bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Soybean Cultivars Moderately Resistant to Soybean Cyst Nematode on SCN Populations and Yield
Authors: Adee Eric A. , Johnson Martin L. , Niblack Terry L. 
Published: June 2008

Spread of soybean cyst nematode Heterodera glycines (SCN) to much of the soybean (Glycine max) growing region in the Midwest has created a persistent and significant annual yield loss for soybean. Host resistance has been the primary means of reducing yield loss to SCN. It is not known how moderately resistant cultivars fit into the management of SCN. Moderately resistant cultivars can have high yield potential, but nematode reproduction is greater than on resistant cultivars. Moderate resistance is defined by a SCN female index (FI) of 10 to 29 in standardized tests, whereas cultivars with an FI < 10 are considered resistant. Two each of SCN-resistant, moderately resistant, and susceptible (FI > 60) cultivars were planted in the same plots for two soybean crops in annual rotation with corn. The SCN population was reduced 80 and 54% by resistant and moderately resistant cultivars, respectively, and increased 189% by the susceptible. Yields of the resistant and moderately resistant were 8.2 and 11.8 bu/acre better, respectively, than for the susceptible. All plots were planted to a susceptible cultivar in the final year of the study, and demonstrated there was a carry-over effect from previous cultivars. Following resistant and moderately resistant cultivars, yields of the susceptible were 6.6 and 4.3 bu/acre above following susceptible cultivars. This study showed that moderately resistant soybean cultivars can be an effective tool for improving profitability of soybean. Accepted for publication 9 April 2008. Published 18 June 2008.
Modelling thrombosis using dissipative particle dynamics method
Authors: Filipovic N , Kojic M , Tsuda A 
Published: July 2008

Aim. Arterial occlusion is a leading cause of cardiovascular disease. The main mechanism causing vessel occlusion is thrombus formation, which may be initiated by the activation of platelets. The focus of this study is on the mechanical aspects of platelet-mediated thrombosis which includes the motion, collision, adhesion and aggregation of activated platelets in the blood. A review of the existing continuum-based models is given. A mechanical model of platelet accumulation onto the vessel wall is developed using the dissipative particle dynamics (DPD) method in which the blood (i.e. colloidal-composed medium) is treated as a group of mesoscale particles interacting through conservative, dissipative, attractive and random forces.Methods. Colloidal fluid components (plasma and platelets) are discretized by mesoscopic (micrometre-size) particles that move according to Newton's law. The size of each mesoscopic particle is small enough to allow tracking of each constituent of the colloidal fluid, but significantly larger than the size of atoms such that, in contrast to the molecular dynamics approach, detailed atomic level analysis is not required.Results. To test this model, we simulated the deposition of platelets onto the wall of an expanded tube and compared our computed results with the experimental data of Karinoet al. (Miscrovasc. Res.17, 238–269, 1977). By matching our simulations to the experimental results, the platelet aggregation/adhesion binding force (characterized by an effective spring constant) was determined and found to be within a physiologically reasonable range.Conclusion. Our results suggest that the DPD method offers a promising new approach to the modelling of platelet-mediated thrombosis. The DPD model includes interaction forces between platelets both when they are in the resting state (non-activated) and when they are activated, and therefore it can be extended to the analysis of kinetics of binding and other phenomena relevant to thrombosis.
Identification of Differential Genes by Suppression Subtractive Hybridization: VI. Differential Hybridization with Tester and Driver DNA Probes
Authors: Rebrikov Denis V. 
Published: July 2008

INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes a method for screening a subtracted cDNA library by differential hybridization using (1) a tester-specific subtracted probe (forward-subtracted probe), (2) a driver-specific subtracted probe (reverse-subtracted probe), (3) a cDNA probe synthesized directly from tester mRNA (or tester genomic DNA), and (4) a cDNA probe synthesized directly from driver mRNA (or driver genomic DNA).
In Vitro Screening for Regulated Transcription Factors with Differential Display of DNA-Binding Proteins (DDDP)
Authors: Reinke Hans , Schibler Ueli 
Published: July 2008

INTRODUCTIONStrict regulation of transcription factor activity is essential to establish and maintain gene expression. Eukaryotic cells control transcription factors at many different levels. Post-translational regulatory mechanisms (e.g., phosphorylation, nuclear translocation, multimerization, regulated degradation, etc.) play particularly important roles because they enable cells to respond to various intra- and extracellular stimuli quickly and without prior protein synthesis. However, extensive post-translational changes can make it difficult to identify differentially regulated transcription factors. Common genomic screening techniques such as DNA microarray analysis are unable to detect any mode of regulation beyond that of mRNA stability. This protocol describes the differential display of DNA-binding proteins (DDDP), which is based on the electrophoretic mobility shift assay (EMSA) and detects DNA-binding transcription factors, independent of the number or nature of regulatory steps required for activation. DDDP is an unbiased screening technique that can be used in any experimental system that uses concentrated protein extracts. A plasmid library containing random DNA sequences is constructed. This library is then used to generate radioactive DNA probes to test protein extracts from different sources in parallel for differentially regulated DNA-binding proteins. Plasmids corresponding to probes that display differential DNA-binding activity can be sequenced, and the binding sequence can be narrowed down in a two-step procedure. The corresponding transcription factors can then be identified by bioinformatic and/or biochemical methods.
Two Distinct Interacting Classes of Nuclear Envelope–Associated Coiled-Coil Proteins Are Required for the Tissue-Specific Nuclear Envelope Targeting ofArabidopsisRanGAP
Authors: Zhao Qiao , Brkljacic Jelena , Meier Iris 
Published: July 2008

AbstractRan GTPase plays essential roles in multiple cellular processes, including nucleocytoplasmic transport, spindle formation, and postmitotic nuclear envelope (NE) reassembly. The cytoplasmic Ran GTPase activating protein RanGAP is critical to establish a functional RanGTP/RanGDP gradient across the NE and is associated with the outer surface of the NE in metazoan and higher plant cells. Arabidopsis thaliana RanGAP association with the root tip NE requires a family of likely plant-specific nucleoporins combining coiled-coil and transmembrane domains (CC-TMD) and WPP domain–interacting proteins (WIPs). We have now identified, by tandem affinity purification coupled with mass spectrometry, a second family of CC-TMD proteins, structurally similar, yet clearly distinct from the WIP family, that is required for RanGAP NE association in root tip cells. A combination of loss-of-function mutant analysis and protein interaction data indicates that at least one member of each NE-associated CC-TMD protein family is required for RanGAP targeting in root tip cells, while both families are dispensable in other plant tissues. This suggests an unanticipated complexity of RanGAP NE targeting in higher plant cells, contrasting both the single nucleoporin anchor in metazoans and the lack of targeting in fungi and proposes an early evolutionary divergence of the underlying plant and animal mechanisms.
In Vitro Activity of Ceftobiprole against Pathogens from Two Phase 3 Clinical Trials of Complicated Skin and Skin Structure Infections
Authors: Amsler Karen M. , Davies Todd A. , Shang Wenchi , Jacobs Michael R. , Bush Karen 
Published: July 2008

ABSTRACT

In phase 3 clinical trials for ceftobiprole treatment of complicated skin and skin structure infections, 1,219 gram-positive and 276 gram-negative aerobic baseline pathogens were identified. Ceftobiprole inhibited all staphylococcal isolates, including methicillin-resistant strains, at MICs of ≤4 μg/ml. Against
Enterobacteriaceae
and
Pseudomonas aeruginosa
isolates, the potency of ceftobiprole was similar to that of cefepime.
Anti-Human Immunodeficiency Virus Type 1 Activities of Antimicrobial Peptides Derived from Human and Bovine Cathelicidins
Authors: Wang Guangshun , Watson Karen M. , Buckheit Robert W. 
Published: July 2008

ABSTRACT
From among 15 human cathelicidin LL-37-derived peptides, FK-13 was identified as the smallest peptide active against human immunodeficiency virus (HIV) and GI-20 had the highest therapeutic index, which was twice that of LL-37. BMAP-18, which is derived from bovine cathelicidin BMAP-27, possessed a therapeutic index similar to that of GI-20. Peptide sequence order, helical structures, and aromatic residues are important in HIV inhibition.
Staurosporine aglycone bilaterally regulates ERK1/2 phosphorylation in rat pulmonary arterial smooth muscle cells
Authors: Zhang Jianing , Tang Xiaobo , Lu Changlian , Guo Lei , Zhang Shuang , Chu Xiaojie , Zhu Daling 
Published: July 2008

Staurosporine, a protein kinase C (PKC) inhibitor, has been reported to regulate the phosphorylation of ERK1/2 in several cell lines. It is still unknown, however, whether its derivative staurosporine aglycone (SA) has the same effect on ERK1/2 activation. In this study, we investigated the effect of SA on ERK1/2 activity in rat pulmonary arteries and pulmonary arterial smooth muscle cells (PASMCs). The pulmonary arteries and PASMCs were treated with SA at different time points and concentrations, and the activation of ERK1/2 was analyzed by Western blotting. The results showed that SA at nanomolar concentrations suppressed ERK1/2 phosphorylation through the PKC pathway alone, but SA at 30 µmol/L for 2 h enhanced the phosphorylation of ERK1/2. The activation of ERK1/2 was inhibited by the MAPK/ERK kinase inhibitor PD98059 or the protein kinase A (PKA) activator isoproterenol. Together, these results suggest that SA has a strong dual regulating effect on ERK1/2 through the PKC and (or) PKA pathways in rat PASMCs.
Deep-crust strike-slip earthquake faulting in southern Italy aided by high fluid pressure: insights from rheological analysis
Authors: Boncio Paolo 
Published: July 2008

Abstract

I present the results of a crustal rheological analysis of the Potenza 1990 and Molise 2002 (southern Italy) deep foci (10–25 km) strike–slip earthquake sequences (
M
max
=5.7) located in the upper half of the middle crust. The analysis consists of geotherms and two-mechanism (brittle frictional v. ductile plastic flow) strength envelopes. Strength envelopes are calculated along a sub-vertical E–W-striking inherited crustal-scale fault zone reactivated under a strike–slip tectonic regime. The effects of high pore-fluid pressure (
Pf
) and strain rate increase due to afterslip processes during the co-seismic and early post-seismic phases are evaluated. The results are compared with the depth-distribution of seismicity. Under long-term strain rates, the rheology predicts a brittle layer in the upper part of the middle crust embedded by two plastic horizons: the base of the carbonates and the Verrucano layer (above) and the lower part of middle crust (below). The best rheological model for the observed seismicity is that considering high
Pf
in the middle crust (λ≥0.65). Brittle faulting aided by high
Pf
in the middle crust is in agreement with the focal depths and magnitudes of the main shocks. The upward and downward widening of the brittle layer in the middle crust, due to the increased strain rate in the co-seismic and early post-seismic phases (afterslip), agrees with the width of the aftershock zones. The weak ductile layer at the base of the carbonates (and possibly within the Verrucano) appears to have an important role in delimiting the seismogenic faulting upwards and probably played a role in defining a seal to fluid up-flow along the fault zone.
The distribution of faults and fractures and their importance in accommodating extensional strain at Kimmeridge Bay, Dorset, UK
Authors: Putz-Perrier Martin W. , Sanderson David J. 
Published: July 2008

Abstract
The spatial distribution of extensional strain in interbedded mudstones and carbonates from around Kimmeridge Bay in southern England is examined using a variety of line samples. Normal faults and tensile fractures (veins) from the same deformation event show displacements ranging over 6 orders of magnitude. The relative contribution of these structures to the overall extension varies, with large faults (>10 m heave) accommodating about 65%, smaller faults (1–10 m heave) about 25% and veins less than 10% of the overall extension. The heterogeneity of fracture density and strain can be quantified from cumulative plots by applying a non-parametric method based on Kuiper's test. Both the degree and statistical significance of strain heterogeneity can be determined and are shown to be scale-dependent. Thin veins accommodate a fairly constant background strain across the region, whilst thick veins and small faults take up localized higher strains in damage zones around larger faults. Fault-strain is relatively homogenously distributed across the region. The faults and veins do not share the same scaling relationship. Thus, this study shows that it is not possible to simply extrapolate fracture frequencies and strain from fault scale to vein scale, and that the heterogeneity of extensional strain is scale dependent.
Counter braids
Authors: Lu Yi , Montanari Andrea , Prabhakar Balaji , Dharmapurikar Sarang , Kabbani Abdul 
Published: July 2008

Fine-grained network measurement requires routers and switches to update large arrays of counters at very high link speed (e.g. 40 Gbps). A naive algorithm needs an infeasible amount of SRAM to store both the counters and a flow-to-counter association rule, so that arriving packets can update corresponding counters at link speed. This has made accurate per-flow measurement complex and expensive, and motivated approximate methods that detect and measure only the large flows.
This paper revisits the problem of accurate per-flow measurement. We present a counter architecture, called Counter Braids, inspired by sparse random graph codes. In a nutshell, Counter Braids "compresses while counting". It solves the central problems (counter space and flow-to-counter association) of per-flow measurement by "braiding" a hierarchy of counters with random graphs. Braiding results in drastic space reduction by sharing counters among flows; and using random graphs generated on-the-fly with hash functions avoids the storage of flow-to-counter association.
The Counter Braids architecture is optimal (albeit with a complex decoder) as it achieves the maximum compression rate asymptotically. For implementation, we present a low-complexity message passing decoding algorithm, which can recover flow sizes with essentially zero error. Evaluation on Internet traces demonstrates that almost all flow sizes are recovered exactly with only a few bits of counter space per flow.
HMTT
Authors: Bao Yungang , Chen Mingyu , Ruan Yuan , Liu Li , Fan Jianping , Yuan Qingbo , Song Bo , Xu Jianwei 
Published: July 2008

Memory trace analysis is an important technology for architecture research, system software (i.e., OS, compiler) optimization, and application performance improvements. Many approaches have been used to track memory trace, such as simulation, binary instrumentation and hardware snooping. However, they usually have limitations of time, accuracy and capacity.
In this paper we propose a platform independent memory trace monitoring system, which is able to track virtual memory reference trace of full systems (including OS, VMMs, libraries, and applications). The system adopts a DIMM-snooping mechanism that uses hardware boards plugged in DIMM slots to snoop. There are several advantages in this approach, such as fast, complete, undistorted, and portable. Three key techniques are proposed to address the system design challenges with this mechanism: (1) To keep up with memory speeds, the DDR protocol state machine is simplified, and large FIFOs are added between the state machine and the trace transmitting logic to handle burst memory accesses; (2) To reconstruct physical-tovirtual mapping and distinguish one process' address space from others, an OS kernel module, which collects page table information, and a synchronization mechanism, which synchronizes the page table information with the memory race, are developed; (3) To dump massive trace data, we employ a straightforward method to compress the trace and use Gigabit Ethernet and RAID to send and receive the compressed trace.
We present our implementation of an initial monitoring system, named HMTT (Hyper Memory Trace Tracker). Using HMTT, we have observed that burst bandwidth utilization is much larger than average bandwidth utilization, by up to 5X in desktop applications. We have also confirmed that the stream memory accesses of many applications contribute even more than 40% of L2 Cache misses and OS virtual memory management may decrease stream accesses in view of memory controller (or L2 Cache), by up to 30.2%. Moreover, we have evaluated OS impact on memory performance in real systems. The evaluations and case studies show the feasibility and effectiveness of our proposed monitoring mechanism and techniques.
DARC
Authors: Traeger Avishay , Deras Ivan , Zadok Erez 
Published: July 2008

OSprof is a versatile, portable, and efficient profiling methodology based on the analysis of latency distributions. Although OSprof has offers several unique benefits and has been used to uncover several interesting performance problems, the latency distributions that it provides must be analyzed manually. These latency distributions are presented as histograms and contain distinct groups of data, called peaks, that characterize the overall behavior of the running code. By automating the analysis process, we make it easier to take advantage of OSprof's unique features.
We have developed the Dynamic Analysis of Root Causes system (DARC), which finds root cause paths in a running program's call-graph using runtime latency analysis. A root cause path is a call-path that starts at a given function and includes the largest latency contributors to a given peak. These paths are the main causes for the high-level behavior that is represented as a peak in an OSprof histogram. DARC performs PID and call-path filtering to reduce overheads and perturbations, and can handle recursive and indirect calls. DARC can analyze preemptive behavior and asynchronous call-paths, and can also resume its analysis from a previous state, which is useful when analyzing short-running programs or specific phases of a program's execution.
We present DARC and show its usefulness by analyzing behaviors that were observed in several interesting scenarios. We also show that DARC has negligible elapsed time overheads for normal use cases.
Identification of Novel Isoforms of theEML4-ALKTransforming Gene in Non–Small Cell Lung Cancer
Authors: Choi Young Lim , Takeuchi Kengo , Soda Manabu , Inamura Kentaro , Togashi Yuki , Hatano Satoko , Enomoto Munehiro , Hamada Toru , Haruta Hidenori , Watanabe Hideki , Kurashina Kentaro , Hatanaka Hisashi , Ueno Toshihide , Takada Shuji , Yamashita Yoshihiro , Sugiyama Yukihiko , Ishikawa Yuichi , Mano Hiroyuki 
Published: July 2008

AbstractThe genome of a subset of non–small-cell lung cancers (NSCLC) harbors a small inversion within chromosome 2 that gives rise to a transforming fusion gene, EML4-ALK, which encodes an activated protein tyrosine kinase. Although breakpoints within EML4 have been identified in introns 13 and 20, giving rise to variants 1 and 2, respectively, of EML4-ALK, it has remained unclear whether other isoforms of the fusion gene are present in NSCLC cells. We have now screened NSCLC specimens for other in-frame fusion cDNAs that contain both EML4 and ALK sequences. Two slightly different fusion cDNAs in which exon 6 of EML4 was joined to exon 20 of ALK were each identified in two individuals of the cohort. Whereas one cDNA contained only exons 1 to 6 of EML4 (variant 3a), the other also contained an additional 33-bp sequence derived from intron 6 of EML4 (variant 3b). The protein encoded by the latter cDNA thus contained an insertion of 11 amino acids between the EML4 and ALK sequences of that encoded by the former. Both variants 3a and 3b of EML4-ALK exhibited marked transforming activity in vitro as well as oncogenic activity in vivo. A lung cancer cell line expressing endogenous variant 3 of EML4-ALK underwent cell death on exposure to a specific inhibitor of ALK catalytic activity. These data increase the frequency of EML4-ALK–positive NSCLC tumors and bolster the clinical relevance of this oncogenic kinase. [Cancer Res 2008;68(13):4971–6]
Triptolide-Induced Transcriptional Arrest Is Associated with Changes in Nuclear Substructure
Authors: Leuenroth Stephanie J. , Crews Craig M. 
Published: July 2008

Abstract
Triptolide, an active component of the medicinal herb lei gong teng, is a potent anticancer and anti-inflammatory therapeutic. It potently inhibits nuclear factor-κB transcriptional activation after DNA binding, although a precise mechanism is as yet unknown. Here, we report that triptolide also induces distinct nuclear substructural changes in HeLa cells. These changes in the nucleolus and nuclear speckles are reversible and dependent on both time and concentration. Furthermore, nuclear changes occurred within hours of triptolide treatment and were calcium and caspase independent. Rounding of nuclear speckles, an indication of transcriptional arrest, was evident and was associated with a decrease in RNA polymerase II (RNA Pol II) COOH-terminal domain Ser2 phosphorylation. Additionally, the nucleolus disassembled and RNA Pol I activity declined after RNA Pol II inhibition. We therefore conclude that triptolide causes global transcriptional arrest as evidenced by inactivity of RNA Pol I and II and the subsequent alteration in nuclear substructure. [Cancer Res 2008;68(13):5257–66]