bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation of cell membrane dynamics and cell motility
Authors: Veronika Merlin , Welsch Roy , Ng Alvin , Matsudaira Paul , Rajapakse Jagath C 
Published: December 2011

Abstract

Background
Essential events of cell development and homeostasis are revealed by the associated changes of cell morphology and therefore have been widely used as a key indicator of physiological states and molecular pathways affecting various cellular functions via cytoskeleton. Cell motility is a complex phenomenon primarily driven by the actin network, which plays an important role in shaping the morphology of the cells. Most of the morphology based features are approximated from cell periphery but its dynamics have received none to scant attention. We aim to bridge the gap between membrane dynamics and cell states from the perspective of whole cell movement by identifying cell edge patterns and its correlation with cell dynamics.

Results
We present a systematic study to extract, classify, and compare cell dynamics in terms of cell motility and edge activity. Cell motility features extracted by fitting a persistent random walk were used to identify the initial set of cell subpopulations. We propose algorithms to extract edge features along the entire cell periphery such as protrusion and retraction velocity. These constitute a unique set of multivariate time-lapse edge features that are then used to profile subclasses of cell dynamics by unsupervised clustering.

Conclusions
By comparing membrane dynamic patterns exhibited by each subclass of cells, correlated trends of edge and cell movements were identified. Our findings are consistent with published literature and we also identified that motility patterns are influenced by edge features from initial time points compared to later sampling intervals.
Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression
Authors: Lee Sheng-An , Tsao Theresa Tsun-Hui , Yang Ko-Chun , Lin Han , Kuo Yu-Lun , Hsu Chien-Hsiang , Lee Wen-Kuei , Huang Kuo-Chuan , Kao Cheng-Yan 
Published: December 2011

Abstract

Background
Schizophrenia, bipolar disorder, and major depression are devastating mental diseases, each with distinctive yet overlapping epidemiologic characteristics. Microarray and proteomics data have revealed genes which expressed abnormally in patients. Several single nucleotide polymorphisms (SNPs) and mutations are associated with one or more of the three diseases. Nevertheless, there are few studies on the interactions among the disease-associated genes and proteins.

Results
This study, for the first time, incorporated microarray and protein-protein interaction (PPI) databases to construct the PPI network of abnormally expressed genes in postmortem brain samples of schizophrenia, bipolar disorder, and major depression patients. The samples were collected from Brodmann area (BA) 10 of the prefrontal cortex. Abnormally expressed disease genes were selected by t-tests comparing the disease and control samples. These genes were involved in housekeeping functions (e.g. translation, transcription, energy conversion, and metabolism), in brain specific functions (e.g. signal transduction, neuron cell differentiation, and cytoskeleton), or in stress responses (e.g. heat shocks and biotic stress).
The diseases were interconnected through several “switchboard”-like nodes in the PPI network or shared abnormally expressed genes. A “core” functional module which consisted of a tightly knitted sub-network of clique-5 and -4s was also observed. These cliques were formed by 12 genes highly expressed in both disease and control samples.

Conclusions
Several previously unidentified disease marker genes and drug targets, such as SBNO2 (schizophrenia), SEC24C (bipolar disorder), and SRRT (major depression), were identified based on statistical and topological analyses of the PPI network. The shared or interconnecting marker genes may explain the shared symptoms of the studied diseases. Furthermore, the “switchboard” genes, such as APP, UBC, and YWHAZ, are proposed as potential targets for developing new treatments due to their functional and topological significance.
Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes
Authors: Zhang Anding , Yang Ming , Hu Pan , Wu Jiayan , Chen Bo , Hua Yafeng , Yu Jun , Chen Huanchun , Xiao Jingfa , Jin Meilin 
Published: December 2011

AbstractBackgroundStreptococcus suis(S. suis) is a major swine pathogen and an emerging zoonotic agent. Serotypes 1, 2, 3, 7, 9, 14 and 1/2 are the most prevalent serotypes of this pathogen. However, almost all studies were carried out on serotype 2 strains. Therefore, characterization of genomic features of other serotypes will be required to better understand their virulence potential and phylogenetic relationships among different serotypes.ResultsFour ChineseS. suisstrains belonging to serotypes 1, 7, 9 and 1/2 were sequenced using a rapid, high-throughput approach. Based on the 13 corresponding serotype strains, including 9 previously completed genomes of this bacterium, a full comparative genomic analysis was performed. The results provide evidence that (i) the pan-genome of this species is open and the size increases with addition of new sequenced genomes, (ii) strains of serotypes 1, 3, 7 and 9 are phylogenetically distinct from serotype 2 strains, but all serotype 2 strains, plus the serotype 1/2 and 14 strains, are very closely related. (iii) all these strains, except for the serotype 1 strain, could harbor a recombinant site for a pathogenic island (89 K) mediated by conjugal transfer, and may have the ability to gain the 89 K sequence.ConclusionsThere is significant genomic diversity among different strains inS. suis, and the gain and loss of large amount of genes are involved in shaping their genomes. This is indicated by (i) pairwise gene content comparisons between every pair of these strains, (ii) the open pan-genome of this species, (iii) the observed indels, invertions and rearrangements in the collinearity analysis. Phylogenetic relationships may be associated with serotype, as serotype 2 strains are closely related and distinct from other serotypes like 1, 3, 7 and 9, but more strains need to be sequenced to confirm this.
i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets
Authors: Mohammed Monzoorul Haque , Ghosh Tarini Shankar , Chadaram Sudha , Mande Sharmila S 
Published: December 2011

Abstract

Background
Obtaining accurate estimates of microbial diversity using rDNA profiling is the first step in most metagenomics projects. Consequently, most metagenomic projects spend considerable amounts of time, money and manpower for experimentally cloning, amplifying and sequencing the rDNA content in a metagenomic sample. In the second step, the entire genomic content of the metagenome is extracted, sequenced and analyzed. Since DNA sequences obtained in this second step also contain rDNA fragments, rapid in silico identification of these rDNA fragments would drastically reduce the cost, time and effort of current metagenomic projects by entirely bypassing the experimental steps of primer based rDNA amplification, cloning and sequencing. In this study, we present an algorithm called i-rDNA that can facilitate the rapid detection of 16S rDNA fragments from amongst millions of sequences in metagenomic data sets with high detection sensitivity.

Results
Performance evaluation with data sets/database variants simulating typical metagenomic scenarios indicates the significantly high detection sensitivity of i-rDNA. Moreover, i-rDNA can process a million sequences in less than an hour on a simple desktop with modest hardware specifications.

Conclusions
In addition to the speed of execution, high sensitivity and low false positive rate, the utility of the algorithmic approach discussed in this paper is immense given that it would help in bypassing the entire experimental step of primer-based rDNA amplification, cloning and sequencing. Application of this algorithmic approach would thus drastically reduce the cost, time and human efforts invested in all metagenomic projects.

Availability
A web-server for the i-rDNA algorithm is available at http://metagenomics.atc.tcs.com/i-rDNA/
Kannan-type contractions and fixed points in uniform spaces
Authors: Włodarczyk Kazimierz , Plebaniak Robert 
Published: December 2011

AbstractIn uniform spaces, usingJ-families of generalized pseudodistances, we construct four kinds of contractions of Kannan type and, by techniques based on these generalized pseudodistances, we prove fixed point theorems for such contractions. The results are new in uniform and locally convex spaces and even in metric spaces. Examples are given.MSC:47H10; 47H09; 54E15; 46A03; 54E35.
Anti-tumor activity and toxicokinetics analysis of MGAH22, an anti-HER2 monoclonal antibody with enhanced Fcγ receptor binding properties
Authors: Nordstrom Jeffrey L , Gorlatov Sergey , Zhang Wenjun , Yang Yinhua , Huang Ling , Burke Steve , Li Hua , Ciccarone Valentina , Zhang Tengfei , Stavenhagen Jeffrey , Koenig Scott , Stewart Stanford J , Moore Paul A , Johnson Syd , Bonvini Ezio 
Published: December 2011

Abstract
Introduction
Response to trastuzumab in metastatic breast cancer correlates with expression of the high binding variant (158V) of the activating Fcγ receptor IIIA (CD16A). We engineered MGAH22, a chimeric anti-HER2 monoclonal antibody with specificity and affinity similar to trastuzumab, with an Fc domain engineered for increased binding to both alleles of human CD16A.

Methods
MGAH22 was compared to an identical anti-HER2 mAb except for a wild type Fc domain. Antibody-dependent cell cytotoxicity (ADCC) assays were performed with HER2-expressing cancer cells as targets and human PBMC or purified NK cells as effectors. Xenograft studies were conducted in mice with wild type murine FcγRs; in mice lacking murine CD16; or in mice lacking murine CD16 but transgenic for human CD16A-158F, the low-binding variant. The latter model reproduces the differential binding between wild type and the Fc-optimized mAb for human CD16A. The JIMT-1 human breast tumor line, derived from a patient that progressed on trastuzumab therapy, was used in these studies. Single and repeat dose toxicology studies with MGAH22 administered intravenously at high dose were conducted in cynomolgus monkeys.

Results
The optimized Fc domain confers enhanced ADCC against all HER2-positive tumor cells tested, including cells resistant to trastuzumab's anti-proliferative activity or expressing low HER2 levels. The greatest improvement occurs with effector cells isolated from donors homozygous or heterozygous for CD16A-158F, the low-binding allele. MGAH22 demonstrates increased activity against HER2-expressing tumors in mice transgenic for human CD16A-158F. In single and repeat-dose toxicology studies in cynomolgus monkeys, a species with a HER2 expression pattern comparable to that in humans and Fcγ receptors that exhibit enhanced binding to the optimized Fc domain, MGAH22 was well tolerated at all doses tested (15-150 mg/kg) and exhibited pharmacokinetic parameters similar to that of other anti-HER2 antibodies. Induction of cytokine release by MGAH22 in vivo or in vitro was similar to that induced by the corresponding wild type mAb or trastuzumab.

Conclusions
The data support the clinical development of MGAH22, which may have utility in patients with low HER2 expressing tumors or carrying the CD16A low-binding allele.
Oxidative stress-related enzyme gene polymorphisms and susceptibility to breast cancer in non-smoking, non-alcohol-consuming Taiwanese women: a case-control study
Authors: Tsai Shih-Meng , Wu Szu-Hsien , Hou Ming-Feng , Chen Yueh-Ling , Ma Hsu , Tsai Li-Yu 
Published: December 2011

Background Mitochondrial manganese superoxide dismutase (MnSOD) converts superoxide anion into H2O2, which is neutralized sequentially by either catalase (CAT) or glutathione peroxidase 1 (Gpx 1) into water or converted into highly reactive hypochlorous acid by myeloperoxidase (MPO). We hypothesize that gene variants for these enzymes might be associated with the risk of breast cancer in non-smoking, non-alcohol-consuming women. Methods Genotypes of oxidative stress-related enzymes ( MnSOD1183T>C, MPO-463G>A, GPx1Pro198Leu and CAT-262C>T) were analysed in 260 non-smoking and non-alcohol-consuming female patients with breast cancer and 224 habit-matched controls. Results Subjects with the MnSOD1183T>C C carrier or those with the GPx1Pro198Leu CT genotype had significantly decreased age-adjusted risks (odds ratio [OR]: 0.56 and 0.16 with 95% confidence intervals [95% CI]: 0.38–0.83 and 0.08–0.29, respectively) for breast cancer. Certain combined genotypes of the polymorphisms also significantly modulated the age-adjusted risk. Conclusions We conclude that oxidative stress-related enzyme genetic variants, especially GPx1Pro198Leu CT, modify the risk of breast cancer development in non-smoking and non-alcohol-consuming women. The role of unidentified environmental factors predisposing to breast cancer development through an oxidative stress mechanism merits further investigation.
Characterization of Adhesive Joints for Hybrid Steel-Glass Beams by Means of Simplified Small Scale Tests
Authors: Feldmann M. , Abeln B. , Preckwinkel E. 
Published: December 2011

Abstract
In the recent past there have been calls for transparent and filigree structures in the building industry. Therefore, glass plays an increasing role not only in a classic way, as a space enclosing element, but also more and more in terms of offering load carrying functions. Glass beams for façade elements or floor girders, glass columns, or bracing façade elements are examples of this. To realize such architecturally attractive structures, bonded hybrid steel-glass elements have been developed in which each material is used in an optimized way according to its material properties. Promising examples for such bonded structures are I-beams in which steel flanges and glass webs are connected by linear adhesive bonds. The shear force is carried by the glass web, whereas the bending capacity of the hybrid beam is significantly increased by slender steel flanges compared to the pure glass pane. The shear forces between steel and glass are sustained only by the adhesive between them. In order to maximize the exploitation of both steel and glass, the adhesive on the one hand has to ensure an adequate stiffness but on the other hand has to be flexible enough to allow for a reduction or redistribution of local stress peaks, as well as other constraints such as thermal dilatation. However, the load-bearing capacity of such beams is governed, besides by the mechanical and geometrical characteristics of the adhesive joint, by aging, temperature, and creeping. In this contribution, an approach is shown for characterizing the adhesive joints for hybrid steel-glass beams by means of simplified small-scale tests. Standardized specimens (block shear and tension bulk specimens) and small-scale push-out tests are used to derive adequate mechanical values for analytical and numerical calculations, allowing one to draw conclusions regarding the general load carrying behavior of large-scale hybrid steel-glass beams. The results show that full-scale hybrid steel-glass beams, especially those with butt splice bonded and U-bonded geometries, are feasible using new structural adhesives, predominantly elasto-plastics such as polyurethanes or epoxy resins.
Algorithm Engineering Challenges in Multicore and Manycore Systems
Authors: Kang Seunghwa , Ediger David , Bader David A. 
Published: December 2011

Abstract
Modern multicore and manycore systems have the strong potential to deliver both high performance and high power efficiency. The large variance in memory access latency, resource sharing, and the heterogeneity of processor architectures in modern multicore and manycore systems raise significant algorithm engineering challenges. In this article, we overview important algorithm engineering issues for modern multicore and manycore systems, and we present algorithm engineering techniques to address such problems as a guideline for practitioners.
Internationale Zertifizierung der industriellen Prozessmesstechnik
Authors: Klotz-Engmann Gerold , Klausmeyer Uwe 
Published: December 2011

Zusammenfassung
Sensoren der industriellen Prozessmesstechnik werden in verschiedensten Branchen und globalen Märkten eingesetzt. Daraus entstehen weitreichende Anforderungen an Produktzertifizierungen. Grundsätzlich muss jedes Messgerät, das in den Europäischen Mitgliedsländern in Verkehr gebracht wird, den zutreffenden Europäischen Richtlinien entsprechen. Der Hersteller bestätigt die Einhaltung aller Anforderungen mit der Ausstellung einer EG-Konformitätserklärung und der CE-Kennzeichnung des Geräts. Voraussetzung ist bei einigen Richtlinien die Produktzertifizierung durch eine “benannte Stelle”. Werden Geräte international vermarktet, dann müssen sehr viele länderspezifische Zertifizierungen außerhalb Europas durchgeführt werden, z. B. in Nordamerika, Russland, China, Japan oder Australien. Mittlerweile werden diese Zertifizierungen teilweise durch internationale Zertifizierungssysteme harmonisiert.
Patterning of the Adult Mandibulate Mouthparts in the Red Flour Beetle, Tribolium castaneum
Authors: Angelini David R , Smith Frank W , Aspiras Ariel C , Kikuchi Moto , Jockusch Elizabeth L 
Published: December 2011

Abstract
Specialized insect mouthparts, such as those of Drosophila, are derived from an ancestral mandibulate state, but little is known about the developmental genetics of mandibulate mouthparts. Here, we study the metamorphic patterning of mandibulate mouthparts of the beetle Tribolium castaneum, using RNA interference to deplete the expression of 13 genes involved in mouthpart patterning. These data were used to test three hypotheses related to mouthpart development and evolution. First, we tested the prediction that maxillary and labial palps are patterned using conserved components of the leg-patterning network. This hypothesis was strongly supported: depletion of Distal-less and dachshund led to distal and intermediate deletions of these structures while depletion of homothorax led to homeotic transformation of the proximal maxilla and labium, joint formation required the action of Notch signaling components and odd-skipped paralogs, and distal growth and patterning required epidermal growth factor (EGF) signaling. Additionally, depletion of abrupt or pdm/nubbin caused fusions of palp segments. Second, we tested hypotheses for how adult endites, the inner branches of the maxillary and labial appendages, are formed at metamorphosis. Our data reveal that Distal-less, Notch signaling components, and odd-skipped paralogs, but not dachshund, are required for metamorphosis of the maxillary endites. Endite development thus requires components of the limb proximal–distal axis patterning and joint segmentation networks. Finally, adult mandible development is considered in light of the gnathobasic hypothesis. Interestingly, while EGF activity is required for distal, but not proximal, patterning of other appendages, it is required for normal metamorphic growth of the mandibles.
Characteristics of Black and White Suicide Decedents in Fulton County, Georgia, 1988–2002
Authors: Abe Karon , Mertz Kristen J. , Powell Kenneth E. , Hanzlick Randy L. 
Published: December 2011

Objectives. We compared the prevalence of risk factors for Black and White suicide decedents in Fulton County, Georgia, from 1988–2002.Methods. We used data from the Fulton County Medical Examiner’s Office to compile information on suicides that occurred in Fulton County between 1988 and 2002. We used the χ2test and logistic regression to identify associations between suicide risk factors and race.Results. Black suicide decedents were more likely than White suicide decedents to be male (odds ratio [OR]=2.06; 95% confidence interval [CI]=1.38, 3.09), to be younger, (≥24 y [OR = 4.74; 95% CI = 2.88, 7.81]; 25–34 y [OR = 2.79; 95% CI = 1.74, 4.47]; 35–44 y [OR = 1.86; 95% CI = 1.13, 3.07]), and to hurt others in a suicide (OR = 4.22; 95% CI = 1.60, 11.15) but less likely to report depression (OR=0.63; 95% CI=0.48, 0.83), to have a family history of suicide (OR=0.08; 95% CI=0.01, 0.61), or to leave a suicide note (OR=0.37; 95% CI=0.26, 0.52).Conclusions. Future research should consider that Black suicide decedents are less likely to report depression than White suicide decedents. This suicide risk difference is important when developing effective suicide prevention programs.
A “Health Commons” Approach to Oral Health for Low-Income Populations in a Rural State
Authors: Beetstra Stephen , Derksen Daniel , Ro Marguerite , Powell Wayne , Fry Donald E. , Kaufman Arthur 
Published: December 2011

Oral health needs are urgent in rural states. Creative, broad-based, and collaborative solutions can alleviate these needs. “Health commons” sites are enhanced, community-based, primary care safety net practices that include medical, behavioral, social, public, and oral health services. Successful intervention requires a comprehensive approach, including attention to enhancing dental service capacity, broadening the scope of the dental skills of locally available providers, expanding the pool of dental providers, creating new interdisciplinary teams in enhanced community-based sites, and developing more comprehensive oral health policy. By incorporating oral health services into the health commons primary care model, access for uninsured and underserved populations is increased. A coalition of motivated stakeholders includes community leaders, safety net providers, legislators, insurers, and medical, dental, and public health providers.
Innovations and Lifelong Learning in Sustainable Organization
Authors: Žnidaršič Jasmina , Jereb Eva 
Published: December 2011

Innovations and Lifelong Learning in Sustainable Organization
Innovation and knowledge are two of key factors for sustainable development of company or organization. Particularly in the current period of economic crisis it is crucial to promote lifelong learning and creativity to contribute innovative solutions to various problems. Lifelong learning makes a significant contribution to awareness of the importance of innovation and creativity for sustainable development of organization. In this paper we explore if respondents from Slovenian companies think that innovation and lifelong learning is important for sustainable development of company. Presented are the results of a survey conducted in 67 large and medium-sized enterprises in Slovenia where we upon respondents' judgment examine the correlation between the innovativeness level and lifelong learning, investing in innovativeness and competitive advantage and the promotion of lifelong learning and competitive advantage of the organization. Also the answers to the questions if lifelong learning contributes to the sustainable development of organization and if more the organization takes care of sustainable development the bigger is its competitive advantage before equal bidders are given.