, nursing homes, and telling the patient “bad news.” Hispanic and black women were against assisted suicide and in favor of extending life, whereas the men in these groups felt the opposite. Hispanic women spoke of not wanting a feeding tube and would consider alternative medicine. Blacks were least opposed to nursing homes. For whites, it was important to have choices. When asked about discrimination related to end‐of‐life care, Muslim women spoke of cultural barriers, blacks spoke of inequities in the past, and whites spoke of age discrimination and abandonment when dying.As the population becomes more diverse and continues to age, it will be important to provide culturally and sex‐sensitive end‐of‐life interventions to increase patient/family satisfaction and allocate resources appropriately.
Cardiac troponin C‐L29Q, related to hypertrophic cardiomyopathy, hinders the transduction of the protein kinase A dependent phosphorylation signal from cardiac troponin I to C
Authors: Schmidtmann Anja , Lindow Christopher , Villard Sylvie , Heuser Arnd , Mügge Andreas , Geßner Reinhard , Granier Claude , Jaquet Kornelia 
Published: November 2005

We investigated structural and functional aspects of the first mutation in TNNC1, coding for the calcium‐binding subunit (cTnC) of cardiac troponin, which was detected in a patient with hypertrophic cardiomyopathy [ Hoffmann B, Schmidt‐Traub H, Perrot A, Osterziel KJ & Gessner R (2001) Hum Mut17, 524]. This mutation leads to a leucine–glutamine exchange at position 29 in the nonfunctional calcium‐binding site of cTnC. Interestingly, the mutation is located in a putative interaction site for the nonphosphorylated N‐terminal arm of cardiac troponin I (cTnI) [ Finley NL, Abbott MB, Abusamhadneh E, Gaponenko V, Dong W, Seabrook G, Howarth JW, Rana M, Solaro RJ, Cheung HC et al. (1999) EJB Lett453, 107–112]. According to peptide array experiments, the nonphosphorylated cTnI arm interacts with cTnC around L29. This interaction is almost abolished by L29Q, as observed upon protein kinase A‐dependent phosphorylation of cTnI at serine 22 and serine 23 in wild‐type troponin. With CD spectroscopy, minor changes are observed in the backbone of Ca2+‐free and Ca2+‐saturated cTnC upon the L29Q replacement. A small, but significant, reduction in calcium sensitivity was detected upon measuring the Ca2+‐dependent actomyosin subfragment 1 (actoS1)‐ATPase activity and the sliding velocity of thin filaments. The maximum actoS1‐ATPase activity, but not the maximum sliding velocity, was significantly enhanced. In addition, we performed our investigations at different levels of protein kinase A‐dependent phosphorylation of cTnI. The in vitro assays mainly showed that the Ca2+ sensitivity of the actoS1‐ATPase activity, and the mean sliding velocity of thin filaments, were no longer affected by protein kinase A‐dependent phosphorylation of cTnI owing to the L29Q exchange in cTnC. The findings imply a hindered transduction of the phosphorylation signal from cTnI to cTnC.
Accelerated Cell Death in
Podospora
Autophagy Mutants
Authors: Pinan-Lucarré Bérangère , Balguerie Axelle , Clavé Corinne 
Published: November 2005

ABSTRACT

Although autophagy is characteristic of type II programmed cell death (PCD), its role in cell death is currently debated. Both cell death-promoting and prosurvival roles of autophagy have been reported depending on the organism and the cell type. In filamentous fungi, a cell death reaction known as an incompatibility reaction occurs when cells of unlike genotype fuse. Cell death by incompatibility is characterized by a dramatic vacuolar enlargement and cell lysis. In
Podospora anserina
, autophagy is induced early during this cell death reaction. Cell death by incompatibility in
Podospora
is a model of type II PCD used here to assess the role of autophagy in this type of cell death. We have inactivated Pa
ATG1
, the
Podospora
ortholog of the
Saccharomyces cerevisiae ATG1
gene involved in the early steps of autophagy in yeast. The ΔPa
ATG1
mutant displays developmental defects characteristic of abrogated autophagy in
Podospora
. Using the green fluorescent protein-PaATG8 autophagosome marker, we show that autophagy is abolished in this mutant. Neither cell death by incompatibility nor vacuolization are suppressed in ΔPa
ATG1
and ΔPa
ATG8
autophagy mutants, indicating that a vacuolar cell death reaction without autophagy occurs in
Podospora
. Our results thus provide a novel example of a type II PCD reaction in which autophagy is not the cause of cell death. In addition, we found that cell death is accelerated in ΔPa
ATG
null mutants, suggesting that autophagy has a protective role in this type II PCD reaction.
Involvement of a Short Interspersed Element in Epigenetic Transcriptional Silencing of the Amoebapore Gene in
Entamoeba histolytica
Authors: Anbar Michael , Bracha Rivka , Nuchamowitz Yael , Li Yan , Florentin Anat , Mirelman David 
Published: November 2005

ABSTRACT

Transcriptional silencing of an amoebapore (
ap-a
) gene occurred in
Entamoeba histolytica
following the transfection of plasmids containing a DNA segment (473 bp) homologous to the 5′ upstream region of the gene (R. Bracha, Y. Nuchamowitz, and D. Mirelman, Eukaryot. Cell
2:
295-305, 2003). This segment contains the promoter region of the
ap-a
gene, a T-rich stretch, followed by a truncated SINE1 (short interspersed element 1) that is transcribed from the antisense strand. Transfection of plasmids containing truncated SINE1 sequences which lack their 3′ regulatory elements upstream of the
ap-a
gene was essential for the downstream silencing of the
ap-a
gene while transfection with plasmids containing the entire SINE1 sequence or without the T-rich stretch promoted the overexpression of the
ap-a
gene. Both the T-rich stretch and sequences of the 5′ SINE1 were essential for the transcription of SINE1. RNA extracts from gene-silenced cultures showed small amounts of short (∼140-nucleotide), single-stranded molecules with homology to SINE1 but no short interfering RNA. Chromatin immunoprecipitation analysis with an antibody against methylated K4 of histone H3 showed a demethylation of K4 at the domain of the
ap-a
gene, indicating transcriptional inactivation. These results suggest the involvement of SINE1 in triggering the gene silencing and the role of histone modification in its epigenetic maintenance.
Stress-Activated Protein Kinase Pathway Functions To Support Protein Synthesis and Translational Adaptation in Response to Environmental Stress in Fission Yeast
Authors: Dunand-Sauthier Isabelle , Walker Carol A. , Narasimhan Jana , Pearce Amanda K. , Wek Ronald C. , Humphrey Tim C. 
Published: November 2005

ABSTRACT

The stress-activated protein kinase (SAPK) pathway plays a central role in coordinating gene expression in response to diverse environmental stress stimuli. We examined the role of this pathway in the translational response to stress in
Schizosaccharomyces pombe
. Exposing wild-type cells to osmotic stress (KCl) resulted in a rapid but transient reduction in protein synthesis. Protein synthesis was further reduced in mutants disrupting the SAPK pathway, including the mitogen-activated protein kinase Wis1 or the mitogen-activated protein kinase Spc1/Sty1, suggesting a role for these stress response factors in this translational control. Further polysome analyses revealed a role for Spc1 in supporting translation initiation during osmotic stress, and additionally in facilitating translational adaptation. Exposure to oxidative stress (H
2
O
2
) resulted in a striking reduction in translation initiation in wild-type cells, which was further reduced in
spc1
−
cells. Reduced translation initiation correlated with phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α) in wild-type cells. Disruption of Wis1 or Spc1 kinase or the downstream bZip transcription factors Atf1 and Pap1 resulted in a marked increase in eIF2α phosphorylation which was dependent on the eIF2α kinases Hri2 and Gcn2. These findings suggest a role for the SAPK pathway in supporting translation initiation and facilitating adaptation to environmental stress in part through reducing eIF2α phosphorylation in fission yeast.
N-Terminal Arm of Mcm1 Is Required for Transcription of a Subset of Genes Involved in Maintenance of the Cell Wall
Authors: Abraham Deepu S. , Vershon Andrew K. 
Published: November 2005

ABSTRACT

The yeast Mcm1 protein is a member of the MADS box family of transcription factors that interacts with several cofactors to differentially regulate genes involved in cell-type determination, mating, cell cycle control and arginine metabolism. Residues 18 to 96 of the protein, which form the core DNA-binding domain of Mcm1, are sufficient to carry out many Mcm1-dependent functions. However, deletion of residues 2 to 17, which form the nonessential N-terminal (NT) arm, confers a salt-sensitive phenotype, suggesting that the NT arm is required for the activation of salt response genes. We used a strategy that combined information from the mutational analysis of the Mcm1-binding site with microarray expression data under salt stress conditions to identify a new subset of Mcm1-regulated genes. Northern blot analysis showed that the transcript levels of several genes encoding associated with the cell wall, especially
YGP1
, decrease significantly upon deletion of the Mcm1 NT arm. Deletion of the Mcm1 NT arm results in a calcofluor white-sensitive phenotype, which is often associated with defects in transcription of cell wall genes. In addition, the deletion makes cells sensitive to CaCl
2
and alkaline pH. We found that the defect caused by removal of the NT arm is not due to changes in Mcm1 protein level, stability, DNA-binding affinity, or DNA bending. This suggests that residues 2 to 17 of Mcm1 may be involved in recruiting a cofactor to the promoters of these genes to activate transcription.
Activation of AP-1-Dependent Transcription by a Truncated Translation Initiation Factor
Authors: Jenkins Caroline C. L. , Mata Juan , Crane Richard F. , Thomas Benjamin , Akoulitchev Alexandre , Bähler Jürg , Norbury Chris J. 
Published: November 2005

ABSTRACT

Int6/eIF3e is a highly conserved subunit of eukaryotic translation initiation factor 3 (eIF3) that has also been reported to interact with subunits of the proteasome and the COP9 signalosome. Overexpression of full-length Int6 or a 13-kDa C-terminal fragment, Int6CT, in the fission yeast
Schizosaccharomyces pombe
causes multidrug resistance that requires the otherwise inessential AP-1 transcription factor Pap1. Here we show for the first time that Int6CT acts to increase the transcriptional activity of Pap1. Microarray hybridization data indicate that Int6CT overexpression resulted in the up-regulation of 67 genes; this expression profile closely matched that of cells overexpressing Pap1. Analysis of the upstream regulatory sequences of these genes showed that the majority contained AP-1 consensus binding sites. Partial defects in ubiquitin-dependent proteolysis have been suggested to confer Pap1-dependent multidrug resistance, but no such defect was seen on Int6CT overexpression. Indeed, none of the previously identified interactions of endogenous Int6 was required for the activation of Pap1 transcription described here. Moreover, Int6CT-induced activation of Pap1-responsive gene expression was independent of the ability of Pap1 to undergo a redox-regulated conformational change which mediates its relocalization to the nucleus and expression of oxidative stress response genes. Int6CT therefore activates Pap1-dependent transcription by a novel mechanism.
Pho5p and Newly Identified Nucleotide Pyrophosphatases/ Phosphodiesterases Regulate Extracellular Nucleotide Phosphate Metabolism inSaccharomyces cerevisiae
Authors: Kennedy Eileen J. , Pillus Lorraine , Ghosh Gourisankar 
Published: November 2005

ABSTRACTExtracellular nucleotides play many biological roles, including intercellular communication and modulation of nucleotide receptor signaling, and are dependent on the phosphorylation state of the nucleotide. Regulation of nucleotide phosphorylation is necessary, and a specialized class of enzymes, nucleotide pyrophosphatases/phosphodiesterases (E-NPPs), has been identified in mammals to perform this function. Although the E-NPP class is conserved among complex eukaryotes, this system has not yet been identified inSaccharomyces cerevisiae.Using genetic and biochemical experiments, we show that two orthologs of the E-NPP family, referred to as Npp1p and Npp2p, exist in budding yeast and can perform nucleotide phosphate hydrolysis. This activity is enhanced during phosphate starvation, where hydrolyzed phosphates can be imported from extracellular sources and utilized to overcome phosphate starvation through the activity of the Pho5p acid phosphatase. The added compensatory effect by Pho5p is also a newly established role for Pho5p. This study demonstrates that extracellular nucleotide phosphate metabolism appears to be controlled by at least two independent regulatory mechanisms, uniting phosphate starvation with extracellular nucleotide regulation.
snRNA and Heterochromatin Formation Are Involved in DNA Excision during Macronuclear Development in Stichotrichous Ciliates
Authors: Juranek Stefan A. , Rupprecht Sina , Postberg Jan , Lipps Hans J. 
Published: November 2005

ABSTRACT

Several models for specific excision of micronucleus-specific DNA sequences during macronuclear development in ciliates exist. While the template-guided recombination model suggests recombination events resulting in specific DNA excision and reordering of macronucleus-destined sequences (MDS) guided by a template, there is evidence that an RNA interference-related mechanism is involved in DNA elimination in holotrichous ciliates. We describe that in the stichotrichous ciliate
Stylonychia
, snRNAs homologous to micronucleus-specific sequences are synthesized during macronuclear differentiation. Western and in situ analyses demonstrate that histone H3 becomes methylated at K9 de novo during macronuclear differentiation, and chromatin immunoprecipitation revealed that micronucleus-specific sequences are associated with methylated H3. To link both observations, expression of a PIWI homolog, member of the RNA-induced silencing complex, was silenced. In these cells, the methylated micronucleus-specific histone H3 variant “X” is still present in macronuclear anlagen and no K9 methylation of histone H3 is observed. We suggest that snRNA recruits chromatin-modifying enzymes to sequences to be excised. Based on our and earlier observations, we believe that this mechanism is not sufficient for specific excision of sequences and reordering of MDS in the developing macronucleus and propose a model for internal eliminated sequence excision and MDS reordering in stichotrichous ciliates.
The
NIT1
Promoter Allows Inducible and Reversible Silencing of Centrin in
Chlamydomonas reinhardtii
Authors: Koblenz Bettina , Lechtreck Karl-Ferdinand 
Published: November 2005

ABSTRACT

An inverted repeat corresponding to parts of the centrin gene of
Chlamydomonas reinhardtii
was placed downstream of the
NIT1
promoter, which is induced by ammonium starvation. After induction, transformants developed centrin deficiency as assayed by immunofluorescence, Western blotting, and Northern blotting. The effect was reversible, demonstrating that the
NIT1
promoter allowed controlled RNA interference in
Chlamydomonas reinhardtii
.
Report on the 9th ACM symposium on access control models and technologies (SACMAT'04)
Authors: Ferrari Elena 
Published: November 2005

SACMAT'04 was held on June 2--4, 2004, at Yorktown Heights, New York, USA and was hosted by IBM T.J. Watson Research Center. The symposium, which was colocated with the IEEE International Workshop on Policies for Distributed Systems and Networks (POLICY 2004), continues its tradition of being the premier forum for presentation of research results and experience reports on leading edge issues of access control and related technologies, including models, systems, applications, and theory. SACMAT gives researchers and practitioners a unique opportunity to share their perspectives with others interested in the various aspects of access control.
The call for papers attracted 65 submissions, from all over the world. The program committee selected 18 papers for presentation. The 18 papers, organized in seven sessions, were presented over two and an half days. The selected papers cover a wide range of topics, ranging from next generation access control models, to security analysis, role administration, policy specification and implementation, and access control for distributed environments and XML data. All the accepted papers were included in a volume published by ACM, whereas best papers from the symposium have been invited for possible publication in ACM Transactions on Information and System Security (TISSEC). Besides the technical sessions, this year program included a keynote speech on Access Control for Databases, and a panel on Security for Grid-based Computing Systems.
The term retrieval abstract machine
Authors: Ley Michael 
Published: November 2005

Scans through large collections of complex objects often cannot be avoided. Even if sohphisticated indexing mechanisms are provided, it may be necessary to evaluate simple predicates against data stored on disk for filtering. For traditional record oriented data models i/o and buffer management are the main bottlenecks for this operation, the interpretation of data structures is straightforward and usually not an important cost factor. For heterogeneously shaped complex objects it may become a dominant cost factor.
In this paper we demonstrate a technique to make data structure traversal inside of complex objects much cheaper than naive interpretation. We compile navigation necessary to evaluate condition predicates and physical schema information into a program to be executed by a specialized abstract machine. Our approach is demonstrated for the Feature Term Data Model (FTDM), but the technique is applicable to many other complex data models. Main parts of this paper are dedicated to the method we used to design the Term Retrieval Abstract Machine (TRAM) architecture by partial evaluation of a tuned interpreter.
Parallel R-trees
Authors: Kamel Ibrahim , Faloutsos Christos 
Published: November 2005

We consider the problem of exploiting parallelism to accelerate the performance of spacial access methods and specifically, R-trees [11]. Our goal is to design a server for spatial data, so that to maximize the throughput of range queries. This can be achieved by (a) maximizing parallelism for large range queries, and (b) by engaging as few disks as possible on point queries [22].
We propose a simple hardware architecture consisting of one processor with several disks attached to it. On this architecture, we propose to distribute the nodes of a traditonal R-tree, with cross-disk pointers (“Multiplexed” R-tree). The R-tree code is identical to the one for a single-disk R-tree, with the only addition that we have to decide which disk a newly created R-tree node should be stored in. We propose and examine several criteria to choose a disk for a new node. The most successful one, termed “proximity index” or PI, estimates the similarity of the new node with the other R-tree nodes already on a disk, and chooses the disk with the lowest similarity. Experimental results show that our scheme consistently outperforms all the other heuristics for node-to-disk assignments, achieving up to 55% gains over the Round Robin one. Experiments also indicate that the multiplexed R-tree with PI heuristic gives better response time than the disk-stripping (=“Super-node”) approach, and imposes lighter load on the I/O sub-system.
The speed up of our method is close to linear speed up, increasing with the size of the queries.
Performance evaluation of ephemeral logging
Authors: Keen John S. , Dally William J. 
Published: November 2005

Ephemeral logging (EL) is a new technique for managing a log of database activity on disk. It does not require periodic checkpoints and does not abort lengthy transactions as frequently as traditional firewall logging for the same amount of disk space. Therefore, it is well suited for highly concurrent databases and applications which have a wide distribution of transaction lifetimes.
This paper briefly explains EL and then analyzes its performance. Simulation studies indicate that it can offer significant savings in disk space, at the expense of slightly higher bandwidth for logging and more main memory. The reduced size of the log implies much faster recovery after a crash as well as cost savings.
EL is the method of choice in some but not all situations. We assess the limitations of our current knowledge about EL and suggest promising directions for further research.
Combinatorial pattern discovery for scientific data
Authors: Wang Jason Tsong-Li , Chirn Gung-Wei , Marr Thomas G. , Shapiro Bruce , Shasha Dennis , Zhang Kaizhong 
Published: November 2005

Suppose you are given a set of natural entities (e.g., proteins, organisms, weather patterns, etc.) that possess some important common externally observable properties. You also have a structural description of the entities (e.g., sequence, topological, or geometrical data) and a distance metric. Combinatorial pattern discovery is the activity of finding patterns in the structural data that might explain these common properties based on the metric.
This paper presents an example of combinatorial pattern discovery: the discovery of patterns in protein databases. The structural representation we consider are strings and the distance metric is string edit distance permitting variable length don't cares. Our techniques incorporate string matching algorithms and novel heuristics for discovery and optimization, most of which generalize to other combinatorial structures. Experimental results of applying the techniques to both generated data and functionally related protein families obtained from the Cold Spring Harbor Laboratory show the effectiveness of the proposed techniques. When we apply the discovered patterns to perform protein classification, they give information that is complementary to the best protein classifier available today.
From structured documents to novel query facilities
Authors: Christophides V. , Abiteboul S. , Cluet S. , Scholl M. 
Published: November 2005

Structured documents (e.g., SGML) can benefit a lot from database support and more specifically from object-oriented database (OODB) management systems. This paper describes a natural mapping from SGML documents into OODB's and a formal extension of two OODB query languages (one SQL-like and the other calculus) in order to deal with SGML document retrieval.
Although motivated by structured documents, the extensions of query languages that we present are general and useful for a variety of other OODB applications. A key element is the introduction of paths as first class citizens. The new features allow to query data (and to some extent schema) without exact knowledge of the schema in a simple and homogeneous fashion.