bluuebunny/crossref_metadata_2025 huggingface dataset:
Mask undercut in deep silicon etch
Authors: Saraf I. , Goeckner M. , Goodlin Brian , Kirmse Karen , Overzet L.
Published: April 2011

Mask undercut in the time-multiplexed deep silicon etch process is becoming an increasingly significant issue as it is used to produce smaller critical dimension features. Models of the process must contain the necessary physics to reproduce the dependencies of mask undercut. We argue that the reason undercut develops is the dependence of the deposition step on ion flux. Our experiments of C4F8 (and CHF3 not shown) plasmas show that the film growth is dominantly ion-enhanced. This leads naturally to a mask undercut that increases in time. A more neutral flux dominant deposition step would result in reduced mask undercut.
Nanomanipulation of field emission measurement for vacuum nanodiodes based on uniform silicon nanowire emitters
Authors: Chen Pai-Yen , Cheng Tsung-Chieh , Shieh Jiann , Luo Yun-Cin
Published: April 2011

We performed in situ field emission (FE) measurements on vacuum nanodiodes with a dynamically tunable nanogap, ranging from 20 to 150 nm. The nanogap was precisely controlled by a scanning tungsten probe (anode) attached on the nanomotor, thereby allowing the accurate and flexible three-dimensional FE characterization for silicon nanowire emitters (cold cathode). Our experimental results show that the local field enhancement factor and the onset voltage are sensitively dependent on the nanogap size, agreeing quite well with the theoretical fitting curve. Moreover, efficient and low-power driving FE nanodevices are envisioned by aggressively reducing the nanogap and squeezing nanodiodes.
Hall effect-induced acceleration of electromigration failures in spin valve multilayers under magnetic field
Authors: Jiang Jing , Zeng Ding Gui , Chung Kyung-Won , Kim Jongryoul , Bae Seongtae
Published: April 2011

It was observed that electromigration (EM)-induced failures in spin valve multilayers were severely accelerated by an externally applied magnetic field. The theoretical and experimental analysis results confirmed that Hall effect-induced Lorentz force applied to the perpendicular-to-the-film-plane direction is primarily responsible for the severe acceleration of the EM failures due to its dominant contribution to abruptly increasing local temperature and current density. The proposed failure model and the theoretical calculations were demonstrated to agree well with the experimental observations.
Label-free cell aggregate formation based on the magneto-Archimedes effect
Authors: Akiyama Yoshitake , Morishima Keisuke
Published: April 2011

This letter demonstrates formation of cell aggregates by a label-free three-dimensional (3D) cell assembly method, which is based on the magneto-Archimedes effect. Gadolinium complex was added to the culturing medium to enhance the diamagnetic property of the cells, by which label-free magnetic manipulation became possible. Cytotoxicity of the gadolinium complex was confirmed to be sufficiently low for exposure less than one day. With this method, the cells aggregated into an egg-shape in about 20 min and became a spheroid in one day. These results suggest that this method is a promising approach to construct arbitrarily-shaped 3D tissues.
Thermal stability of amorphous GaN1−xAsx alloys
Authors: Levander A. X. , Liliental-Weber Z. , Broesler R. , Hawkridge M. E. , Novikov S. V. , Foxon C. T. , Dubon O. D. , Wu J. , Walukiewicz W. , Yu K. M.
Published: April 2011

GaN 1 − x As x alloys grown across the composition range by low temperature molecular beam epitaxy have great technological potential for photovoltaic applications owing to their strong absorption coefficient and wide tunability of band gap and band edges. We found that amorphous GaN1−xAsx alloys that are formed for the compositions x, in the range of x∼0.3–0.7 are stable up to 700 °C. This is surprising since growth of GaN1−xAsx above 400 °C results in phase segregation. At annealing temperatures higher than 700 °C the alloy phase segregates into GaAs:N and GaN:As. The relative size of the nanocrystals depends on the initial film composition and annealing conditions.
Microfluidic resonant waveguide grating biosensor system for whole cell sensing
Authors: Zaytseva Natalya , Miller William , Goral Vasily , Hepburn Jerry , Fang Ye
Published: April 2011

We report on a fluidic resonant waveguide grating (RWG) biosensor system that enables medium throughput measurements of cellular responses under microfluidics in a 32-well format. Dynamic mass redistribution assays under microfluidics differentiate the cross-desensitization process between the β2-adrenoceptor agonist epinephrine and the adenylate cyclase activator forskolin mediated signaling. This system opens new possibility to study cellular processes that are otherwise difficult to achieve using conventional RWG configurations.
Soil organic carbon and total nitrogen under Leucaena leucocephala pastures in Queensland
Authors: Radrizzani Alejandro , Shelton H. Max , Dalzell Scott A. , Kirchhof Gunnar
Published: April 2011

Soil organic carbon (OC) and total nitrogen (TN) accumulation in the top 0–0.15 m of leucaena–grass pastures were compared with native pastures and with continuously cropped land. OC and TN levels were highest under long-term leucaena–grass pasture (P < 0.05). For leucaena–grass pastures that had been established for 20, 31, and 38 years, OC accumulated at rates that exceeded those of the adjacent native grass pasture by 267, 140, and 79 kg/ha.year, respectively, while TN accumulated at rates that exceeded those of the native grass pastures by 16.7, 10.8, and 14.0 kg/ha.year, respectively. At a site where 14-year-old leucaena–grass pasture was adjacent to continuously cropped land, there were benefits in OC accumulation of 762 kg/ha.year and in TN accumulation of 61.9 kg/ha.year associated with the establishment of leucaena–grass pastures. Similar C : N ratios (range 12.7–14.5) of soil OC in leucaena and grass-only pastures indicated that plant-available N limited soil OC accumulation in pure grass swards. Higher OC accumulation occurred near leucaena hedgerows than in the middle of the inter-row in most leucaena–grass pastures.
Rates of C sequestration were compared with simple models of greenhouse gas (GHG) emissions from the grazed pastures. The amount of carbon dioxide equivalent (CO2-e) accumulated in additional topsoil OC of leucaena–grass pastures ≤20 years old offset estimates of the amount of CO2-e emitted in methane and nitrous oxide from beef cattle grazing these pastures, thus giving positive GHG balances. Less productive, aging leucaena pastures >20 years old had negative GHG balances; lower additional topsoil OC accumulation rates compared with native grass pastures failed to offset animal emissions.
Indirect selection using reference and probe genotype performance in multi-environment trials
Authors: Mathews Ky L. , Trethowan Richard , Milgate Andrew W. , Payne Thomas , van Ginkel Maarten , Crossa Jose , DeLacy Ian , Cooper Mark , Chapman Scott C.
Published: April 2011

There is a substantial challenge in identifying appropriate cultivars from databases for introduction into a breeding program. We propose an indirect selection procedure that illustrates how strategically designed multi-environment trials, linked to historical performance databases, can identify germplasm to meet objectives of plant breeding programs.
Two strategies for indirect selection of germplasm from the International Wheat and Maize Improvement Center’s (CIMMYT) trial database were developed based on reference and probe genotype sets included in the International Adaptation Trial (IAT). The IAT was designed to improve the understanding of relationships among global spring wheat (Triticum spp.) locations. Grain yield (t/ha) data were collated from 183 IAT trials grown in 40 countries (including Australia) between 2001 and 2004.
The reference genotype set strategy used the genetic correlations among locations in the IAT to identify locations similar to a target environment. For a key southern Australian breeding location, Roseworthy, the number of cultivars targeted for selection was reduced to 35% of the original 1252. The Irrigated Winter Cereals Trials (2008–09) aimed to identify high yield potential lines in south-eastern Australian irrigated environments. Thirty-five CIMMYT cultivars identified using the reference genotype selection strategy were grown in this trial series. In all trials, the proportion of CIMMYT cultivars in the top 20% yielding lines exceeded the expected proportion, 0.20.
The probe genotype strategy utilised contrasting line yield responses to assess the occurrence of soil-borne stresses such as root lesion nematode (Pratylenchus thorneii) and boron toxicity. For these stresses, the number of targeted cultivars was reduced to 25% and 83% of the original 1252, respectively.
Community extraction for social networks
Authors: Zhao Yunpeng , Levina Elizaveta , Zhu Ji
Published: April 2011

Analysis of networks and in particular discovering communities within networks has been a focus of recent work in several fields and has diverse applications. Most community detection methods focus on partitioning the entire network into communities, with the expectation of many ties within communities and few ties between. However, many networks contain nodes that do not fit in with any of the communities, and forcing every node into a community can distort results. Here we propose a new framework that extracts one community at a time, allowing for arbitrary structure in the remainder of the network, which can include weakly connected nodes. The main idea is that the strength of a community should depend on ties between its members and ties to the outside world, but not on ties between nonmembers. The proposed extraction criterion has a natural probabilistic interpretation in a wide class of models and performs well on simulated and real networks. For the case of the block model, we establish asymptotic consistency of estimated node labels and propose a hypothesis test for determining the number of communities.
Emergence of long timescales and stereotyped behaviors in
Caenorhabditis elegans
Authors: Stephens Greg J. , Bueno de Mesquita Matthew , Ryu William S. , Bialek William
Published: April 2011

Animal behaviors often are decomposable into discrete, stereotyped elements, well separated in time. In one model, such behaviors are triggered by specific commands; in the extreme case, the discreteness of behavior is traced to the discreteness of action potentials in the individual command neurons. Here, we use the crawling behavior of the nematode
Caenorhabditis elegans
to demonstrate the opposite view, in which discreteness, stereotypy, and long timescales emerge from the collective dynamics of the behavior itself. In previous work, we found that as
C. elegans
crawls, its body moves through a “shape space” in which four dimensions capture approximately 95% of the variance in body shape. Here we show that stochastic dynamics within this shape space predicts transitions between attractors corresponding to abrupt reversals in crawling direction. With no free parameters, our inferred stochastic dynamical system generates reversal timescales and stereotyped trajectories in close agreement with experimental observations. We use the stochastic dynamics to show that the noise amplitude decreases systematically with increasing time away from food, resulting in longer bouts of forward crawling and suggesting that worms can use noise to modify their locomotory behavior.
Pitch perception beyond the traditional existence region of pitch
Authors: Oxenham Andrew J. , Micheyl Christophe , Keebler Michael V. , Loper Adam , Santurette Sébastien
Published: April 2011

Humans’ ability to recognize musical melodies is generally limited to pure-tone frequencies below 4 or 5 kHz. This limit coincides with the highest notes on modern musical instruments and is widely believed to reflect the upper limit of precise stimulus-driven spike timing in the auditory nerve. We tested the upper limits of pitch and melody perception in humans using pure and harmonic complex tones, such as those produced by the human voice and musical instruments, in melody recognition and pitch-matching tasks. We found that robust pitch perception can be elicited by harmonic complex tones with fundamental frequencies below 2 kHz, even when all of the individual harmonics are above 6 kHz—well above the currently accepted existence region of pitch and above the currently accepted limits of neural phase locking. The results suggest that the perception of musical pitch at high frequencies is not constrained by temporal phase locking in the auditory nerve but may instead stem from higher-level constraints shaped by prior exposure to harmonic sounds.
Discovery and molecular basis of potent noncovalent inhibitors of fatty acid amide hydrolase (FAAH)
Authors: Min Xiaoshan , Thibault Stephen T. , Porter Amy C. , Gustin Darin J. , Carlson Timothy J. , Xu Haoda , Lindstrom Michelle , Xu Guifen , Uyeda Craig , Ma Zhihua , Li Yihong , Kayser Frank , Walker Nigel P. C. , Wang Zhulun
Published: April 2011

Fatty acid amide hydrolase (FAAH), an amidase-signature family member, is an integral membrane enzyme that degrades lipid amides including the endogenous cannabinoid anandamide and the sleep-inducing molecule oleamide. Both genetic knock out and pharmacological administration of FAAH inhibitors in rodent models result in analgesic, anxiolytic, and antiinflammatory phenotypes. Targeting FAAH activity, therefore, presents a promising new therapeutic strategy for the treatment of pain and other neurological-related or inflammatory disorders. Nearly all FAAH inhibitors known to date attain their binding potency through a reversible or irreversible covalent modification of the nucleophile Ser241 in the unusual Ser-Ser-Lys catalytic triad. Here, we report the discovery and mechanism of action of a series of ketobenzimidazoles as unique and potent noncovalent FAAH inhibitors. Compound
2
, a representative of these ketobenzimidazoles, was designed from a series of ureas that were identified from high-throughput screening. While urea compound
1
is characterized as an irreversible covalent inhibitor, the cocrystal structure of FAAH complexed with compound
2
reveals that these ketobenzimidazoles, though containing a carbonyl moiety, do not covalently modify Ser241. These inhibitors achieve potent inhibition of FAAH activity primarily from shape complementarity to the active site and through numerous hydrophobic interactions. These noncovalent compounds exhibit excellent selectivity and good pharmacokinetic properties. The discovery of this distinctive class of inhibitors opens a new avenue for modulating FAAH activity through nonmechanism-based inhibition.
Roles for class IIA phosphatidylinositol transfer protein in neurotransmission and behavioral plasticity at the sensory neuron synapses of
Caenorhabditis elegans
Authors: Iwata Ryo , Oda Shigekazu , Kunitomo Hirofumi , Iino Yuichi
Published: April 2011

Growing evidence suggests that sensory neuron synapses not merely pass, but actively encode sensory information and convey it to the central nervous system. The chemosensory preferences of
Caenorhabditis elegans
, as manifested in the direction of chemotaxis, are reversibly regulated by prior experience at the level of sensory neurons; the attractive drive is promoted by diacylglycerol (DAG) signaling, whereas the counteracting repulsive drive requires PtdIns(3,4,5)P
3
signaling. Here we report that the two opposing drives require a class IIA phosphatidylinositol transfer protein (PITP), PITP-1, which localizes to the sensory neuron synapses. In
pitp-1
mutants, attraction behavior to salt is reduced, whereas conditioned repulsion from salt is eliminated: the mutants inflexibly show weak attraction behavior to salt, irrespective of prior experience. To generate flexible behavioral outputs, attraction and repulsion, PITP-1 acts in the gustatory neuron ASER and likely regulates neurotransmission from ASER, as
pitp-1
mutations do not affect the ASER Ca
2+
response to sensory stimulus. Furthermore, full attraction to salt is restored in
pitp-1
mutants by expression of the phosphatidylinositol transfer domain alone, and also by mutations of a DGK gene that cause accumulation of DAG, suggesting that PITP-1 serves for DAG production via phosphatidylinositol transport and, hence, regulates synaptic transmission. In addition to gustatory behavior, olfactory behaviors and osmotic avoidance are also regulated by PITP-1 in the sensory neurons that detect each sensory stimulus. Thus, PITP-1–dependent phosphatidylinositol transport is essential for sensory neuron synapses to couple sensory inputs to effective behavioral responses.
Three chemokine receptors cooperatively regulate homing of hematopoietic progenitors to the embryonic mouse thymus
Authors: Calderón Lesly , Boehm Thomas
Published: April 2011

The thymus lacks self-renewing hematopoietic cells, and thymopoiesis fails rapidly when the migration of progenitor cells to the thymus ceases. Hence, the process of thymus homing is an essential step for T-cell development and cellular immunity. Despite decades of research, the molecular details of thymus homing have not been elucidated fully. Here, we show that chemotaxis is the key mechanism regulating thymus homing in the mouse embryo. We determined the number of early thymic progenitors in the thymic rudiments of mice deficient for one, two, or three of the chemokine receptor genes, chemokine (C-C motif) receptor 9 (
Ccr9
), chemokine (C-C motif) receptor 7 (
Ccr7
), and chemokine (C-X-C motif) receptor 4 (
Cxcr4
). In the absence of all three chemokine receptors, thymus homing was reduced about 100-fold both before and after vascularization of the thymic rudiment. In the absence of only two of these three chemokine receptor genes, thymus homing was much less affected (only two- to 10-fold), indicating that the chemotactic regulation of thymus homing is remarkably robust. Our results reveal the redundant roles of Ccr9, Ccr7, and Cxcr4 for thymic homing and provide a framework to examine the regulation of progenitor homing in the postnatal thymus.
Modeling high-grade serous ovarian carcinogenesis from the fallopian tube
Authors: Karst Alison M. , Levanon Keren , Drapkin Ronny
Published: April 2011

High-grade serous ovarian carcinoma (HGSOC) is a lethal disease for which improved screening and treatment strategies are urgently needed. Progress in these areas is impeded by our poor understanding of HGSOC pathogenesis. Most ovarian cancer research is based on the hypothesis that HGSOC arises from ovarian surface epithelial cells. However, recent studies suggest that >50% of high-grade serous carcinomas involving the ovary likely arise from fallopian tube epithelium. Therefore, limiting HGSOC research to modeling based on ovarian surface epithelium alone is inadequate. To address the need for a fallopian tube–based model of HGSOC, we have developed a system for studying human fallopian tube secretory epithelial cell (FTSEC) transformation. Our model is based on (
i
) immortalization of FTSECs isolated from primary samples of normal, nondiseased human fallopian tubes, (
ii
) transformation of FTSECs with defined genetic elements, and (
iii
) xenograft-based tumorigenic assays. We use our model to show that FTSECs immortalized with human telomerase reverse transcriptase (hTERT) plus SV40 large T and small T antigens are transformed by either oncogenic Ras (H-Ras
V12
) or c-Myc expression, leading to increased proliferation, clonogenicity, and anchorage-independent growth. Additionally, we demonstrate that FTSECs remain susceptible to c-Myc–mediated transformation in the absence of viral oncoproteins, by replacing SV40 large T and small T antigens with sh-p53, mutant CDK4 (CDK4
R24C
), and sh-PP2A-B56γ. Importantly, all transformed FTSECs gave rise to high-grade Müllerian carcinomas that were grossly, histologically, immunophenotypically, and genomically similar to human HGSOC. With this model, we will now be able to assess the transformative effects of specific genetic alterations on FTSECs in order to characterize their respective roles in HGSOC development.
Modular coherence of protein dynamics in yeast cell polarity system
Authors: Gao Juntao Tony , Guimerà Roger , Li Hua , Pinto Inês Mendes , Sales-Pardo Marta , Wai Stephanie C. , Rubinstein Boris , Li Rong
Published: April 2011

In this study, we investigated on a systems level how complex protein interactions underlying cell polarity in yeast determine the dynamic association of proteins with the polar cortical domain (PCD) where they localize and perform morphogenetic functions. We constructed a network of physical interactions among >100 proteins localized to the PCD. This network was further divided into five robust modules correlating with distinct subprocesses associated with cell polarity. Based on this reconstructed network, we proposed a simple model that approximates a PCD protein's molecular residence time as the sum of the characteristic time constants of the functional modules with which it interacts, weighted by the number of edges forming these interactions. Regression analyses showed excellent fitting of the model with experimentally measured residence times for a large subset of the PCD proteins. The model is able to predict residence times using small training sets. Our analysis also revealed a scaffold protein that imposes a local constraint of dynamics for certain interacting proteins.
Role of mass-kill hunting strategies in the extirpation of Persian gazelle (
Gazella subgutturosa
) in the northern Levant
Authors: Bar-Oz Guy , Zeder Melinda , Hole Frank
Published: April 2011

Continuous and intensive exploitation of wildlife resources by early agricultural societies had major ecological consequences in the ancient Near East. In particular, hunting strategies of post-Neolithic societies involving the mass killing of wild ungulates contributed to the eventual extirpation of a number of wild species. A remarkable deposit of bones of Persian gazelle (
Gazella subgutarosa
) from fourth millennium BCE levels at Tell Kuran in northeastern Syria provides insight into the unsustainable hunting practices that disrupted gazelle migratory patterns and helped set the course for the virtual extinction of this species and possibly other steppe species in the Levant. The social context of mass kills conducted during periods when people relied primarily on domestic livestock for animal resources sets them apart from the more targeted and sustainable practices of earlier periods, when wild animals were the major or sole source of animal protein.
Torsional elasticity and energetics of F
1
-ATPase
Authors: Czub Jacek , Grubmüller Helmut
Published: April 2011

F
o
F
1
-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded F
o
generates the rotary torque that drives the rotation of the asymmetric shaft of F
1
. Mechanical energy of the rotating shaft is used by the F
1
catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant part of the shaft is required for the observed high turnover rate. We used atomistic simulations to study the spatial distribution and structural determinants of the F
1
torsional elasticity at the molecular level and to comprehensively characterize the elastic properties of F
1
-ATPase. Our fluctuation analysis revealed an unexpected heterogeneity of the F
1
shaft elasticity. Further, we found that the measured overall torsional moduli of the shaft arise from two distinct contributions, the intrinsic elasticity and the effective potential imposed on the shaft by the catalytic subunit. Separation of these two contributions provided a quantitative description of the coupling between the rotor and the catalytic subunit. This description enabled us to propose a minimal quantitative model of the F
1
energetics along the rotary degrees of freedom near the resting state observed in the crystal structures. As opposed to the usually employed models where the motor mechanical progression is described by a single angular variable, our multidimensional treatment incorporates the spatially inhomogeneous nature of the shaft and its interactions with the stator and offers new insight into the mechanoenzymatics of F
1
-ATPase.
Extensive DNA-binding specificity divergence of a conserved transcription regulator
Authors: Baker Christopher R. , Tuch Brian B. , Johnson Alexander D.
Published: April 2011

The DNA sequence recognized by a transcription regulator can be conserved across large evolutionary distances. For example, it is known that many homologous regulators in yeasts and mammals can recognize the same (or closely related) DNA sequences. In contrast to this paradigm, we describe a case in which the DNA-binding specificity of a transcription regulator has changed so extensively (and over a much smaller evolutionary distance) that its
cis
-regulatory sequence appears unrelated in different species. Bioinformatic, genetic, and biochemical approaches were used to document and analyze a major change in the DNA-binding specificity of Matα1, a regulator of cell-type specification in ascomycete fungi. Despite this change, Matα1 controls the same core set of genes in the hemiascomycetes because its DNA recognition site has evolved with it, preserving the protein-DNA interaction but significantly changing its molecular details. Matα1 and its recognition sequence diverged most dramatically in the common ancestor of the CTG-clade (
Candida albicans, Candida lusitaniae,
and related species), apparently without the aid of a gene duplication event. Our findings suggest that DNA-binding specificity divergence between orthologous transcription regulators may be more prevalent than previously thought and that seemingly unrelated
cis
-regulatory sequences can nonetheless be homologous. These findings have important implications for understanding transcriptional network evolution and for the bioinformatic analysis of regulatory circuits.
Site-specific enzymatic polysialylation of therapeutic proteins using bacterial enzymes
Authors: Lindhout Theresa , Iqbal Umar , Willis Lisa M. , Reid Anne N. , Li Jianjun , Liu Xin , Moreno Maria , Wakarchuk Warren W.
Published: April 2011

The posttranslational modification of therapeutic proteins with terminal sialic acids is one means of improving their circulating half-life, thereby improving their efficiency. We have developed a two-step in vitro enzymatic modification of glycoproteins, which has previously only been achieved by chemical means [Gregoriadis G, Jain S, Papaioannou I, Laing P (2005)
Int J Pharm
300:125–130). This two-step procedure uses the
Campylobacter jejuni
Cst-II α2,8-sialyltransferase to provide a primer on N-linked glycans, followed by polysialylation using the
Neisseria meningitidis
α2,8-polysialyltransferase. Here, we have demonstrated the ability of this system to modify three glycoproteins with varying N-linked glycan compositions: the human therapeutic proteins alpha-1-antitrypsin (A1AT) and factor IX, as well as bovine fetuin. The chain length of the polysialic acid addition was optimized by controlling reaction conditions. After demonstrating the ability of this system to modify a variety of proteins, the effect of polysialylation on the activity and serum half-life of A1AT was examined. The polysialylation of A1AT did not adversely affect its in vitro inhibition activity against human neutrophil elastase. The polysialylation of A1AT resulted in a significantly improved pharmacokinetic profile when the modified proteins were injected into CD-1 mice. Together, these results suggest that polysialylated A1AT may be useful for improved augmentation therapy for patients with a deficiency in this protein and that this modification may be applied to other therapeutic proteins.
Therapeutic strategies to overcome crizotinib resistance in non-small cell lung cancers harboring the fusion oncogene EML4-ALK
Authors: Katayama Ryohei , Khan Tahsin M. , Benes Cyril , Lifshits Eugene , Ebi Hiromichi , Rivera Victor M. , Shakespeare William C. , Iafrate A. John , Engelman Jeffrey A. , Shaw Alice T.
Published: April 2011

The echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) fusion oncogene represents a molecular target in a small subset of non-small cell lung cancers (NSCLCs). This fusion leads to constitutive ALK activation with potent transforming activity. In a pivotal phase 1 clinical trial, the ALK tyrosine kinase inhibitor (TKI) crizotinib (PF-02341066) demonstrated impressive antitumor activity in the majority of patients with NSCLC harboring ALK fusions. However, despite these remarkable initial responses, cancers eventually develop resistance to crizotinib, usually within 1 y, thereby limiting the potential clinical benefit. To determine how cancers acquire resistance to ALK inhibitors, we established a model of acquired resistance to crizotinib by exposing a highly sensitive EML4-ALK–positive NSCLC cell line to increasing doses of crizotinib until resistance emerged. We found that cells resistant to intermediate doses of crizotinib developed amplification of the EML4-ALK gene. Cells resistant to higher doses (1 μM) also developed a gatekeeper mutation, L1196M, within the kinase domain, rendering EML4-ALK insensitive to crizotinib. This gatekeeper mutation was readily detected using a unique and highly sensitive allele-specific PCR assay. Although crizotinib was ineffectual against EML4-ALK harboring the gatekeeper mutation, we observed that two structurally different ALK inhibitors, NVP-TAE684 and AP26113, were highly active against the resistant cancer cells in vitro and in vivo. Furthermore, these resistant cells remained highly sensitive to the Hsp90 inhibitor 17-AAG. Thus, we have developed a model of acquired resistance to ALK inhibitors and have shown that second-generation ALK TKIs or Hsp90 inhibitors are effective in treating crizotinib-resistant tumors harboring secondary gatekeeper mutations.
Aprataxin localizes to mitochondria and preserves mitochondrial function
Authors: Sykora Peter , Croteau Deborah L. , Bohr Vilhelm A. , Wilson David M.
Published: April 2011

Ataxia with oculomotor apraxia 1 is caused by mutation in theAPTXgene, which encodes the DNA strand-break repair protein aprataxin. Aprataxin exhibits homology to the histidine triad superfamily of nucleotide hydrolases and transferases and removes 5′-adenylate groups from DNA that arise from aborted ligation reactions. We report herein that aprataxin localizes to mitochondria in human cells and we identify an N-terminal amino acid sequence that targets certain isoforms of the protein to this intracellular compartment. We also show that transcripts encoding this unique N-terminal stretch are expressed in the human brain, with highest production in the cerebellum. Depletion of aprataxin in human SH-SY5Y neuroblastoma cells and primary skeletal muscle myoblasts results in mitochondrial dysfunction, which is revealed by reduced citrate synthase activity and mtDNA copy number. Moreover, mtDNA, not nuclear DNA, was found to have higher levels of background DNA damage on aprataxin knockdown, suggesting a direct role for the enzyme in mtDNA processing.
Mice with behavioral evidence of tinnitus exhibit dorsal cochlear nucleus hyperactivity because of decreased GABAergic inhibition
Authors: Middleton Jason W. , Kiritani Taro , Pedersen Courtney , Turner Jeremy G. , Shepherd Gordon M. G. , Tzounopoulos Thanos
Published: April 2011

Tinnitus has been associated with increased spontaneous and evoked activity, increased neural synchrony, and reorganization of tonotopic maps of auditory nuclei. However, the neurotransmitter systems mediating these changes are poorly understood. Here, we developed an in vitro assay that allows us to evaluate the roles of excitation and inhibition in determining the neural correlates of tinnitus. To measure the magnitude and spatial spread of evoked circuit activity, we used flavoprotein autofluorescence (FA) imaging, a metabolic indicator of neuronal activity. We measured FA responses after electrical stimulation of glutamatergic axons in slices containing the dorsal cochlear nucleus, an auditory brainstem nucleus hypothesized to be crucial in the triggering and modulation of tinnitus. FA imaging in dorsal cochlear nucleus brain slices from mice with behavioral evidence of tinnitus (tinnitus mice) revealed enhanced evoked FA response at the site of stimulation and enhanced spatial propagation of FA response to surrounding sites. Blockers of GABAergic inhibition enhanced FA response to a greater extent in control mice than in tinnitus mice. Blockers of excitation decreased FA response to a similar extent in tinnitus and control mice. These findings indicate that auditory circuits in mice with behavioral evidence of tinnitus respond to stimuli in a more robust and spatially distributed manner because of a decrease in GABAergic inhibition.
Impact of daily temperature fluctuations on dengue virus transmission by
Aedes aegypti
Authors: Lambrechts Louis , Paaijmans Krijn P. , Fansiri Thanyalak , Carrington Lauren B. , Kramer Laura D. , Thomas Matthew B. , Scott Thomas W.
Published: April 2011

Most studies on the ability of insect populations to transmit pathogens consider only constant temperatures and do not account for realistic daily temperature fluctuations that can impact vector–pathogen interactions. Here, we show that diurnal temperature range (DTR) affects two important parameters underlying dengue virus (DENV) transmission by
Aedes aegypti
. In two independent experiments using different DENV serotypes, mosquitoes were less susceptible to virus infection and died faster under larger DTR around the same mean temperature. Large DTR (20 °C) decreased the probability of midgut infection, but not duration of the virus extrinsic incubation period (EIP), compared with moderate DTR (10 °C) or constant temperature. A thermodynamic model predicted that at mean temperatures <18 °C, DENV transmission increases as DTR increases, whereas at mean temperatures >18 °C, larger DTR reduces DENV transmission. The negative impact of DTR on
Ae. aegypti
survival indicates that large temperature fluctuations will reduce the probability of vector survival through EIP and expectation of infectious life. Seasonal variation in the amplitude of daily temperature fluctuations helps to explain seasonal forcing of DENV transmission at locations where average temperature does not vary seasonally and mosquito abundance is not associated with dengue incidence. Mosquitoes lived longer and were more likely to become infected under moderate temperature fluctuations, which is typical of the high DENV transmission season than under large temperature fluctuations, which is typical of the low DENV transmission season. Our findings reveal the importance of considering short-term temperature variations when studying DENV transmission dynamics.
Territorial behavior in Taiwanese kukrisnakes (Oligodon formosanus)
Authors: Huang Wen-San , Greene Harry W. , Chang Tien-Jye , Shine Richard
Published: April 2011

The independent evolutionary origin of a complex trait, within a lineage otherwise lacking it, provides a powerful opportunity to test hypotheses on selective forces. Territorial defense of an area containing resources (such as food or shelter) is widespread in lizards but not snakes. Our studies on an insular population of Taiwanese kukrisnakes (Oligodon formosanus) show that females of this species actively defend sea turtle nests by repelling conspecifics for long periods (weeks) until the turtle eggs hatch or are consumed. A clutch of turtle eggs comprises a large, long-lasting food resource, unlike the prey types exploited by other types of snakes. Snakes of this species have formidable weaponry (massively enlarged teeth that are used for slitting eggshells), and when threatened, these snakes wave their tails toward the aggressor (an apparent case of head-tail mimicry). Bites to the tail during intraspecific combat bouts thus can have high fitness costs for males (because the hemipenes are housed in the tail). In combination, unusual features of the species (ability to inflict severe damage to male conspecifics) and the local environment (a persistent prey resource, large relative to the snakes consuming it) render resource defense both feasible and advantageous for female kukrisnakes. The (apparently unique) evolution of territorial behavior in this snake species thus provides strong support for the hypothesis that resource defensibility is critical to the evolution of territoriality.
Normal and neoplastic nonstem cells can spontaneously convert to a stem-like state
Authors: Chaffer Christine L. , Brueckmann Ines , Scheel Christina , Kaestli Alicia J. , Wiggins Paul A. , Rodrigues Leonardo O. , Brooks Mary , Reinhardt Ferenc , Su Ying , Polyak Kornelia , Arendt Lisa M. , Kuperwasser Charlotte , Bierie Brian , Weinberg Robert A.
Published: April 2011

Current models of stem cell biology assume that normal and neoplastic stem cells reside at the apices of hierarchies and differentiate into nonstem progeny in a unidirectional manner. Here we identify a subpopulation of basal-like human mammary epithelial cells that departs from that assumption, spontaneously dedifferentiating into stem-like cells. Moreover, oncogenic transformation enhances the spontaneous conversion, so that nonstem cancer cells give rise to cancer stem cell (CSC)-like cells in vitro and in vivo. We further show that the differentiation state of normal cells-of-origin is a strong determinant of posttransformation behavior. These findings demonstrate that normal and CSC-like cells can arise de novo from more differentiated cell types and that hierarchical models of mammary stem cell biology should encompass bidirectional interconversions between stem and nonstem compartments. The observed plasticity may allow derivation of patient-specific adult stem cells without genetic manipulation and holds important implications for therapeutic strategies to eradicate cancer.
Perspectives of matrix convex functions
Authors: Ebadian Ali , Nikoufar Ismail , Eshaghi Gordji Madjid
Published: April 2011

In this paper, we generalize the main results of [Effros EG, (2009)
Proc Natl Acad. Sci USA
106:1006–1008]. Namely, we provide the necessary and sufficient conditions for jointly convexity of perspective functions and generalized perspective functions.
CD4
+
CD25
+
regulatory T cells control CD8
+
T-cell effector differentiation by modulating IL-2 homeostasis
Authors: McNally Alice , Hill Geoffrey R. , Sparwasser Tim , Thomas Ranjeny , Steptoe Raymond J.
Published: April 2011

CD4
+
CD25
+
regulatory T cells (Treg) play a crucial role in the regulation of immune responses. Although many mechanisms of Treg suppression in vitro have been described, the mechanisms by which Treg modulate CD8
+
T cell differentiation and effector function in vivo are more poorly defined. It has been proposed, in many instances, that modulation of cytokine homeostasis could be an important mechanism by which Treg regulate adaptive immunity; however, direct experimental evidence is sparse. Here we demonstrate that CD4
+
CD25
+
Treg, by critically regulating IL-2 homeostasis, modulate CD8
+
T-cell effector differentiation. Expansion and effector differentiation of CD8
+
T cells is promoted by autocrine IL-2 but, by competing for IL-2, Treg limit CD8
+
effector differentiation. Furthermore, a regulatory loop exists between Treg and CD8
+
effector T cells, where IL-2 produced during CD8
+
T-cell effector differentiation promotes Treg expansion.
Evidence for erythrocyte-binding antigen 175 as a component of a ligand-blocking blood-stage malaria vaccine
Authors: Jiang Lubin , Gaur Deepak , Mu Jianbing , Zhou Hong , Long Carole A. , Miller Louis H.
Published: April 2011

The ligands that pathogens use to invade their target cells have often proven to be good targets for vaccine development. However,
Plasmodium falciparum
has redundant ligands that mediate invasion of erythrocytes. The first requirement for the development of a successful ligand-blocking malaria vaccine is the demonstration that antibodies induced to each ligand can block the erythrocyte invasion of parasites with polymorphic sequences. Because of
P. falciparum
’s redundancy in erythrocyte invasion, each ligand needs to be studied under artificial conditions in which parasite invasion is restricted in its use of alternative pathways. Here we investigate the role of erythrocyte-binding antigen 175 (EBA-175), a parasite ligand that binds to sialic acid on glycophorin A, in the invasion of erythrocytes by 10
P. falciparum
clones under conditions in which invasion is partially limited to the EBA-175–glycophorin A pathway, using chymotrypsin-treated erythrocytes. We show that the ability to invade erythrocytes for both sialic acid–independent and sialic acid–dependent pathways requires the EBA-175–glycophorin A pathway for erythrocyte invasion. Importantly, antibodies against region II of EBA-175 from the 3D7 clone blocked invasion of chymotrypsin-treated erythrocytes by >50% by all parasite clones studied, including those with multiple different mutations described in the literature. The one exception was FCR3, which had a similar sequence to 3D7 but only 30% inhibition of invasion of chymotrypsin-treated erythrocytes, indicating alternative pathways for invasion of chymotrypsin-treated erythrocytes. Our findings suggest that antibodies to region II of EBA-175, as one component of a ligand-blocking malaria vaccine, are largely unaffected by polymorphism in EBA-175.
Ac conductivity and dielectric properties of CuFe1−xCrxO2 : Mg delafossite
Authors: Lalanne M , Demont P , Barnabé A
Published: April 2011

The electrical and dielectric properties of CuFe1−x
Cr
x
O2 (0 ⩽ x ⩽ 1) powders, doped with 3% of Mg and prepared by solid-state reaction, were studied by broadband dielectric spectroscopy in the temperature range from −100 to 150 °C. The frequency-dependent electrical and dielectric data have been discussed in the framework of a power law conductivity and complex impedance and dielectric modulus. At room temperature, the ac conductivity behaviour is characteristic of the charge transport in CuFe1−x
Cr
x
O2 powders. The substitution of Fe3+ by Cr3+ results in an increase in dc conductivity and a decrease in the Cu+–Cu+ distance. Dc conductivity, characteristic onset frequency and Havriliak–Negami characteristics relaxation times are thermally activated above −40 °C for x = 0.835. The associated activation energies obtained from dc and ac conductivity and from impedance and modulus losses are similar and show that CuFe1−x
Cr
x
O2 delafossite powders satisfy the BNN relation. Dc and ac conductivities have the same transport mechanism, namely thermally activated nearest neighbour hopping and tunnelling hopping above and below −40 °C, respectively.
Towards the accurate electronic structure descriptions of typical high-constant dielectrics
Authors: Jiang Ting-Ting , Sun Qing-Qing , Li Ye , Guo Jiao-Jiao , Zhou Peng , Ding Shi-Jin , Zhang David Wei
Published: April 2011

High-constant dielectrics have gained considerable attention due to their wide applications in advanced devices, such as gate oxides in metal–oxide–semiconductor devices and insulators in high-density metal–insulator–metal capacitors. However, the theoretical investigations of these materials cannot fulfil the requirement of experimental development, especially the requirement for the accurate description of band structures. We performed first-principles calculations based on the hybrid density functionals theory to investigate several typical high-k dielectrics such as Al2O3, HfO2, ZrSiO4, HfSiO4, La2O3 and ZrO2. The band structures of these materials are well described within the framework of hybrid density functionals theory. The band gaps of Al2O3, HfO2, ZrSiO4, HfSiO4, La2O3 and ZrO2are calculated to be 8.0 eV, 5.6 eV, 6.2 eV, 7.1 eV, 5.3 eV and 5.0 eV, respectively, which are very close to the experimental values and far more accurate than those obtained by the traditional generalized gradient approximation method.
Expansion of the Surgical Apgar Score across All Surgical Subspecialties as a Means to Predict Postoperative Mortality
Authors: Reynolds Paul Q. , Sanders Neal W. , Schildcrout Jonathan S. , Mercaldo Nathaniel D. , St. Jacques Paul J.
Published: April 2011

Background

A surgical scoring system, akin to the obstetrician's Apgar score, has been developed to assess postoperative risk. To date, evaluation of this scoring system has been limited to general and vascular services. The authors attempt to externally validate and expand the Surgical Apgar Score across a wide breadth of surgical subspecialties.

Methods

Intraoperative data for 123,864 procedures including all surgical subspecialties were collected and associated with Surgical Apgar Scores (created by the summation of point values associated with the lowest mean arterial pressure, lowest heart rate, and estimated blood loss). Patients' death records were matched to the corresponding score, and logistic regression models were created in which mortality within 7, 30, and 90 days was regressed on the Apgar score.

Results

Lower Surgical Apgar Scores were associated with an increased risk of death. The magnitude of this association varied by subspecialty. Some subspecialties exhibited higher odds ratios, suggesting that the score is not as useful for them. For most of the subspecialties the association between the Apgar score and mortality decreased as the time since surgery increased, suggesting that predictive ability ceases to be helpful over time. After adjusting for the patient's American Society of Anesthesiologists classification, Apgar scores remained associated with death among most of the subspecialties.

Conclusion

A previously published methodology for calculating risk among general and vascular surgical patients can be applied across many surgical services to provide an objective means of predicting and communicating patient outcomes in surgery as well as planning potential interventions.
VATS Thymectomy for Nonthymomatous Myasthenia Gravis Standardized Outcome Assessment Using the Myasthenia Gravis Foundation of America Clinical Classification
Authors: Keating Cameron P. , Kong Yu X. , Tay Valerie , Knight Simon R. , Clarke C. Peter , Wright Gavin M.
Published: April 2011

Objective

Video-assisted thoracoscopic (VATS) thymectomy has been practiced in Australia for nearly two decades. Our aim was to assess the complete stable remission and asymptomatic disease rates after VATS thymectomy in nonthymomatous myasthenia gravis. There remains doubt that minimally invasive techniques achieve equal remission rates to open maximal operations. Therefore, we report our outcomes using the Myasthenia Gravis Foundation of America (MGFA) Clinical Classification and Kaplan-Meier analysis and compare the results to the literature.

Methods

A retrospective analysis of 78 consecutive patients undergoing right VATS thymectomy between April 1994 and March 2007 at two Thoracic Surgery Units in Melbourne, Australia, was undertaken. Patients with thymoma were excluded. Therefore, 57 patients were followed-up for a minimum of 12 months to apply the MGFA Clinical Classification. VATS thymectomy was performed by a three-port right side technique.

Results

The complete stable remission rate was 15% at 3 years and 28% at 5 years. The asymptomatic disease rate was 59% at 5 years. Median follow-up was 32 months. No prognostic factors for remission were identified. The overall morbidity rate was 14% (8/57).

Conclusions

Right VATS thymectomy achieves comparable remission and asymptomatic disease rates to other minimally invasive and open techniques when compared with studies using either MGFA or older criteria.