bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perception of complex aggregates
Authors: Ramanarayanan Ganesh , Bala Kavita , Ferwerda James A. 
Published: August 2008

Aggregates of individual objects, such as forests, crowds, and piles of fruit, are a common source of complexity in computer graphics scenes. When viewing an aggregate, observers attend less to individual objects and focus more on overall properties such as numerosity, variety, and arrangement. Paradoxically, rendering and modeling costs increase with aggregate complexity, exactly when observers are attending less to individual objects.
In this paper we take some first steps to characterize the limits of visual coding of aggregates to efficiently represent their appearance in scenes. We describe psychophysical experiments that explore the roles played by the geometric and material properties of individual objects in observers' abilities to discriminate different aggregate collections. Based on these experiments we derive metrics to predict when two aggregates have the same appearance, even when composed of different objects. In a follow-up experiment we confirm that these metrics can be used to predict the appearance of a range of realistic aggregates. Finally, as a proof-of-concept we show how these new aggregate perception metrics can be applied to simplify scenes by allowing substitution of geometrically simpler aggregates for more complex ones without changing appearance.
Using prototypes in early pervasive game development
Authors: Ollila Elina M. I. , Suomela Riku , Holopainen Jussi 
Published: August 2008

In this article we discuss various prototyping methods in early pervasive game development. The focus is on pervasive games that are played with mobile phones. Choosing the right prototyping method is crucial in achieving results that can be used for validating or developing further design ideas. In this article we give guidelines that help the selection process and give ideas on methods that can be used in different situations.
We have play-tested pervasive game prototypes using agile software prototype development methods, forum prototypes, and guided paper prototyping methods. We give examples of five pervasive games where these kinds of prototyping methods are used. In concluding, we compare the results and discuss their benefits and disadvantages in the game development process, that is, when the methods should be used and what should be considered when using them.
Types for atomicity
Authors: Flanagan Cormac , Freund Stephen N. , Lifshin Marina , Qadeer Shaz 
Published: August 2008

Atomicity is a fundamental correctness property in multithreaded programs. A method is atomic if, for every execution, there is an equivalent serial execution in which the actions of the method are not interleaved with actions of other threads. Atomic methods are amenable to sequential reasoning, which significantly facilitates subsequent analysis and verification.
This article presents a type system for specifying and verifying the atomicity of methods in multithreaded Java programs using a synthesis of Lipton's theory of reduction and type systems for race detection. The type system supports guarded, write-guarded, and unguarded fields, as well as thread-local data, parameterized classes and methods, and protected locks. We also present an algorithm for verifying atomicity via type inference.
We have applied our type checker and type inference tools to a number of commonly used Java library classes and programs. These tools were able to verify the vast majority of methods in these benchmarks as atomic, indicating that atomicity is a widespread methodology for multithreaded programming. In addition, reported atomicity violations revealed some subtle errors in the synchronization disciplines of these programs.
Noncoherence of a Causal Wiener Algebra Used in Control Theory
Authors: Sasane Amol 
Published: August 2008

Let ℂ≥0 : = {s ∈ ℂ | Re (s) ≥ 0}, and let 𝒲+ denote the ring of all functions
f : ℂ≥0→ℂ
such that  (s ∈ ℂ≥0), where , and
0 = t0 < t1 < t2 < ⋯ equipped with pointwise operations. (Here denotes the Laplace transform.) It is shown that the ring 𝒲+ is not coherent, answering a question of Alban Quadrat. In fact, we present two principal ideals in the domain 𝒲+ whose intersection is not finitely generated.
Evaluation of genomic island predictors using a comparative genomics approach
Authors: Langille Morgan GI , Hsiao William WL , Brinkman Fiona SL 
Published: August 2008

Abstract

Background
Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest. Recently, multiple programs for automated detection of GIs have been developed that utilize sequence composition characteristics, such as G+C ratio and dinucleotide bias. To robustly evaluate the accuracy of such methods, we propose that a dataset of GIs be constructed using criteria that are independent of sequence composition-based analysis approaches.

Results
We developed a comparative genomics approach (IslandPick) that identifies both very probable islands and non-island regions. The approach involves 1) flexible, automated selection of comparative genomes for each query genome, using a distance function that picks appropriate genomes for identification of GIs, 2) identification of regions unique to the query genome, compared with the chosen genomes (positive dataset) and 3) identification of regions conserved across all genomes (negative dataset). Using our constructed datasets, we investigated the accuracy of several sequence composition-based GI prediction tools.

Conclusion
Our results indicate that AlienHunter has the highest recall, but the lowest measured precision, while SIGI-HMM is the most precise method. SIGI-HMM and IslandPath/DIMOB have comparable overall highest accuracy. Our comparative genomics approach, IslandPick, was the most accurate, compared with a curated list of GIs, indicating that we have constructed suitable datasets. This represents the first evaluation, using diverse and, independent datasets that were not artificially constructed, of the accuracy of several sequence composition-based GI predictors. The caveats associated with this analysis and proposals for optimal island prediction are discussed.
Can modeling of HIV treatment processes improve outcomes? Capitalizing on an operations research approach to the global pandemic
Authors: Xiong Wei , Hupert Nathaniel , Hollingsworth Eric B , O'Brien Megan E , Fast Jessica , Rodriguez William R 
Published: August 2008

Abstract

Background
Mathematical modeling has been applied to a range of policy-level decisions on resource allocation for HIV care and treatment. We describe the application of classic operations research (OR) techniques to address logistical and resource management challenges in HIV treatment scale-up activities in resource-limited countries.

Methods
We review and categorize several of the major logistical and operational problems encountered over the last decade in the global scale-up of HIV care and antiretroviral treatment for people with AIDS. While there are unique features of HIV care and treatment that pose significant challenges to effective modeling and service improvement, we identify several analogous OR-based solutions that have been developed in the service, industrial, and health sectors.

Results
HIV treatment scale-up includes many processes that are amenable to mathematical and simulation modeling, including forecasting future demand for services; locating and sizing facilities for maximal efficiency; and determining optimal staffing levels at clinical centers. Optimization of clinical and logistical processes through modeling may improve outcomes, but successful OR-based interventions will require contextualization of response strategies, including appreciation of both existing health care systems and limitations in local health workforces.

Conclusion
The modeling techniques developed in the engineering field of operations research have wide potential application to the variety of logistical problems encountered in HIV treatment scale-up in resource-limited settings. Increasing the number of cross-disciplinary collaborations between engineering and public health will help speed the appropriate development and application of these tools.
First detection, isolation and molecular characterization of infectious salmon anaemia virus associated with clinical disease in farmed Atlantic salmon (Salmo salar) in Chile
Authors: Godoy Marcos G , Aedo Alejandra , Kibenge Molly JT , Groman David B , Yason Carmencita V , Grothusen Horts , Lisperguer Angelica , Calbucura Marlene , Avendaño Fernando , Imilán Marcelo , Jarpa Miguel , Kibenge Frederick SB 
Published: August 2008

Abstract

Background
Infectious salmon anaemia (ISA) is a viral disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), which belongs to the genus Isavirus, family Orthomyxoviridae. The virus is considered to be carried by marine wild fish and for over 25 years has caused major disease outbreaks in marine-farmed Atlantic salmon in the Northern hemisphere. In the Southern hemisphere, ISAV was first detected in Chile in 1999 in marine-farmed Coho salmon (Oncorhynchus kisutch). In contrast to the classical presentation of ISA in Atlantic salmon, the presence of ISAV in Chile until now has only been associated with a clinical condition called Icterus Syndrome in Coho salmon and virus isolation has not always been possible. During the winter of 2007, unexplained mortalities were registered in market-size Atlantic salmon in a grow-out site located in Chiloé in Region X of Chile. We report here the diagnostic findings of the first significant clinical outbreak of ISA in marine-farmed Atlantic salmon in Chile and the first characterization of the ISAV isolated from the affected fish.

Results
In mid-June 2007, an Atlantic salmon marine farm site located in central Chiloé Island in Region X of Chile registered a sudden increase in mortality following recovery from an outbreak of Pisciricketsiosis, which rose to a cumulative mortality of 13.6% by harvest time. Based on the clinical signs and lesions in the affected fish, and laboratory tests performed on the fish tissues, a confirmatory diagnosis of ISA was made; the first time ISA in its classical presentation and for the first time affecting farmed Atlantic salmon in Chile. Rapid sequencing of the virus-specific RT-PCR products amplified from the fish tissues identified the virus to belong to the European genotype (Genotype I) of the highly polymorphic region (HPR) group HPR 7b, but with an 11-amino acid insert in the fusion glycoprotein, and ability to cause cytopathic effects (CPE) in CHSE-214 cell line, characteristics which make it distinct from common European Genotype ISAV isolates from Europe and North America.

Conclusion
In conclusion, the present work constitutes the first report of a case of ISA in farmed Atlantic salmon in Chile. The clinical signs and lesions are consistent with the classical descriptions of the disease in marine-farmed Atlantic salmon in the Northern hemisphere. The outbreak was caused by ISAV of European genotype (or Genotype I) of HPR 7b but distinct from common European Genotype ISAV isolates.
RNase footprinting demonstrates antigenomic hepatitis delta virus ribozyme structural rearrangement as a result of self-cleavage reaction
Authors: Savochkina Larissa , Alekseenkova Victoria , Belyanko Tatyana , Dobrynina Nadezhda , Beabealashvilli Robert 
Published: August 2008

Abstract

Background
Hepatitis delta virus (HDV) is a satellite virus of hepatitis B. During viral replication the 1700-nucleotide-long genomic RNA and its complement, the antigenomic RNA, undergo self-cleavage catalyzed by internal ribozyme motifs that are essential for propagation of the virus in vivo. These self-cleavage activities are provided by 85-nucleotide-long sequence elements, the genomic and antigenomic forms of HDV ribozyme. Recently four permuted variants of the antigenomic HDV cis-ribozyme with a self-cleavage site located at the 5' proximity, in the middle, or nearby the 3' end of the molecule were constructed and synthesized. These constructs exhibit equal activity, a bi-phasic kinetics of self-cleavage reaction and reaction products with low and high stability. We have used ribonuclease probing to footprint the structures of uncleaved and post-cleaved forms of the antigenomic HDV ribozymes in solution. Uncleaved ribozymes, associated and individual products of the self-cleavage reaction were analyzed using ribonuclease and Fe(II)-EDTA protection assays to reveal the differences in the structure of pre- and post-cleaved antigenomic HDV ribozyme in solution.

Findings
Our findings demonstrate that a significant conformational change accompanies catalysis in the antigenomic HDV ribozyme in solution, in contrast to minor conformational switch observed in crystals of the genomic form. This study indicates that changes in the structure of stem P1 and stem P4 are minor, those of the region ascribed to stem P2, stem P3 and loop l3 are dramatic, while stem P1.1 results from the self-cleavage reaction.

Conclusion
Our data agree with the structure of post-cleaved and disagree with that of pre-cleaved forms of HDV ribozyme published elsewhere.
Brain region-specificity of palmitic acid-induced abnormalities associated with Alzheimer's disease
Authors: Patil Sachin , Balu Deebika , Melrose Joseph , Chan Christina 
Published: August 2008

Abstract

Background
Alzheimer's disease (AD) is a progressive, neurodegenerative disease mostly affecting the basal forebrain, cortex and hippocampus whereas the cerebellum is relatively spared. The reason behind this region-specific brain damage in AD is not well understood. Here, we report our data suggesting "differential free fatty acid metabolism in the different brain areas" as a potentially important factor in causing the region-specific damage observed in AD brain.

Findings
The astroglia from two different rat brain regions, cortex (region affected in AD) and cerebellum (unaffected region), were treated with 0.2 mM of palmitic acid. The conditioned media were then transferred to the cortical neurons to study the possible effects on the two main, AD-associated protein abnormalities, viz. BACE1 upregulation and hyperphosphorylation of tau. The conditioned media from palmitic-acid treated cortical astroglia, but not the cerebellar astroglia, significantly elevated levels of phosphorylated tau and BACE1 in cortical neurons as compared to controls (47 ± 7% and 45 ± 4%, respectively).

Conclusion
The present data provide an experimental explanation for the region-specific damage observed in AD brain; higher fatty acid-metabolizing capacity of cortical astroglia as compared to cerebellar astroglia, may play a causal role in increasing vulnerability of cortex in AD, while sparing cerebellum.
Calculation of Splicing Potential from the Alternative Splicing Mutation Database
Authors: Bechtel Jason M , Rajesh Preeti , Ilikchyan Irina , Deng Ying , Mishra Pankaj K , Wang Qi , Wu Xiaochun , Afonin Kirill A , Grose William E , Wang Ye , Khuder Sadik , Fedorov Alexei 
Published: August 2008

Abstract

Background
The Alternative Splicing Mutation Database (ASMD) presents a collection of all known mutations inside human exons which affect splicing enhancers and silencers and cause changes in the alternative splicing pattern of the corresponding genes.

Findings
An algorithm was developed to derive a Splicing Potential (SP) table from the ASMD information. This table characterizes the influence of each oligonucleotide on the splicing effectiveness of the exon containing it. If the SP value for an oligonucleotide is positive, it promotes exon retention, while negative SP values mean the sequence favors exon skipping. The merit of the SP approach is the ability to separate splicing signals from a wide range of sequence motifs enriched in exonic sequences that are attributed to protein-coding properties and/or translation efficiency. Due to its direct derivation from observed splice site selection, SP has an advantage over other computational approaches for predicting alternative splicing.

Conclusion
We show that a vast majority of known exonic splicing enhancers have highly positive cumulative SP values, while known splicing silencers have core motifs with strongly negative cumulative SP values. Our approach allows for computation of the cumulative SP value of any sequence segment and, thus, gives researchers the ability to measure the possible contribution of any sequence to the pattern of splicing.
Whole genome amplification and its impact on CGH array profiles
Authors: Talseth-Palmer Bente A , Bowden Nikola A , Hill Alyssa , Meldrum Cliff , Scott Rodney J 
Published: August 2008

Abstract

Background
Some array comparative genomic hybridisation (array CGH) platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA) is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of starting material. A range of WGA methods are available and the multiple displacement amplification (MDA) approach has been shown to be highly accurate, although amplification bias has been reported. In the current study, WGA was used to amplify DNA extracted from whole blood. In total, six array CGH experiments were performed to investigate whether the use of whole genome amplified DNA (wgaDNA) produces reliable and reproducible results. Four experiments were conducted on amplified DNA compared to unamplified DNA and two experiments on unamplified DNA compared to unamplified DNA.

Findings
All the experiments involving wgaDNA resulted in a high proportion of losses and gains of genomic material. Previously, amplification bias has been overcome by using amplified DNA in both the test and reference DNA. Our data suggests that this approach may not be effective, as the gains and losses introduced by WGA appears to be random and are not reproducible between different experiments using the same DNA.

Conclusion
In light of these findings, the use of both amplified test and reference DNA on CGH arrays may not provide an accurate representation of copy number variation in the DNA.
Conservation of CD44 exon v3 functional elements in mammals
Authors: Vela Elena , Hilari Josep M , Delclaux María , Fernández-Bellon Hugo , Isamat Marcos 
Published: August 2008

Abstract

Background
The human CD44 gene contains 10 variable exons (v1 to v10) that can be alternatively spliced to generate hundreds of different CD44 protein isoforms. Human CD44 variable exon v3 inclusion in the final mRNA depends on a multisite bipartite splicing enhancer located within the exon itself, which we have recently described, and provides the protein domain responsible for growth factor binding to CD44.

Findings
We have analyzed the sequence of CD44v3 in 95 mammalian species to report high conservation levels for both its splicing regulatory elements (the 3' splice site and the exonic splicing enhancer), and the functional glycosaminglycan binding site coded by v3. We also report the functional expression of CD44v3 isoforms in peripheral blood cells of different mammalian taxa with both consensus and variant v3 sequences.

Conclusion
CD44v3 mammalian sequences maintain all functional splicing regulatory elements as well as the GAG binding site with the same relative positions and sequence identity previously described during alternative splicing of human CD44. The sequence within the GAG attachment site, which in turn contains the Y motif of the exonic splicing enhancer, is more conserved relative to the rest of exon. Amplification of CD44v3 sequence from mammalian species but not from birds, fish or reptiles, may lead to classify CD44v3 as an exclusive mammalian gene trait.
Dark Aberrant Crypt Foci with activated Wnt pathway are related to tumorigenesis in the colon of AOM-treated rat
Authors: Lu Qing , Jiang Bo , Lin Chen , Shan Tao 
Published: August 2008

Abstract

Background
To evaluate the relationship between Aberrant Crypt Foci (ACF) and tumorigenesis, we observed the sequential development from ACF to tumor in the colon of azoxymethane-exposed wistar rats.

Methods
Sixty wistar rats were sacrificed at different time points after exposure to azoxymethane and the colons were stained with methylene blue for stereomicroscopic analysis.

Results
We found two types of early lesions: classic ACF and dark ACF. Dark ACF were characterized by dark blue staining, mildly enlarged or small compressed crypts that are not elevated from the surrounding epithelium. Large dark ACF and nascent tumors displayed the same surface morphology. Furthermore, dark ACF grew significantly faster than classic ACF and showed dysplasia without hyperplasia. In contrast, classic ACF showed hyperplasia without dysplasia. Dark ACF has significant higher expression rate of β-catenin (100%) and MMP-7 (81.82%) compared with the expression of β-catenin and MMP-7 in classic ACF (4.84% and 7.87%, respectively).

Conclusion
Our data indicated that dark ACF is closely related to tumorigenesis while classic ACF is not. Furthermore, Wnt signal pathway was activated during the early period of dark ACF.
Combined milrinone and enteral metoprolol therapy in patients with septic myocardial depression
Authors: Schmittinger Christian A , Dünser Martin W , Haller Maria , Ulmer Hanno , Luckner Günter , Torgersen Christian , Jochberger Stefan , Hasibeder Walter R 
Published: August 2008

Abstract
Introduction
The multifactorial etiology of septic cardiomyopathy is not fully elucidated. Recently, high catecholamine levels have been suggested to contribute to impaired myocardial function.

Methods
This retrospective analysis summarizes our preliminary clinical experience with the combined use of milrinone and enteral metoprolol therapy in 40 patients with septic shock and cardiac depression. Patients with other causes of shock or cardiac failure, patients with beta-blocker therapy initiated more than 48 hours after shock onset, and patients with pre-existent decompensated congestive heart failure were excluded. In all study patients, beta blockers were initiated only after stabilization of cardiovascular function (17.7 ± 15.5 hours after shock onset or intensive care unit admission) in order to decrease the heart rate to less than 95 beats per minute (bpm). Hemodynamic data and laboratory parameters were extracted from medical charts and documented before and 6, 12, 24, 48, 72, and 96 hours after the first metoprolol dosage. Adverse cardiovascular events were documented. Descriptive statistical methods and a linear mixed-effects model were used for statistical analysis.

Results
Heart rate control (65 to 95 bpm) was achieved in 97.5% of patients (n = 39) within 12.2 ± 12.4 hours. Heart rate, central venous pressure, and norepinephrine, arginine vasopressin, and milrinone dosages decreased (all P < 0.001). Cardiac index and cardiac power index remained unchanged whereas stroke volume index increased (P = 0.002). In two patients (5%), metoprolol was discontinued because of asymptomatic bradycardia. Norepinephrine and milrinone dosages were increased in nine (22.5%) and six (15%) patients, respectively. pH increased (P < 0.001) whereas arterial lactate (P < 0.001), serum C-reactive protein (P = 0.001), and creatinine (P = 0.02) levels decreased during the observation period. Twenty-eight-day mortality was 33%.

Conclusion
Low doses of enteral metoprolol in combination with phosphodiesterase inhibitors are feasible in patients with septic shock and cardiac depression but no overt heart failure. Future prospective controlled trials on the use of beta blockers for septic cardiomyopathy and their influence on proinflammatory cytokines are warranted.