bluuebunny/crossref_metadata_2025_split huggingface dataset:
A role of Rab7 in stabilizing EGFR‐Her2 and in sustaining Akt survival signal
Authors: Wang Tuanlao , Zhang Ming , Ma Zexu , Guo Ke , Tergaonkar Vinay , Zeng Qi , Hong Wanjin 
Published: September 2011

AbstractRab7 plays an important role in regulating endocytic traffic. In view of an emerging role of membrane traffic in signaling and diseases, we have examined the possible role of Rab7 in oncogenesis. The role of Rab7 was investigated using shRNA‐mediated knockdown in A431 and MCF7 cancer cells. To our surprise, Rab7 knockdown effectively suppressed anchorage‐independent growth of cancer cells in soft agar. Anoikis (matrix‐detachment triggered apoptosis) was enhanced, while the level of phosphorylated (active) Akt (which is a key survival factor) was significantly reduced. Also intriguing was the observation that EGFR and Her2 levels were significantly reduced when Rab7 was knocked‐down. More robust reduction of EGFR and Her2 levels was observed when knocked‐down cells were treated with HSP90 inhibitor geldanamycin (GA). Low concentration of GA (50–100 nm)‐induced apoptosis of the Rab7 knocked‐down cells but not control cells, suggesting that Rab7 and HSP90 together contribute to the optimal stability of EGFR and Her2 as well as to protect cancer cells from apoptosis. Rab7 seems to protect EGFR and Her2 from proteosome‐mediated degradation. These results suggest that Rab7 is likely involved in protecting EGFR and Her2 from being degraded by the proteosome and in maintaining optimal Akt survival signal (especially during cell detachment or when HSP90 is inhibited). Rab7 is potentially a novel target for combinatory therapy with Hsp90 inhibitors. J. Cell. Physiol. 227: 2788–2797, 2012. © 2011 Wiley Periodicals, Inc.
Threaded behavior protocols
Authors: Poch Tomáš , Šerý Ondřej , Plášil František , Kofroň Jan 
Published: September 2011

Abstract
Component-based development is a well-established methodology of software development. Nevertheless, some of the benefits that the component based development offers are often neglected. One of them is modeling and subsequent analysis of component behavior, which can help establish correctness guarantees, such as absence of composition errors and safety of component updates. We believe that application of component behavior modeling in practice is limited due to huge differences between the behavior modeling languages (e.g., process algebras) and the common implementation languages (e.g., Java). As a result, many concepts of the implementation languages are either very different or completely missing in the behavior modeling languages. As an example, even though behavior modeling languages are practical for modeling and analysis of various message-based protocols, they are not well suited for modeling current component applications, where thread-based parallelism, lock-based synchronization, and nested method calls are the essential building blocks. With this in mind, we propose a new behavior modeling language for software components, Threaded Behavior Protocols (TBP). At the model level, TBP provides developers with the concepts known from the implementation languages and essential to most component applications. In addition, the theoretical framework of TBP provides a notion of correctness based on absence of communication errors and a refinement relation to verify correctness of hierarchical components. The main asset of TBP formalism is that it links together the notion of threads as used in imperative object oriented languages and the notion of refinement. For instance, this allows reasoning about hierarchical components composed of primitive components implemented in Java without the need of bridging abstractions and simplifications enforced by the modeling languages.
Study of the SN2 Substitution Reactions Between Methyl Naphtalene‐2‐Sulfonate and Methyl 4‐Nitrobenzene Sulfonate and Bromide Ions in Dodecyl Dibromide Dimeric Micellar Solutions in the Absence and Presence of Alcohols
Authors: del Mar Graciani María , Rodríguez Amalia , Martín Victoria Isabel , Moyá María Luisa 
Published: September 2011

AbstractThe SN2 substitution reactions between methyl naphthalene‐2‐sulfonate and methyl 4‐nitrobenzenesulfonate with bromide ions were studied in alkanediyl‐α,ω‐bis(dimethyldodecylammonium) bromide, 12‐s‐12,2Br− (s = 3, 4, 6), micellar solutions in the absence and in the presence of alcohols. The observed rate constant for the two processes was found to be sensitive to changes in micellar characteristics caused by the presence of alcohols. At high surfactant concentrations, kinetic data made evident the sphere‐to‐rod transition accompanying the increase in the dimeric surfactant concentration in all the micellar reaction media investigated. Kinetic results were quantitatively rationalized within the whole surfactant concentration range, below and above the second CMC, by using a new treatment based on the pseudophase kinetic model.
Developmental dysplasia of the hip: Impact of sonographic newborn hip screening on the outcome of early treated decentered hip joints—a single center retrospective comparative cohort study based on Graf's method of hip ultrasonography
Authors: Tschauner Christian , Fürntrath Frank , Saba Yasaman , Berghold Andrea , Radl Roman 
Published: September 2011

Purpose/Background/Introduction The aim of this study was to retrospectively evaluate the impact of neonatal sonographic hip screening using Graf's method for the management and outcome of orthopaedic treatment of decentered hip joints with developmental dysplasia of the hip (DDH), using three decades (1978–2007) of clinical information compiled in a medical database. Methods Three representative cohorts of consecutive cases of decentered hip joints were selected according to different search criteria and inclusion and exclusion parameters: (1) cohort 1 (1978–1982; n = 80), without sonographic screening; (2) cohort 2.1 (1994–1996; n = 91), with nationwide established general sonographic screening according to the Graf-method; (3) cohort 2.2 (2003–2005; n = 91), with sonographic screening including referred cases for open reduction from non-screened populations. These three cohorts were compared for the following parameters: age at initial treatment, successful closed reduction, necessary overhead traction, necessary adductor-tenotomy, rate of open reduction, rate of avascular necrosis (AVN) and rate of secondary acetabuloplasty. Results The age at initial treatment was reduced from 5.5 months in the first cohort to 2 months in the two subsequent two cohorts and the rate of successful closed reduction increased from 88.7 to 98.9 and 95.6%, respectively. There was a statistically significant improvement in six out of seven parameters with sonographic hip screening; only the rate of secondary acetabuloplasty did not improve significantly. Conclusion Compared to the era before the institution of a sonographic hip screening programme according to the Graf-method in Austria in 1992, ultrasound screening based-treatment of decentered hip joints has become safer, shorter and simpler: “safer” means lower rate of AVN, “shorter” means less treatment time due to earlier onset and “simpler” means that the devices are now less invasive and highly standardized.
The Mediatory Guile of the Nanny in Persian Romance
Authors: Milani Farzaneh 
Published: September 2011

The Word for Guile (Kayd) Itself Seems to be Shifty. Sometimes it is positive, sometimes negative, at times divine. It seems to assume its significance from its context. It becomes positive or negative according to the point of view of the one who uses it. It has a variety of meanings: Steingass's listing “deceiving, laying snares, entrapping, plotting mischief; applying a remedy, vomiting; being menstruous; the croak of a raven; war, warfare; deceit, fraud, stratagem; treachery, malignity, malice” illustrates its large semantic field. Kayd can also be a divine attribute. In the Qur˒anic chapter in which the Egyptian ruler admonishes his wife and utters the often repeated verse 29, “Indeed your guile is great,” verse 76 links kayd with God who “did devise a plan for Joseph.” “There are at least thirty-four uses of the Arabic root K.Y.D in the Qur˒an, and a number of them refer to God's action.”Some of the most admired heroes and heroines of Persian literature are guileful. Most writers, however, have formulated their paradigms of guile with women in mind. Kayd and its numerous synonyms, although not gendered words, are frequently “feminized.”
Simulations of combined neutral beam injection and ion cyclotron heating with the TORIC-SSFPQL package
Authors: Bilato R. , Brambilla M. , Maj O. , Horton L.D. , Maggi C.F. , Stober J. 
Published: September 2011

A source describing the injection of fast ions due to the ionization of high-energy neutral beams has been added to the surface-averaged quasilinear Fokker–Planck code SSFPQL (Brambilla 1994 Nucl. Fusion
34 1121). For this purpose, the multiple-beam NBI code SINBAD (Feng et al 1995 Comput. Phys. Commun.
88 161) has been included as a module in SSFPQL, with the modifications required to handle arbitrary axisymmetric equilibria. Alternatively, the neutral beam injection (NBI) source can be built using the output of a Monte Carlo NBI code. We have also added a term describing losses of fast ions during thermalization, and a subroutine evaluating the neutron production rate by nuclear reactions. With these extensions, iterations between SSFPQL and the full-wave solver TORIC (Brambilla 1999 Plasma Phys. Control. Fusion
41 1) can now be used to investigate the strong interplay between NBI and ion cyclotron (IC) heating.
By comparing the predicted and measured neutron production rates from D–D reactions in a discharge with combined NBI and IC heating in ASDEX Upgrade we obtain a plausible estimate of the importance of fast-ion losses (FILs), even if their cause cannot be identified. We find, however, that the plasma composition, in particular the presence of low Z impurities, plays a more critical role than FILs in limiting the efficiency of this heating scheme.
Bambus 2: scaffolding metagenomes
Authors: Koren Sergey , Treangen Todd J. , Pop Mihai 
Published: September 2011

Abstract
Motivation: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.
Results: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly.
Availability: Bambus 2 is open source and available from http://amos.sf.net.
Contact: mpop@umiacs.umd.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
An efficient network querying method based on conditional random fields
Authors: Huang Qiang , Wu Ling-Yun , Zhang Xiang-Sun 
Published: September 2011

Abstract
Motivation: A large amount of biomolecular network data for multiple species have been generated by high-throughput experimental techniques, including undirected and directed networks such as protein–protein interaction networks, gene regulatory networks and metabolic networks. There are many conserved functionally similar modules and pathways among multiple biomolecular networks in different species; therefore, it is important to analyze the similarity between the biomolecular networks. Network querying approaches aim at efficiently discovering the similar subnetworks among different species. However, many existing methods only partially solve this problem.
Results: In this article, a novel approach for network querying problem based on conditional random fields (CRFs) model is presented, which can handle both undirected and directed networks, acyclic and cyclic networks and any number of insertions/deletions. The CRF method is fast and can query pathways in a large network in seconds using a PC. To evaluate the CRF method, extensive computational experiments are conducted on the simulated and real data, and the results are compared with the existing network querying methods. All results show that the CRF method is very useful and efficient to find the conserved functionally similar modules and pathways in multiple biomolecular networks.
Availability: Code and data are available at http://doc.aporc.org/wiki/CNetQ
Contact: lywu@amt.ac.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Discovering relational-based association rules with multiple minimum supports on microarray datasets
Authors: Liu Yu-Cheng , Cheng Chun-Pei , Tseng Vincent S. 
Published: September 2011

Abstract
Motivation: Association rule analysis methods are important techniques applied to gene expression data for finding expression relationships between genes. However, previous methods implicitly assume that all genes have similar importance, or they ignore the individual importance of each gene. The relation intensity between any two items has never been taken into consideration. Therefore, we proposed a technique named REMMAR (RElational-based Multiple Minimum supports Association Rules) algorithm to tackle this problem. This method adjusts the minimum relation support (MRS) for each gene pair depending on the regulatory relation intensity to discover more important association rules with stronger biological meaning.
Results: In the actual case study of this research, REMMAR utilized the shortest distance between any two genes in the Saccharomyces cerevisiae gene regulatory network (GRN) as the relation intensity to discover the association rules from two S.cerevisiae gene expression datasets. Under experimental evaluation, REMMAR can generate more rules with stronger relation intensity, and filter out rules without biological meaning in the protein–protein interaction network (PPIN). Furthermore, the proposed method has a higher precision (100%) than the precision of reference Apriori method (87.5%) for the discovered rules use a literature survey. Therefore, the proposed REMMAR algorithm can discover stronger association rules in biological relationships dissimilated by traditional methods to assist biologists in complicated genetic exploration.
Availability: The source code in Java and other materials used in this study are available at http://websystem.csie.ncku.edu.tw/REMMAR_Program.rar
Contact: tsengsm@mail.ncku.edu.tw
Supplementary Information: Supplementary data are available at Bioinformatics online.
Influence of renal dysfunction phenotype on mortality in the setting of cardiac dysfunction: analysis of three randomized controlled trials
Authors: Testani Jeffrey M. , Coca Steven G. , Shannon Richard P. , Kimmel Stephen E. , Cappola Thomas P. 
Published: September 2011

AimsRenal neurohormonal activation leading to a reduction in glomerular filtration rate (GFR) has been suggested as a mechanism for renal insufficiency (RI) in the setting of heart failure. We hypothesized that RI occurring in the presence of renal neurohormonal activation may be prognostically more important than RI in the absence of renal neurohormonal activation.Methods and resultsSubjects in the Evaluation Study of Congestive Heart Failure and Pulmonary Artery Catheterization Effectiveness (ESCAPE) trial (n = 429), Beta‐Blocker Evaluation of Survival Trial (BEST) (n = 2691), and Studies Of Left Ventricular Dysfunction (SOLVD) trial (n = 6782) limited datasets were studied. The blood urea nitrogen to creatinine ratio (BUN/Creatinine) was employed as a surrogate for renal neurohormonal activation and the primary outcome was the interaction between BUN/Creatinine and RI associated mortality. Baseline RI (GFR < 60 mL/min/1.73 m²) was associated with mortality in all study populations (P < 0.001). In patients with higher BUN/Creatinine, the risk of mortality was consistently greater in patients with RI [adjusted hazard ratio (HR) ESCAPE = 2.8, 95% confidence interval (CI) 1.3–14.3, P = 0.019; BEST = 1.6, 95% CI 1.2–2.2, P = 0.002; SOLVD = 1.6, 95% CI 1.3–2.0, P = 0.001]. However, in patients with lower BUN/Creatinine, the risk of mortality was not elevated in patients with RI (adjusted HR ESCAPE = 0.94, 95% CI 0.35–2.4, P = 0.90, P interaction = 0.005; BEST = 0.97, 95% CI 0.64–1.4, P = 0.90, P interaction = 0.02; SOLVD = 1.0, 95% CI 0.8–1.3, P = 0.71, P interaction = 0.005).ConclusionThe association between RI and poor survival observed in heart failure populations appears to be contingent not simply on the presence of a reduced GFR, but possibly on the mechanism by which GFR is reduced.
Analysis of match–mismatch between commercial fishing periods and spawning ecology of Pacific halibut (Hippoglossus stenolepis), based on winter surveys and behavioural data from electronic archival tags
Authors: Loher Timothy 
Published: September 2011

Abstract
Loher, T. 2011. Analysis of match–mismatch between commercial fishing periods and spawning ecology of Pacific halibut (Hippoglossus stenolepis), based on winter surveys and behavioural data from electronic archival tags. – ICES Journal of Marine Science, 68: 2240–2251. The fishery for halibut (Hippoglossus stenolepis) in the eastern Pacific is closed during the boreal winter, roughly corresponding to the seasonal spawning of the species. Opening and closing dates for each season are stipulated annually based on economics and biology. Historical surveys and data from electronic tags are analysed to assess the extent to which recent closures have encompassed the annual spawning cycle of the species, as defined by migration to offshore spawning sites, active spawning, and return to feeding areas. These were assessed by calculating mean maximum daily depth profiles for fish exhibiting seasonal migration, calculating the date-specific proportions of the tagged population either migrating to or resident on their feeding or spawning grounds, and examining the temporal distribution of spent and running fish in historical surveys along with evidence of spawning contained in high-resolution tag data. The data indicate that fishery closures over the past 20 years have been consistently too short to protect the entirety of a migration period that begins as early as September and is not substantially completed until May. Additionally, some recent season openings have encroached on the active spawning season. Failure to fully protect spawning migrations may allow seasonal interception fisheries, and the selective removal of early and late spawners could cause changes in stock demographics, restrict effective spawning, and influence long-term stock productivity, especially in the face of environmental variability.
WOX4 Imparts Auxin Responsiveness to Cambium Cells in Arabidopsis
Authors: Suer Stefanie , Agusti Javier , Sanchez Pablo , Schwarz Martina , Greb Thomas 
Published: September 2011

Abstract
Multipotent stem cell populations, the meristems, are fundamental for the indeterminate growth of plant bodies. One of these meristems, the cambium, is responsible for extended root and stem thickening. Strikingly, although the pivotal role of the plant hormone auxin in promoting cambium activity has been known for decades, the molecular basis of auxin responsiveness on the level of cambium cells has so far been elusive. Here, we reveal that auxin-dependent cambium stimulation requires the homeobox transcription factor WOX4. In Arabidopsis thaliana inflorescence stems, 1-N-naphthylphthalamic acid–induced auxin accumulation stimulates cambium activity in the wild type but not in wox4 mutants, although basal cambium activity is not abolished. This conclusion is confirmed by the analysis of cellular markers and genome-wide transcriptional profiling, which revealed only a small overlap between WOX4-dependent and cambium-specific genes. Furthermore, the receptor-like kinase PXY is required for a stable auxin-dependent increase in WOX4 mRNA abundance and the stimulation of cambium activity, suggesting a concerted role of PXY and WOX4 in auxin-dependent cambium stimulation. Thus, in spite of large anatomical differences, our findings uncover parallels between the regulation of lateral and apical plant meristems by demonstrating the requirement for a WOX family member for auxin-dependent regulation of lateral plant growth.
Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory
Authors: Gilardoni Paola A. , Hettenhausen Christian , Baldwin Ian T. , Bonaventure Gustavo 
Published: September 2011

Abstract
Nicotiana attenuata has the capacity to respond specifically to herbivory by its natural herbivore, Manduca sexta, through the perception of elicitors in larval oral secretions. We demonstrate that Lectin receptor kinase 1 (LecRK1) functions during M. sexta herbivory to suppress the insect-mediated inhibition of jasmonic acid (JA)–induced defense responses. Gene function analysis performed by reducing LecRK1 expression in N. attenuata by both virus-induced gene silencing and inverted repeated RNA interference (ir-lecRK1 plants) revealed that LecRK1 was essential to mount a full defense response against M. sexta folivory; larvae growing on ir-lecRK1 plants were 40 to 100% larger than those growing on wild-type plants. The insect-induced accumulation of nicotine, diterpene-glucosides, and trypsin protease inhibitors, as well as the expression of Thr deaminase, was severalfold reduced in ir-lecRK1 plants compared with the wild type. The accumulation of JA and JA-Ile was unaffected during herbivory in ir-lecRK1 plants; however, salicylic acid (SA) accumulation was increased by twofold. The expression of nahG in ir-lecRK1 plants prevented the increased accumulation of SA and restored the defense response against M. sexta herbivory. The results suggest that LecRK1 inhibits the accumulation of SA during herbivory, although other mechanisms may also be affected.