bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Factors and Mechanisms Underlying the Improved Photodynamic Cell Killing with Silicon Phthalocyanine Photosensitizers Directed to Lysosomes Versus Mitochondria
Authors: Rodriguez Myriam E. , Zhang Ping , Azizuddin Kashif , Delos Santos Grace B. , Chiu Song‐mao , Xue Liang‐yan , Berlin Jeffery C. , Peng Xinzhan , Wu Hongqiao , Lam Minh , Nieminen Anna‐Liisa , Kenney Malcolm E. , Oleinick Nancy L. 
Published: April 2009

AbstractThe phthalocyanine photosensitizer Pc 4 has been shown to bind preferentially to mitochondrial and endoplasmic reticulum membranes. Upon photoirradiation of Pc 4‐loaded cells, membrane components, especially Bcl‐2, are photodamaged and apoptosis, as indicated by activation of caspase‐3 and cleavage of poly(ADP‐ribose) polymerase, is triggered. A series of analogs of Pc 4 were synthesized, and the results demonstrate that Pcs with the aminopropylsiloxy ligand of Pc 4 or a similar one on one side of the Pc ring and a second large axial ligand on the other side of the ring have unexpected properties, including enhanced cell uptake, greater monomerization resulting in greater intracellular fluorescence and three‐fold higher affinity constants for liposomes. The hydroxyl‐bearing axial ligands tend to reduce aggregation of the Pc and direct it to lysosomes, resulting in four to six times more killing of cells, as defined by loss of clonogenicity, than with Pc 4. Whereas Pc 4‐PDT photodamages Bcl‐2 and Bcl‐xL, Pc 181‐PDT causes much less photodamage to Bcl‐2 over the same dose–response range relative to cell killing, with earlier cleavage of Bid and slower caspase‐3‐dependent apoptosis. Therefore, within this series of photosensitizers, these hydroxyl‐bearing axial ligands are less aggregated than is Pc 4, tend to localize to lysosomes and are more effective in overall cell killing than is Pc 4, but induce apoptosis more slowly and by a modified pathway.
Does the DNA Binding Mode of a Molecule Affect its Ability to Interact With Singlet Oxygen?
Authors: Lau Vivian , Heyne Belinda 
Published: April 2009

AbstractSinglet oxygen is known to be a potent mutagenic agent and several biologically relevant molecules have been proposed to act as scavengers for this noxious species. However, numerous studies have been conducted in homogenous solution and the reactivity of singlet oxygen scavengers known to bind DNA has never been investigated in double‐stranded DNA. In the following paper, we present the results obtained regarding the interaction between 4′,6‐diamidino‐2‐phenylindole (DAPI) and singlet oxygen. We show the molecule to be a potent scavenger of singlet oxygen in aqueous solution with an absolute rate constant (chemical and physical quenching of singlet oxygen) of (1.7 ± 0.3) × 107 m−1 s−1. In addition, we demonstrate that the binding mode of a singlet oxygen scavenger to DNA can strongly influence its reactivity toward singlet oxygen. In the case of DAPI, while the molecule exhibits a chemical reaction with singlet oxygen when the molecule is free in aqueous solution or intercalated in GC sequences of DNA, DAPI becomes chemically unreactive toward singlet oxygen when bound in the minor groove of DNA AT sequences.
Agrobacterium tumefaciens and A. rhizogenes use different proteins to transport bacterial DNA into the plant cell nucleus
Authors: Ream Walt 
Published: April 2009

Summary Agrobacterium tumefaciens and A. rhizogenes transport single‐stranded DNA (ssDNA; T‐strands) and virulence proteins into plant cells through a type IV secretion system. DNA transfer initiates when VirD2 nicks border sequences in the tumour‐inducing plasmid, attaches to the 5′ end, and pilots T‐strands into plant cells. Agrobacterium tumefaciens translocates ssDNA‐binding protein VirE2 into plant cells where it targets T‐strands into the nucleus. Some A. rhizogenes strains lack VirE2 but transfer T‐strands efficiently due to the GALLS gene, which complements an A. tumefaciens virE2 mutant. VirE2 and full‐length GALLS (GALLS‐FL) contain nuclear localization sequences that target these proteins to the plant cell nucleus. VirE2 binds cooperatively to T‐strands allowing it to move ssDNA without ATP hydrolysis. Unlike VirE2, GALLS‐FL contains ATP‐binding and helicase motifs similar to those in TraA, a strand transferase involved in conjugation. VirE2 may accumulate in the nucleus and pull T‐strands into the nucleus using the force generated by cooperative DNA binding. GALLS‐FL accumulates inside the nucleus where its predicted ATP‐dependent strand transferase may pull T‐strands into the nucleus. These different mechanisms for nuclear import of T‐strands may affect the efficiency and quality of transgenic events in plant biotechnology applications.
A Social‐Cognitive Framework of Multidisciplinary Team Innovation
Authors: Paletz Susannah B. F. , Schunn Christian D. 
Published: April 2009

AbstractThe psychology of science typically lacks integration between cognitive and social variables. We present a new framework of team innovation in multidisciplinary science and engineering groups that ties factors from both literatures together. We focus on the effects of a particularly challenging social factor, knowledge diversity, which has a history of mixed effects on creativity, most likely because those effects are mediated and moderated by cognitive and additional social variables. In addition, we highlight the distinction between team innovative processes that are primarily divergent versus convergent; we propose that the social and cognitive implications are different for each, providing a possible explanation for knowledge diversity’s mixed results on team outcomes. Social variables mapped out include formal roles, communication norms, sufficient participation and information sharing, and task conflict; cognitive variables include analogy, information search, and evaluation. This framework provides a roadmap for research that aims to harness the power of multidisciplinary teams.
Temperature influences the population structure of nitrite‐oxidizing bacteria in activated sludge
Authors: Alawi M. , Off S. , Kaya M. , Spieck E. 
Published: April 2009

SummaryActivated sludge from the municipal waste water treatment plant in Hamburg was seeded with mineral nitrite medium and incubated at 10°C, 17°C and 28°C. Dominant lithoautotrophic nitrite‐oxidizing bacteria have been identified by electron microscopy, denaturing and temperature gradient gel electrophoresis and PCR with genus‐specific primer pairs. The results have revealed the existence of three different genera of nitrite‐oxidizing bacteria, namely Nitrospira, Nitrobacter and a novel cold‐adapted nitrite oxidizer. As shown by electron microscopy members of the novel genus coexisted in activated sludge together with Nitrospira. A temperature‐dependent shift in the population structure was demonstrated by cultivation‐based approaches. The novel nitrite oxidizer was enriched at temperatures of 10°C and 17°C. Representatives of Nitrospira were able to grow in a broad temperature range between 10°C and 28°C and members of Nitrobacter were enriched during incubations at 17°C and 28°C. By subsequent 16S rDNA sequencing, the cold‐adapted nitrite oxidizer was shown to be closely related to the betaproteobacterium ‘Candidatus Nitrotoga arctica’. These findings demonstrated that the population structure of nitrite‐oxidizing bacteria in activated sludge is more complex than previously thought and responds strongly to long‐term temperature changes.
Validation of the Sysmex XT‐2000iV hematology system for dogs, cats, and horses. II. Differential leukocyte counts
Authors: Lilliehöök Inger , Tvedten Harold 
Published: April 2009

Background: The Sysmex XT‐2000iV is a laser‐based, flow cytometric hematology system that stains nucleic acids in leukocytes with a fluorescent dye. A 4‐part differential is obtained using side fluorescence light and laser side scatter.Objective: The purpose of this study was to validate the Sysmex XT‐2000iV for determining differential leukocyte counts in blood from ill dogs, cats, and horses.Methods: Blood samples from diseased animals (133 dogs, 65 cats, and 73 horses) were analyzed with the Sysmex XT‐2000iV (Auto‐diff) and the CELL‐DYN 3500. Manual differentials were obtained by counting 100 leukocytes in Wright‐stained blood smears.Results: Leukocyte populations in the Sysmex DIFF scattergram were usually well separated in equine samples, but were not as well separated in canine and feline samples. Correlation among the Sysmex XT‐2000iV, CELL‐DYN 3500, and manual counts was excellent for neutrophil counts (r ≥.97) and good for lymphocyte counts (r ≥.87) for all three species. Systematic differences between the 3 methods were seen for lymphocyte and monocyte counts. The Sysmex reported incomplete differential counts on 18% of feline, 13% of canine, and 3% of equine samples, often when a marked left shift (>10% bands) and/or toxic neutrophils were present. Eosinophils were readily identified in cytograms from all 3 species. Neither the Sysmex nor the CELL‐DYN detected basophils in the 7 dogs and 5 cats with basophilia.Conclusions: The Sysmex XT‐2000iV automated differential leukocyte count performed well with most samples from diseased dogs, cats, and horses. Basophils were not detected. Immature neutrophils or prominent toxic changes often induced errors in samples from cats and dogs.
Cytologic interpretation of canine cerebrospinal fluid samples with low total nucleated cell concentration, with and without blood contamination
Authors: Doyle Clare , Solano‐Gallego Laia 
Published: April 2009

Background:Cerebrospinal fluid (CSF) is potentially altered by iatrogenic blood contamination at the time of sampling due to the addition of blood‐associated leukocytes and protein.Objectives:The objective of this study was to assess whether protein concentration, neutrophil percentage, and the presence of activated macrophages, reactive lymphocytes, or eosinophils in CSF samples with low total nucleated cell concentration (TNCC) are affected by blood contamination or associated with central nervous system (CNS) disease.Methods:Case records from the Royal Veterinary College Diagnostic Laboratory were searched retrospectively for dogs with CSF having ≤5 TNCC/μL. TNCC, RBC, and protein concentrations; neutrophil percentage; and the presence of activated macrophages, reactive lymphocytes, and eosinophils were recorded. Results of magnetic resonance imaging (MRI) also were recorded as a marker of CNS disease.Results:Of 906 cases evaluated, 106 (12%) had blood contamination (>500 RBCs/μL) in CSF. Protein concentration and neutrophil percentage were significantly higher and the presence of eosinophils was more likely in blood contaminated vs noncontaminated samples. Non‐blood‐contaminated samples with activated macrophages or reactive lymphocytes had higher protein concentrations and neutrophil percentages, and those with activated macrophages were more likely to have a positive finding on MRI.Conclusions:Protein concentration, neutrophil percentage, and the presence of eosinophils are significantly affected by blood contamination in canine CSF having low TNCC. Activated macrophages and reactive lymphocytes are not affected by blood contamination, however, and may be useful in identifying dogs with CNS abnormalities.
Evaluation of platelet function in dogs with cardiac disease using the PFA‐100 platelet function analyzer
Authors: Clancey Noel , Burton Shelley , Horney Barbara , MacKenzie Allan , Nicastro Andrea , Côté Etienne 
Published: April 2009

Background:Cardiac disease has the potential to alter platelet function in dogs. Evaluation of platelet function using the PFA‐100 analyzer in dogs of multiple breeds and with a broad range of cardiac conditions would help clarify the effect of cardiac disease on platelets.Objectives:The objective of this study was to assess differences in closure time (CT) in dogs with cardiac disease associated with murmurs, when compared with that of healthy dogs.Methods:Thirty‐nine dogs with cardiac murmurs and turbulent blood flow as determined echocardiographically were included in the study. The dogs represented 23 different breeds. Dogs with murmurs were further divided into those with atrioventricular valvular insufficiency (n=23) and subaortic stenosis (n=9). Fifty‐eight clinically healthy dogs were used as controls. CTs were determined in duplicate on a PFA‐100 analyzer using collagen/ADP cartridges.Results:Compared with CTs in the control group (mean±SD, 57.6±5.9 seconds; median, 56.5 seconds; reference interval, 48.0–77.0 seconds), dogs with valvular insufficiency (mean±SD, 81.9±26.3 seconds; median, 78.0 seconds; range, 52.5–187 seconds), subaortic stenosis (71.4±16.5 seconds; median, 66.0 seconds; range, 51.5–95.0 seconds), and all dogs with murmurs combined (79.6±24.1 seconds; median, 74.0 seconds; range, 48.0–187 seconds) had significantly prolonged CTs (P<.01).Conclusions:The PFA‐100 analyzer is useful in detecting platelet function defects in dogs with cardiac murmurs, most notably those caused by mitral and/or tricuspid valvular insufficiency or subaortic stenosis. The form of turbulent blood flow does not appear to be an important factor in platelet hypofunction in these forms of cardiac disease.
Trade-offs in loop transformations
Authors: Palkovic Martin , Catthoor Francky , Corporaal Henk 
Published: April 2009

Nowadays, multimedia systems deal with huge amounts of memory accesses and large memory footprints. To alleviate the impact of these accesses and reduce the memory footprint, high-level memory exploration and optimization techniques have been proposed. These techniques try to more efficiently utilize the memory hierarchy. An important step in these optimization techniques are loop transformations (LT). They have a crucial effect on later data memory footprint optimization steps and code generation. However, the state-of-the-art work has focused only on individual objectives. The main one in literature involves improving the locality of data accesses, and thus reducing the data memory footprint. It does not consider the trade-offs in the LT step in relation to successive optimization steps. Therefore, it is not globally efficient in mapping the application on the target platform.
In this article we will discuss several trade-offs during the loop transformations. To our knowledge, we are the first ones considering these global trade-offs. Previous work always gave mostly one solution, having the best locality and thus the optimized memory footprint, even though some research in two-dimensional trade-offs in this area exists as well. We start from this state-of-the-art solution with minimal footprint. We show that by sacrificing the footprint, we can obtain gains in data reuse (crucial for energy reduction) and reduce the control-flow complexity. We demonstrate our approach on a real-life application, namely the QSDPCM video coder. At the end, we show that considering trade-offs for this application leads to 16% energy reduction in a two-layer memory subsystem and 10% cycle reduction on the ARM platform.
Electromagnetic Radiations of FPGAs
Authors: Sauvage Laurent , Guilley Sylvain , Mathieu Yves 
Published: April 2009

Since the first announcement of a Side Channel Analysis (SCA) about ten years ago, considerable research has been devoted to studying these attacks on Application Specific Integrated Circuits (ASICs), such as smart cards or TPMs. In this article, we compare power-line attacks with ElectroMagnetic (EM) attacks, specifically targeting Field Programmable Gate Array devices (FPGAs), as they are becoming widely used for sensitive applications involving cryptography.
We show experimentally that ElectroMagnetic Analysis (EMA) is always faster than the historical Differential Power Analysis (DPA) in retrieving keys of symmetric ciphers. In addition, these analyses prove to be very convenient to conduct, as they are totally non-invasive.
Research reports indicate that EMA can be conducted globally, typically with macroscopic home-made coils circling the device under attack, with fair results. However, as accurate professional EM antennas are now becoming more accessible, it has become commonplace to carry out EM analyses locally.
Cartography has been carried out by optical means on circuits realized with technology greater than 250 nanometers. Nonetheless, for deep submicron technologies, the feature size of devices that are spied upon is too small to be visible with photographic techniques. In addition, the presence of the 6+ metallization layers obviously prevents a direct observation of the layout. Therefore, EM imaging is emerging as a relevant means to discover the underlying device structure.
In this article, we present the first images of deep-submicron FPGAs. The resolution is not as accurate as photographic pictures: we notably compare the layout of toy design examples placed at the four corners of the FPGAs with the EM images we collected. We observe that EM imaging has the advantage of revealing active regions, which can be useful in locating a particular processor (visible while active---invisible when inactive).
In the context of EM attacks, we stress that the exact localization of the cryptographic target is not necessary: the coarse resolution we obtain is sufficient. We note that the EM imaging does not reveal the exact layout of the FPGA, but instead directly guides the attacker towards the areas which are leaking the most. We achieve attacks with an accurate sensor, both far from (namely on a SMC capacitor on the board) and close to (namely directly over the FPGA) the encryption co-processor. As compared to the previously published attacks, we report a successful attack on a DES module in fewer than 6,300 measurements, which is currently the best cracking performance against this encryption algorithm implemented in FPGAs.
Retrospective-approximation algorithms for the multidimensional stochastic root-finding problem
Authors: Pasupathy Raghu , Schmeiser Bruce W. 
Published: April 2009

The stochastic root-finding problem (SRFP) is that of solving a nonlinear system of equations using only a simulation that provides estimates of the functions at requested points. Equivalently, SRFPs seek locations where an unknown vector function attains a given target using only a simulation capable of providing estimates of the function. SRFPs find application in a wide variety of physical settings.We develop a family of retrospective-approximation (RA) algorithms called Bounding RA that efficiently solves a certain class of multidimensional SRFPs. During each iteration, Bounding RA generates and solves a sample-path problem by identifying a polytope of stipulated diameter, with an image that bounds the given target to within stipulated tolerance. Across iterations, the stipulations become increasingly stringent, resulting in a sequence of shrinking polytopes that approach the correct solution.Efficiency results from: (i) the RA structure, (ii) the idea of using bounding polytopes to exploit problem structure, and (iii) careful step-size and direction choice during algorithm evolution. Bounding RA has good finite-time performance that is robust with respect to the location of the initial solution, and algorithm parameter values. Empirical tests suggest that Bounding RA outperforms Simultaneous Perturbation Stochastic Approximation (SPSA), which is arguably the best-known algorithm for solving SRFPs.
Perspectives on router buffer sizing
Authors: Vishwanath Arun , Sivaraman Vijay , Thottan Marina 
Published: April 2009

The past few years have witnessed a lot of debate on how large Internet router buffers should be. The widely believed rule-of-thumb used by router manufacturers today mandates a buffer size equal to the delay-bandwidth product. This rule was first challenged by researchers in 2004 who argued that if there are a large number of long-lived TCP connections flowing through a router, then the buffer size needed is equal to the delay-bandwidth product divided by the square root of the number of long-lived TCP flows. The publication of this result has since reinvigorated interest in the buffer sizing problem with numerous other papers exploring this topic in further detail - ranging from papers questioning the applicability of this result to proposing alternate schemes to developing new congestion control algorithms, etc.
This paper provides a synopsis of the recently proposed buffer sizing strategies and broadly classifies them according to their desired objective: link utilisation, and per-flow performance. We discuss the pros and cons of these different approaches. These prior works study buffer sizing purely in the context of TCP. Subsequently, we present arguments that take into account both real-time and TCP traffic. We also report on the performance studies of various high-speed TCP variants and experimental results for networks with limited buffers. We conclude this paper by outlining some interesting avenues for further research.
Dietary Sulforaphane-Rich Broccoli Sprouts Reduce Colonization and Attenuate Gastritis inHelicobacter pylori–Infected Mice and Humans
Authors: Yanaka Akinori , Fahey Jed W. , Fukumoto Atsushi , Nakayama Mari , Inoue Souta , Zhang Songhua , Tauchi Masafumi , Suzuki Hideo , Hyodo Ichinosuke , Yamamoto Masayuki 
Published: April 2009

AbstractThe isothiocyanate sulforaphane [SF; 1-isothiocyanato-4(R)-methylsulfinylbutane] is abundant in broccoli sprouts in the form of its glucosinolate precursor (glucoraphanin). SF is powerfully bactericidal against Helicobacter pylori infections, which are strongly associated with the worldwide pandemic of gastric cancer. Oral treatment with SF-rich broccoli sprouts of C57BL/6 female mice infected with H. pylori Sydney strain 1 and maintained on a high-salt (7.5% NaCl) diet reduced gastric bacterial colonization, attenuated mucosal expression of tumor necrosis factor-α and interleukin-1β, mitigated corpus inflammation, and prevented expression of high salt-induced gastric corpus atrophy. This therapeutic effect was not observed in mice in which the nrf2 gene was deleted, strongly implicating the important role of Nrf2-dependent antioxidant and anti-inflammatory proteins in SF-dependent protection. Forty-eight H. pylori–infected patients were randomly assigned to feeding of broccoli sprouts (70 g/d; containing 420 μmol of SF precursor) for 8 weeks or to consumption of an equal weight of alfalfa sprouts (not containing SF) as placebo. Intervention with broccoli sprouts, but not with placebo, decreased the levels of urease measured by the urea breath test and H. pylori stool antigen (both biomarkers of H. pylori colonization) and serum pepsinogens I and II (biomarkers of gastric inflammation). Values recovered to their original levels 2 months after treatment was discontinued. Daily intake of sulforaphane-rich broccoli sprouts for 2 months reduces H. pylori colonization in mice and improves the sequelae of infection in infected mice and in humans. This treatment seems to enhance chemoprotection of the gastric mucosa against H. pylori–induced oxidative stress.