bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct printing of aligned carbon nanotube patterns for high-performance thin film devices
Authors: Im Jiwoon , Lee Il-Ha , Lee Byung Yang , Kim Byeongju , Park June , Yu Woojong , Kim Un Jeong , Lee Young Hee , Seong Maeng-Je , Lee Eun Hong , Min Yo-Sep , Hong Seunghun
Published: February 2009

The aligned assembly of carbon nanotubes (CNTs) on substrate presents a significant bottleneck in the fabrication of high-performance thin film devices. Here, we report a direct printing method to prepare laterally aligned thick CNT patterns over large surface regions. In this method, CNT forests were grown selectively on specific regions of one substrate, and the forest patterns were transferred on another SiO2 substrate in a laterally aligned formation while keeping their original shapes. The degree of alignment was characterized via electrical measurement and polarized Raman spectroscopy. Furthermore, we demonstrated high-performance field-effect transistors and gas sensors using our method.
Depletion of surface accumulation charge in InN by anodic oxidation
Authors: Denisenko A. , Pietzka C. , Chuvilin A. , Kaiser U. , Lu H. , Schaff W. J. , Kohn E.
Published: February 2009

Si-doped InN layer by molecular beam epitaxy was subjected to anodic oxidation in 0.1 M potassium hydroxide (KOH) electrolyte and characterized by electrochemical methods to derive carrier profile at the InN surface. The obtained results were compared to the characteristics of a planar resistor structure and vertical metal-oxide-semiconductor (MOS) diodes with Ni-metal contacts on the oxidized InN. Both measurements in electrolyte and in air confirmed the formation of a surface oxide layer after the anodic treatment and depletion of the surface accumulation charge of the as-grown InN. The upward band bending of InN at the oxide interface was also concluded from the analysis of capacitance-voltage characteristics of the MOS diodes. Transmission electron microscopy revealed a nonuniform oxide layer containing porelike structures of a few nanometers in diameter.
Ionization energy levels in Mn-doped InxGa1−xN alloys
Authors: Tablero C. , Martí A. , Luque A.
Published: February 2009

The Mn-doped InxGa1−xN alloys are very interesting because of the possibility of controlling the gap and the levels induced by the Mn doping. Most of the experimental and theoretical work has been carried out on the wurtzite structure and with x next to zero. However, two possible phases may coexist, although in different proportions, depending on experimental growth conditions. We present total-energy spin-polarized density-functional calculations and analyze some of their electronic properties interesting for both spintronic and optoelectronic applications. In particular, the ionization levels in the entire x range, as well as in the ordered wurtzite and zinc-blende ferromagnetic structures.
Modulating nanomagnetism in Ni80Fe20/(Ni,Fe)O thin films by tuning the interfacial microstructure using ion bombardment
Authors: Su Chyun.-H. , Lo Shen-Chuan , Lin K.-W. , van Lierop J. , Ouyang Hao
Published: February 2009

The strength, polarity, and temperature dependence of the exchange bias field in ferromagnet/antiferromagnet thin film systems depend critically on the nature of the interfacial microstructure. Using ion bombardment during film deposition, we have found a way to modulate the interface microstructure, providing unique control over the exchange bias magnetism. We demonstrate interfacial microstructure modulation in Ni80Fe20/(Ni,Fe)O thin films, where different ion bombardment energies alter the exchange coupling between the (Ni,Fe)O and Ni80Fe20 interfaces. One interface configuration provides positive or negative exchange coupling depending on whether the film was cooled with or without an external magnetic field, while another interface configuration results in the more typical negative exchange coupling independent of the field cooling.
Accumulation of fluorine in CF4 plasma-treated AlGaN∕GaN heterostructure interface: An experimental investigation
Authors: Basu Anirban , Adesida Ilesanmi
Published: February 2009

The impact of CF4 plasma treatment on the transport properties of the two dimensional electron gas (2DEG) in AlGaN∕GaN heterostrustures has been studied. Systematic Hall measurements of the plasma-treated samples show a large degradation in mobility and sheet concentration, which can be partially recovered with short-duration rapid thermal annealing. Further annealing progressively degrades both mobility and sheet concentration. Secondary ion mass spectrometry of the heterostructure reveals accumulation of fluorine at the AlGaN∕GaN interface close to the 2DEG channel as a result of annealing. Following our systematic electrical and analytical studies of the behavior of fluorine incorporated into the heterostructure epilayer due to bombardment, a vacancy-mediated postannealing redistribution of fluorine has been proposed.
Charge trapping induced by plasma in alumina electrode surface investigated by thermoluminescence and optically stimulated luminescence
Authors: Ambrico P. F. , Ambrico M. , Schiavulli L. , Ligonzo T. , Augelli V.
Published: February 2009

The plasma of a dielectric barrier discharge can fill traps in the alumina that cover the electrode. Trap energies and lifetimes are estimated by thermoluminescence and optically stimulated luminescence. Comparison with similar results for traps created by other radiation sources clarifies the mechanisms regulating this effect. Alumina’s trap energies are approximately 1 eV, and the traps remain active for several days after plasma exposure. These results could be important to keep dielectric barrier discharge plasmas uniform since a trapped charge can be an electron reservoir.
Two-photon excited whispering-gallery mode ultraviolet laser from an individual ZnO microneedle
Authors: Zhu G. P. , Xu C. X. , Zhu J. , Lv C. G. , Cui Y. P.
Published: February 2009

Wurtzite structural ZnO microneedles with hexagonal cross section were fabricated by vapor-phase transport method and an individual microneedle was employed as a lasing microcavity. Under excitation of a femtosecond pulse laser with 800 nm wavelength, the ultraviolet (UV) laser emission was obtained, which presented narrow linewidth and high Q value. The UV emission, resonant mechanism, and laser mode characteristics were discussed in detail. The results demonstrated that the UV laser originated from the whispering-gallery mode induced by two-photon absorption assisted by Rabi oscillation.
Multibits magnetic recording using a ferromagnetic element with shifted vortex core position
Authors: Piao Hong-Guang , Djuhana Dede , Oh Suhk-Kun , Yu Seong-Cho , Kim Dong-Hyun
Published: February 2009

We suggest a patterned ferromagnetic multibits element for an ultrahigh density magnetic recording media. The pattern is composed of a circular ferromagnetic disk in contact to four needle-shaped sharp equilateral triangles. By using micromagnetic simulation, we found that a spin configuration of circular ferromagnetic disk is modified with position of magnetic vortex core shifted from the center by selecting a specific combination of spin states of four needles. We explore the possibility of multibits recording by shifting magnetic vortex core position in the ferromagnetic element.
Landau level spectrum in a two-dimensional hole gas in C-doped (100) GaAs/Al0.4Ga0.6As square quantum well
Authors: Yuan Z. Q. , Du R. R. , Manfra M. J. , Pfeiffer L. N. , West K. W.
Published: February 2009

We study the Landau level spectrum of a two-dimensional hole gas in carbon δ-doped (100) GaAs/Al0.4Ga0.6As square quantum well (width of 15 nm) by means of microwave cyclotron resonance (CR) and tilted field magnetotransport. Only one type of hole, with an effective mass of 0.4me, was detected in CR. By analyzing the spin-splitting level coincident conditions at B∼1 T, we find that the effective g-factor is large enough to cause Landau level crossing even in zero tilt, and the product of gm∗ increases with total magnetic field.
Metallic conductivity and the role of copper in ZnO/Cu/ZnO thin films for flexible electronics
Authors: Sivaramakrishnan K. , Alford T. L.
Published: February 2009

ZnO/Cu/ZnO multilayer structures are obtained with the highest conductivity of dielectric-metal-dielectric films reported in literature with a carrier concentration of 1.2×1022 cm−3 and resistivity of 6.9×10−5 Ω-cm at the optimum copper layer thickness. The peak transmittance, photopic averaged transmittance, and Haacke figure of merit are 88%, 75%, and 8.7×10−3 Ω−1, respectively. The conduction mechanism involves metal to oxide carrier injection prior to the formation of a continuous metal conduction pathway. Optical transmission is elucidated in terms of copper’s absorption due to d-band to Fermi surface transitions at short wavelengths and reflectance combined with scattering losses at long wavelengths.
Gate voltage dependence on hot carrier degradation at an elevated temperature in a device with ultrathin silicon oxynitride
Authors: Jo Minseok , Kim Seonghyun , Cho Chunhum , Chang Man , Hwang Hyunsang
Published: February 2009

The effects of hot carrier stress (HCS) at elevated temperature on a device with ultrathin silicon oxynitride have been investigated. It was shown that the degradation of the device was more significant at elevated temperature compared with at room temperature. This behavior attributed to more generation of interface states due to an increase in the high-energy tail electrons. By the theory of electron-electron scattering, the threshold voltage shift was the most severe at the condition of VG>VD. However, based on the results of extrapolating the device lifetime, the worst case stress condition under HCS was the VG=VD condition at elevated temperature due to a higher generation rate.
Electronic transport and colossal electroresistance in SrTiO3:Nb-based Schottky junctions
Authors: Shang D. S. , Sun J. R. , Shi L. , Wang J. , Wang Z. H. , Shen B. G.
Published: February 2009

Current-voltage characteristics and colossal electroresistance (CER) have been experimentally investigated in the temperature range from 293 to 454 K for the Schottky junctions Au/SrTiO3:0.5 wt % Nb and Au/SrTiO3:0.05 wt % Nb. Both junctions show electron tunneling-dominated transport behavior. Postannealing of SrTiO3:0.05 wt % Nb in oxygen atmosphere causes a transition of the transport behavior from electron tunneling to thermionic emission. The CER effect appears in the junctions with the transport behavior dominated by electron tunneling and greatly weakens when thermionic emission prevails after postannealing. This result reveals the presence of a close relation between CER and electron tunneling.
Michigan State wins contest to host DOE’s rare isotope beam lab
Authors: Kramer David
Published: February 2009

The $550 million heavy ion accelerator will be an “incredible toy box” for nuclear physicists, says project director.
Preparing high-school physics teachers
Authors: Hodapp Theodore , Hehn Jack , Hein Warren
Published: February 2009

By taking on a significant part of the education of high-school physics teachers, physics departments in the US can inspire their students and help ensure a scientifically educated population.
Simon Newcomb, America’s first great astronomer
Authors: Carter William E. , Carter Merri Sue
Published: February 2009

In the late 19th century, Newcomb determined the scale of the solar system with an accuracy unrivaled until decades after his death.
Defined tuberculosis vaccine, Mtb72F/AS02A, evidence of protection in cynomolgus monkeys
Authors: Reed Steven G. , Coler Rhea N. , Dalemans Wilfried , Tan Esterlina V. , DeLa Cruz Eduardo C. , Basaraba Randall J. , Orme Ian M. , Skeiky Yasir A. W. , Alderson Mark R. , Cowgill Karen D. , Prieels Jean-Paul , Abalos Rodolfo M. , Dubois Marie-Claude , Cohen Joe , Mettens Pascal , Lobet Yves
Published: February 2009

The development of a vaccine for tuberculosis requires a combination of antigens and adjuvants capable of inducing appropriate and long-lasting T cell immunity. We evaluated Mtb72F formulated in AS02A in the cynomolgus monkey model. The vaccine was immunogenic and caused no adverse reactions. When monkeys were immunized with bacillus Calmette–Guérin (BCG) and then boosted with Mtb72F in AS02A, protection superior to that afforded by using BCG alone was achieved, as measured by clinical parameters, pathology, and survival. We observed long-term survival and evidence of reversal of disease progression in monkeys immunized with the prime-boost regimen. Antigen-specific responses from protected monkeys receiving BCG and Mtb72F/AS02A had a distinctive cytokine profile characterized by an increased ratio between 3 Th1 cytokines, IFN-γ, TNF, and IL-2 and an innate cytokine, IL-6. To our knowledge, this is an initial report of a vaccine capable of inducing long-term protection against tuberculosis in a nonhuman primate model, as determined by protection against severe disease and death, and by other clinical and histopathological parameters.
Early childhood stress is associated with elevated antibody levels to herpes simplex virus type 1
Authors: Shirtcliff Elizabeth A. , Coe Christopher L. , Pollak Seth D.
Published: February 2009

It is well known that children need solicitous parenting and a nurturing rearing environment to ensure their normal behavioral development. Early adversity often negatively impacts emotional and mental well-being, but it is less clearly established how much the maturation and regulation of physiological systems is also compromised. The following research investigated the effect of 2 different types of adverse childhood experiences, early deprivation through institutionalization and physical abuse, on a previously unexplored outcome: the containment of herpes simplex virus (HSV). The presence of HSV-specific antibody in salivary specimens was determined in 155 adolescents, including 41 postinstitutionalized, 34 physically-abused, and 80 demographically-similar control youth. Across 4 school and home days, HSV antibody was higher in both postinstitutionalized and physically-abused adolescents when compared with control participants. Because the prevalence of HSV infection was similar across the groups, the elevated antibody was likely indicative of viral recrudescence from latency. Total secretory Ig-A secretion was associated with HSV, but did not account for the group differences in HSV-specific antibody. These findings are likely caused by a failure of cellular immune processes to limit viral reactivation, indicating a persistent effect of early rearing on immune functioning. The fact that antibody profiles were still altered years after adoption into a more benevolent setting with supportive families suggests these results were not caused by contemporaneous factors, but rather reflect a lingering influence of earlier life experiences.
Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor
Authors: Segura Miguel F. , Hanniford Douglas , Menendez Silvia , Reavie Linsey , Zou Xuanyi , Alvarez-Diaz Silvia , Zakrzewski Jan , Blochin Elen , Rose Amy , Bogunovic Dusan , Polsky David , Wei Jianjun , Lee Peng , Belitskaya-Levy Ilana , Bhardwaj Nina , Osman Iman , Hernando Eva
Published: February 2009

The highly aggressive character of melanoma makes it an excellent model for probing the mechanisms underlying metastasis, which remains one of the most difficult challenges in treating cancer. We find that miR-182, member of a miRNA cluster in a chromosomal locus (7q31–34) frequently amplified in melanoma, is commonly up-regulated in human melanoma cell lines and tissue samples; this up-regulation correlates with gene copy number in a subset of melanoma cell lines. Moreover, miR-182 ectopic expression stimulates migration of melanoma cells in vitro and their metastatic potential in vivo, whereas miR-182 down-regulation impedes invasion and triggers apoptosis. We further show that miR-182 over-expression promotes migration and survival by directly repressing microphthalmia-associated transcription factor-M and FOXO3, whereas enhanced expression of either microphthalmia-associated transcription factor-M or FOXO3 blocks miR-182's proinvasive effects. In human tissues, expression of miR-182 increases with progression from primary to metastatic melanoma and inversely correlates with FOXO3 and microphthalmia-associated transcription factor levels. Our data provide a mechanism for invasion and survival in melanoma that could prove applicable to metastasis of other cancers and suggest that miRNA silencing may be a worthwhile therapeutic strategy.
Prediction of membrane protein structures with complex topologies using limited constraints
Authors: Barth P. , Wallner B. , Baker D.
Published: February 2009

Reliable structure-prediction methods for membrane proteins are important because the experimental determination of high-resolution membrane protein structures remains very difficult, especially for eukaryotic proteins. However, membrane proteins are typically longer than 200 aa and represent a formidable challenge for structure prediction. We have developed a method for predicting the structures of large membrane proteins by constraining helix–helix packing arrangements at particular positions predicted from sequence or identified by experiments. We tested the method on 12 membrane proteins of diverse topologies and functions with lengths ranging between 190 and 300 residues. Enforcing a single constraint during the folding simulations enriched the population of near-native models for 9 proteins. In 4 of the cases in which the constraint was predicted from the sequence, 1 of the 5 lowest energy models was superimposable within 4 Å on the native structure. Near-native structures could also be selected for heme-binding and pore-forming domains from simulations in which pairs of conserved histidine-chelating hemes and one experimentally determined salt bridge were constrained, respectively. These results suggest that models within 4 Å of the native structure can be achieved for complex membrane proteins if even limited information on residue-residue interactions can be obtained from protein structure databases or experiments.
Metamaterials and the Landau–Lifshitz permeability argument: Large permittivity begets high-frequency magnetism
Authors: Merlin Roberto
Published: February 2009

Homogeneous composites, or metamaterials, made of dielectric or metallic particles are known to show magnetic properties that contradict arguments by Landau and Lifshitz [Landau LD, Lifshitz EM (1960)
Electrodynamics of Continuous Media
(Pergamon, Oxford, UK), p 251], indicating that the magnetization and, thus, the permeability, loses its meaning at relatively low frequencies. Here, we show that these arguments do not apply to composites made of substances with Im

ε
S

≫ λ/ℓ or Re

ε
S

∼ λ/ℓ (ε
S
and ℓ are the complex permittivity and the characteristic length of the particles, and λ ≫ ℓ is the vacuum wavelength). Our general analysis is supported by studies of split rings, one of the most common constituents of electromagnetic metamaterials, and spherical inclusions. An analytical solution is given to the problem of scattering by a small and thin split ring of arbitrary permittivity. Results reveal a close relationship between ε
S
and the dynamic magnetic properties of metamaterials. For |

ε
S

| ≪ λ/
a
(
a
is the ring cross-sectional radius), the composites exhibit very weak magnetic activity, consistent with the Landau–Lifshitz argument and similar to that of molecular crystals. In contrast, large values of the permittivity lead to strong diamagnetic or paramagnetic behavior characterized by susceptibilities whose magnitude is significantly larger than that of natural substances. We compiled from the literature a list of materials that show high permittivity at wavelengths in the range 0.3–3000 μm. Calculations for a system of spherical inclusions made of these materials, using the magnetic counterpart to Lorentz–Lorenz formula, uncover large magnetic effects the strength of which diminishes with decreasing wavelength.
The transactivating function 1 of estrogen receptor α is dispensable for the vasculoprotective actions of 17β-estradiol
Authors: Billon-Galés Audrey , Fontaine Coralie , Filipe Cédric , Douin-Echinard Victorine , Fouque Marie-José , Flouriot Gilles , Gourdy Pierre , Lenfant Françoise , Laurell Henrik , Krust Andrée , Chambon Pierre , Arnal Jean-François
Published: February 2009

Full-length 66-kDa estrogen receptor α (ERα) stimulates target gene transcription through two activation functions (AFs), AF-1 in the N-terminal domain and AF-2 in the ligand binding domain. Another physiologically expressed 46-kDa ERα isoform lacks the N-terminal A/B domains and is consequently devoid of AF-1. Previous studies in cultured endothelial cells showed that the N-terminal A/B domain might not be required for estradiol (E2)-elicited NO production. To evaluate the involvement of ERα AF-1 in the vasculoprotective actions of E2, we generated a targeted deletion of the ERα A/B domain in the mouse. In these
ER
α
AF-1
0
mice, both basal endothelial NO production and reendothelialization process were increased by E2 administration to a similar extent than in control mice. Furthermore, exogenous E2 similarly decreased fatty streak deposits at the aortic root from both ovariectomized 18-week-old
ER
α
AF-1
+/+
LDLr
−/−
(low-density lipoprotein receptor) and
ER
α
AF-1
0
LDLr
−/−
mice fed with a hypercholesterolemic diet. In addition, quantification of lesion size on
en face
preparations of the aortic tree of 8-month-old ovariectomized or intact female mice revealed that ERα AF-1 is dispensable for the atheroprotective action of endogenous estrogens. We conclude that ERα AF-1 is not required for three major vasculoprotective actions of E2, whereas it is necessary for the effects of E2 on its reproductive targets. Thus, selective ER modulators stimulating ERα with minimal activation of ERα AF-1 could retain beneficial vascular actions, while minimizing the sexual effects.
Disentangling prenatal and inherited influences in humans with an experimental design
Authors: Rice Frances , Harold Gordon T. , Boivin Jacky , Hay Dale F. , van den Bree Marianne , Thapar Anita
Published: February 2009

Exposure to adversity in utero at a sensitive period of development can bring about physiological, structural, and metabolic changes in the fetus that affect later development and behavior. However, the link between prenatal environment and offspring outcomes could also arise and confound because of the relation between maternal and offspring genomes. As human studies cannot randomly assign offspring to prenatal conditions, it is difficult to test whether in utero events have true causal effects on offspring outcomes. We used an unusual approach to overcome this difficulty whereby pregnant mothers are either biologically unrelated or related to their child as a result of in vitro fertilization (IVF). In this sample, prenatal smoking reduces offspring birth weight in both unrelated and related offspring, consistent with effects arising through prenatal mechanisms independent of the relation between the maternal and offspring genomes. In contrast, the association between prenatal smoking and offspring antisocial behavior depended on inherited factors because association was only present in related mothers and offspring. The results demonstrate that this unusual prenatal cross-fostering design is feasible and informative for disentangling inherited and prenatal effects on human health and behavior. Disentangling these different effects is invaluable for pinpointing markers of prenatal adversity that have a causal effect on offspring outcomes. The origins of behavior and many common complex disorders may begin in early life, therefore this experimental design could pave the way for identifying prenatal factors that affect behavior in future generations.
Protection of synapses against Alzheimer's-linked toxins: Insulin signaling prevents the pathogenic binding of Aβ oligomers
Authors: De Felice Fernanda G. , Vieira Marcelo N. N. , Bomfim Theresa R. , Decker Helena , Velasco Pauline T. , Lambert Mary P. , Viola Kirsten L. , Zhao Wei-Qin , Ferreira Sergio T. , Klein William L.
Published: February 2009

Synapse deterioration underlying severe memory loss in early Alzheimer's disease (AD) is thought to be caused by soluble amyloid beta (Aβ) oligomers. Mechanistically, soluble Aβ oligomers, also referred to as Aβ-derived diffusible ligands (ADDLs), act as highly specific pathogenic ligands, binding to sites localized at particular synapses. This binding triggers oxidative stress, loss of synaptic spines, and ectopic redistribution of receptors critical to plasticity and memory. We report here the existence of a protective mechanism that naturally shields synapses against ADDL-induced deterioration. Synapse pathology was investigated in mature cultures of hippocampal neurons. Before spine loss, ADDLs caused major downregulation of plasma membrane insulin receptors (IRs), via a mechanism sensitive to calcium calmodulin-dependent kinase II (CaMKII) and casein kinase II (CK2) inhibition. Most significantly, this loss of surface IRs, and ADDL-induced oxidative stress and synaptic spine deterioration, could be completely prevented by insulin. At submaximal insulin doses, protection was potentiated by rosiglitazone, an insulin-sensitizing drug used to treat type 2 diabetes. The mechanism of insulin protection entailed a marked reduction in pathogenic ADDL binding. Surprisingly, insulin failed to block ADDL binding when IR tyrosine kinase activity was inhibited; in fact, a significant increase in binding was caused by IR inhibition. The protective role of insulin thus derives from IR signaling-dependent downregulation of ADDL binding sites rather than ligand competition. The finding that synapse vulnerability to ADDLs can be mitigated by insulin suggests that bolstering brain insulin signaling, which can decline with aging and diabetes, could have significant potential to slow or deter AD pathogenesis.
Predicting human resting-state functional connectivity from structural connectivity
Authors: Honey C. J. , Sporns O. , Cammoun L. , Gigandet X. , Thiran J. P. , Meuli R. , Hagmann P.
Published: February 2009

In the cerebral cortex, the activity levels of neuronal populations are continuously fluctuating. When neuronal activity, as measured using functional MRI (fMRI), is temporally coherent across 2 populations, those populations are said to be functionally connected. Functional connectivity has previously been shown to correlate with structural (anatomical) connectivity patterns at an aggregate level. In the present study we investigate, with the aid of computational modeling, whether systems-level properties of functional networks—including their spatial statistics and their persistence across time—can be accounted for by properties of the underlying anatomical network. We measured resting state functional connectivity (using fMRI) and structural connectivity (using diffusion spectrum imaging tractography) in the same individuals at high resolution. Structural connectivity then provided the couplings for a model of macroscopic cortical dynamics. In both model and data, we observed (
i
) that strong functional connections commonly exist between regions with no direct structural connection, rendering the inference of structural connectivity from functional connectivity impractical; (
ii
) that indirect connections and interregional distance accounted for some of the variance in functional connectivity that was unexplained by direct structural connectivity; and (
iii
) that resting-state functional connectivity exhibits variability within and across both scanning sessions and model runs. These empirical and modeling results demonstrate that although resting state functional connectivity is variable and is frequently present between regions without direct structural linkage, its strength, persistence, and spatial statistics are nevertheless constrained by the large-scale anatomical structure of the human cerebral cortex.
Spatiotemporal structures in aging and rejuvenating glasses
Authors: Peter G. Wolynes
Published: February 2009

Complex spatiotemporal structures develop during the process of aging glasses after cooling and of rejuvenating glasses on heating. The key to understanding these structures is the interplay between the activated reconfiguration events that generate mobility and the transport of mobility. These effects are both accounted for by combining the random first-order transition theory of activated events with mode coupling theory in an inhomogeneous setting. The predicted modifications by mobility transport of the time course of the aging regime are modest. In contrast, the rejuvenation process is strongly affected through the propagation of fronts of enhanced mobility originating from the initial reconfiguration events. The structures in a rejuvenating glass resemble flames. An analysis along the lines of combustion theory provides an estimate of the front propagation speed. Heterogeneous rejuvenation naturally should occur for glasses with free surfaces. The analogy with combustion also provides a way of looking at the uptake of diluents by glasses described by case II and super case II diffusion.
Risk assessment in man and mouse
Authors: Balci Fuat , Freestone David , Gallistel Charles R.
Published: February 2009

Human and mouse subjects tried to anticipate at which of 2 locations a reward would appear. On a randomly scheduled fraction of the trials, it appeared with a short latency at one location; on the complementary fraction, it appeared after a longer latency at the other location. Subjects of both species accurately assessed the exogenous uncertainty (the probability of a short versus a long trial) and the endogenous uncertainty (from the scalar variability in their estimates of an elapsed duration) to compute the optimal target latency for a switch from the short- to the long-latency location. The optimal latency was arrived at so rapidly that there was no reliably discernible improvement over trials. Under these nonverbal conditions, humans and mice accurately assess risks and behave nearly optimally. That this capacity is well-developed in the mouse opens up the possibility of a genetic approach to the neurobiological mechanisms underlying risk assessment.
Evidence of cacao use in the Prehispanic American Southwest
Authors: Crown Patricia L. , Hurst W. Jeffrey
Published: February 2009

Chemical analyses of organic residues in fragments of ceramic vessels from Pueblo Bonito in Chaco Canyon, New Mexico, reveal theobromine, a biomarker for cacao. With an estimated 800 rooms, Pueblo Bonito is the largest archaeological site in Chaco Canyon and was the center of a large number of interconnected towns and villages spread over northwestern New Mexico. The cacao residues come from pieces of vessels that are likely cylinder jars, special containers occurring almost solely at Pueblo Bonito and deposited in caches at the site. This first known use of cacao drinks north of the Mexican border indicates exchange with cacao cultivators in Mesoamerica in a time frame of about A.D. 1000–1125. The association of cylinder jars and cacao beverages suggests that the Chacoan ritual involving the drinking of cacao was tied to Mesoamerican rituals incorporating cylindrical vases and cacao. The importance of Pueblo Bonito within the Chacoan world likely lies in part with the integration of Mesoamerican ritual, including critical culinary ingredients.
Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1
Authors: Chan Carol W. M. , Wong Newton A. , Liu Ying , Bicknell David , Turley Helen , Hollins Laura , Miller Crispin J. , Wilding Jennifer L. , Bodmer Walter F.
Published: February 2009

CDX1 is a transcription factor that plays a key role in intestinal development and differentiation. However, the downstream targets of CDX1 are less well defined than those of its close homologue, CDX2. We report here the identification of downstream targets of CDX1 using microarray gene-expression analysis and other approaches. Keratin 20 (KRT20), a member of the intermediate filament and a well-known marker of intestinal differentiation, was initially identified as one of the genes likely to be directly regulated by CDX1. CDX1 and KRT20 mRNA expression were significantly correlated in a panel of 38 colorectal cancer cell lines. Deletion and mutation analysis of the KRT20 promoter showed that the minimum regulatory region for the control of KRT20 expression by CDX1 is within 246 bp upstream of the KRT20 transcription start site. ChIP analysis confirmed that CDX1 binds to the predicted CDX elements in this region of the KRT20 promoter in vivo. In addition, immunohistochemistry showed expression of CDX1 parallels that of KRT20 in the normal crypt, which further supports their close relationship. In summary, our observations strongly imply that KRT20 is directly regulated by CDX1, and therefore suggest a role for CDX1 in maintaining differentiation in intestinal epithelial cells. Because a key feature of the development of a cancer is an unbalanced program of proliferation and differentiation, dysregulation of CDX1 may be an advantage for the development of a colorectal carcinoma. This could, therefore, explain the relatively frequent down regulation of CDX1 in colorectal carcinomas by hypermethylation.
Prevention of autoimmune disease by induction of tolerance to Toll-like receptor 7
Authors: Hayashi Tomoko , Gray Christine S. , Chan Michael , Tawatao Rommel I. , Ronacher Lisa , McGargill Maureen A. , Datta Sandip K. , Carson Dennis A. , Corr Maripat
Published: February 2009

Activation of Toll-like receptors (TLR) contributes to the initiation and maintenance of chronic inflammation in autoimmune diseases, yet repeated exposure to a TLR agonist can induce hyporesponsiveness to subsequent TLR stimulation. Here, we used a synthetic TLR7 agonist, 9-benzyl-8-hydroxy-2-(2-methoxyethoxy) adenine (SM360320, 1V136) to study TLR7 induced attenuation of inflammatory responses and its application to autoimmune diseases. Repeated low dose administration of this TLR7 agonist induced hyporesponsiveness or tolerance to TLR2, -7, and -9 activators and limited the course of neural inflammation in an experimental allergic encephalomyelitis model. The hyporesponsiveness did not depend on T or B lymphocytes, but did require bone marrow derived cells. In addition, TLR7 tolerance reduced inflammation in a passive antibody mediated arthritis model. TLR7 tolerance did not cause global immunosuppression, because susceptibility to Listeria monocytogenes infection was not altered. The mechanism of TLR7 tolerance involved the up-regulation of 2 inhibitors of TLR signaling: Interleukin 1 Receptor Associated Kinase (IRAK) M, and Src homology 2 domain-containing inositol polyphosphate phosphatase (SHIP)-1. These findings suggest that induction of TLR7 tolerance might be a new therapeutic approach to subdue inflammation in autoimmune diseases.
Strong profiling is not mathematically optimal for discovering rare malfeasors
Authors: Press William H.
Published: February 2009

The use of profiling by ethnicity or nationality to trigger secondary security screening is a controversial social and political issue. Overlooked is the question of whether such actuarial methods are in fact mathematically justified, even under the most idealized assumptions of completely accurate prior probabilities, and secondary screenings concentrated on the highest-probablity individuals. We show here that strong profiling (defined as screening at least in proportion to prior probability) is no more efficient than uniform random sampling of the entire population, because resources are wasted on the repeated screening of higher probability, but innocent, individuals. A mathematically optimal strategy would be “square-root biased sampling,” the geometric mean between strong profiling and uniform sampling, with secondary screenings distributed broadly, although not uniformly, over the population. Square-root biased sampling is a general idea that can be applied whenever a “bell-ringer” event must be found by sampling with replacement, but can be recognized (either with certainty, or with some probability) when seen.
Dendritic LSm1/CBP80-mRNPs mark the early steps of transport commitment and translational control
Authors: di Penta Alessandra , Mercaldo Valentina , Florenzano Fulvio , Munck Sebastian , Ciotti M. Teresa , Zalfa Francesca , Mercanti Delio , Molinari Marco , Bagni Claudia , Achsel Tilmann
Published: February 2009

Messenger RNA (mRNA) transport to neuronal dendrites is crucial for synaptic plasticity, but little is known of assembly or translational regulation of dendritic messenger ribonucleoproteins (mRNPs). Here we characterize a novel mRNP complex that is found in neuronal dendrites throughout the central nervous system and in some axonal processes of the spinal cord. The complex is characterized by the LSm1 protein, which so far has been implicated in mRNA degradation in nonneuronal cells. In brain, it associates with intact mRNAs. Interestingly, the LSm1-mRNPs contain the cap-binding protein CBP80 that associates with (pre)mRNAs in the nucleus, suggesting that the dendritic LSm1 complex has been assembled in the nucleus. In support of this notion, neuronal LSm1 is partially nuclear and inhibition of mRNA synthesis increases its nuclear localization. Importantly, CBP80 is also present in the dendrites and both LSm1 and CBP80 shift significantly into the spines upon stimulation of glutamergic receptors, suggesting that these mRNPs are translationally activated and contribute to the regulated local protein synthesis.
Antagonistic regulation of Fus2p nuclear localization by pheromone signaling and the cell cycle
Authors: Ydenberg Casey A. , Rose Mark D.
Published: February 2009

When yeast cells sense mating pheromone, they undergo a characteristic response involving changes in transcription, cell cycle arrest in early G1, and polarization along the pheromone gradient. Cells in G2/M respond to pheromone at the transcriptional level but do not polarize or mate until G1. Fus2p, a key regulator of cell fusion, localizes to the tip of the mating projection during pheromone-induced G1 arrest. Although Fus2p was expressed in G2/M cells after pheromone induction, it accumulated in the nucleus until after cell division. As cells arrested in G1, Fus2p was exported from the nucleus and localized to the nascent tip. Phosphorylation of Fus2p by Fus3p was required for Fus2p export; cyclin/Cdc28p-dependent inhibition of Fus3p during late G1 through S phase was sufficient to block exit. However, during G2/M, when Fus3p was activated by pheromone signaling, Cdc28p activity again blocked Fus2p export. Our results indicate a novel mechanism by which pheromone-induced proteins are regulated during the transition from mitosis to conjugation.
The mitotic spindle mediates inheritance of the Golgi ribbon structure
Authors: Wei Jen-Hsuan , Seemann Joachim
Published: February 2009

The mammalian Golgi ribbon disassembles during mitosis and reforms in both daughter cells after division. Mitotic Golgi membranes concentrate around the spindle poles, suggesting that the spindle may control Golgi partitioning. To test this, cells were induced to divide asymmetrically with the entire spindle segregated into only one daughter cell. A ribbon reforms in the nucleated karyoplasts, whereas the Golgi stacks in the cytoplasts are scattered. However, the scattered Golgi stacks are polarized and transport cargo. Microinjection of Golgi extract together with tubulin or incorporation of spindle materials rescues Golgi ribbon formation. Therefore, the factors required for postmitotic Golgi ribbon assembly are transferred by the spindle, but the constituents of functional stacks are partitioned independently, suggesting that Golgi inheritance is regulated by two distinct mechanisms.
From fish to amphibians to mammals: in search of novel strategies to optimize cardiac regeneration
Authors: Ausoni Simonetta , Sartore Saverio
Published: February 2009

Different vertebrate species have different cardiac regeneration rates: high in teleost fish, moderate in urodele amphibians, and almost negligible in mammals. Regeneration may occur through stem and progenitor cell differentiation or via dedifferentiation with residual cardiomyocytes reentering the cell cycle. In this review, we will examine the ability of zebrafish and newts to respond to cardiac damage with de novo cardiogenesis, whereas rodents and humans respond with a marked fibrogenic response and virtually no cardiomyocyte regeneration. Concerted strategies are needed to overcome this evolutionarily imposed barrier and optimize cardiac regeneration in mammals.
Down-regulation of Gfi-1 expression by TGF-β is important for differentiation of Th17 and CD103+ inducible regulatory T cells
Authors: Zhu Jinfang , Davidson Todd S. , Wei Gang , Jankovic Dragana , Cui Kairong , Schones Dustin E. , Guo Liying , Zhao Keji , Shevach Ethan M. , Paul William E.
Published: February 2009

Growth factor independent 1 (Gfi-1), a transcriptional repressor, is transiently induced during T cell activation. Interleukin (IL) 4 further induces Gfi-1, resulting in optimal Th2 cell expansion. We report a second important function of Gfi-1 in CD4 T cells: prevention of alternative differentiation by Th2 cells, and inhibition of differentiation of naive CD4 T cells to either Th17 or inducible regulatory T (iTreg) cells. In Gfi1−/− Th2 cells, the Rorc, Il23r, and Cd103 loci showed histone 3 lysine 4 trimethylation modifications that were lacking in wild-type Th2 cells, implying that Gfi-1 is critical for epigenetic regulation of Th17 and iTreg cell–related genes in Th2 cells. Enforced Gfi-1 expression inhibited IL-17 production and iTreg cell differentiation. Furthermore, a key inducer of both Th17 and iTreg cell differentiation, transforming growth factor β, repressed Gfi-1 expression, implying a reciprocal negative regulation of CD4 T cell fate determination. Chromatin immunoprecipitation showed direct binding of the Gfi-1–lysine-specific demethylase 1 repressive complex to the intergenic region of Il17a/Il17f loci and to intron 1 of Cd103. T cell–specific Gfi1 conditional knockout mice displayed a striking delay in the onset of experimental allergic encephalitis correlated with a dramatic increase of Foxp3+CD103+ CD4 T cells. Thus, Gfi-1 plays a critical role both in enhancing Th2 cell expansion and in repressing induction of Th17 and CD103+ iTreg cells.
CD4+ regulatory T cells require CTLA-4 for the maintenance of systemic tolerance
Authors: Friedline Randall H. , Brown David S. , Nguyen Hai , Kornfeld Hardy , Lee JinHee , Zhang Yi , Appleby Mark , Der Sandy D. , Kang Joonsoo , Chambers Cynthia A.
Published: February 2009

Cytotoxic T lymphocyte antigen-4 (CTLA-4) plays a critical role in negatively regulating T cell responses and has also been implicated in the development and function of natural FOXP3+ regulatory T cells. CTLA-4–deficient mice develop fatal, early onset lymphoproliferative disease. However, chimeric mice containing both CTLA-4–deficient and –sufficient bone marrow (BM)–derived cells do not develop disease, indicating that CTLA-4 can act in trans to maintain T cell self-tolerance. Using genetically mixed blastocyst and BM chimaeras as well as in vivo T cell transfer systems, we demonstrate that in vivo regulation of Ctla4−/− T cells in trans by CTLA-4–sufficient T cells is a reversible process that requires the persistent presence of FOXP3+ regulatory T cells with a diverse TCR repertoire. Based on gene expression studies, the regulatory T cells do not appear to act directly on T cells, suggesting they may instead modulate the stimulatory activities of antigen-presenting cells. These results demonstrate that CTLA-4 is absolutely required for FOXP3+ regulatory T cell function in vivo.
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
Authors: Hur Junguk , Schuyler Adam D. , States David J. , Feldman Eva L.
Published: February 2009

Summary:SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multiple sources. Ambiguous acronyms are resolved by a scoring scheme based on the co-occurrence of acronyms and corresponding description terms, which incorporates optional user-defined filters. Functional enrichment analyses are used to identify highly relevant targets (genes and proteins), GO (Gene Ontology) terms, MeSH (Medical Subject Headings) terms, pathways and protein–protein interaction networks by comparing identified targets from one search result with those from other searches or to the full HGNC [HUGO (Human Genome Organization) Gene Nomenclature Committee] gene set. The performance of gene/protein name identification was evaluated using the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) version 2 (Year 2006) Gene Normalization Task as a gold standard. SciMiner achieved 87.1% recall, 71.3% precision and 75.8% F-measure. SciMiner's literature mining performance coupled with functional enrichment analyses provides an efficient platform for retrieval and summary of rich biological information from corpora of users' interests.

Availability:  http://jdrf.neurology.med.umich.edu/SciMiner/. A server version of the SciMiner is also available for download and enables users to utilize their institution's journal subscriptions.

Contact:  juhur@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Benchmarking regulatory network reconstruction with GRENDEL
Authors: Haynes Brian C. , Brent Michael R.
Published: February 2009

Motivation: Over the past decade, the prospect of inferring networks of gene regulation from high-throughput experimental data has received a great deal of attention. In contrast to the massive effort that has gone into automated deconvolution of biological networks, relatively little effort has been invested in benchmarking the proposed algorithms. The rate at which new network inference methods are being proposed far outpaces our ability to objectively evaluate and compare them. This is largely due to a lack of fully understood biological networks to use as gold standards.

Results: We have developed the most realistic system to date that generates synthetic regulatory networks for benchmarking reconstruction algorithms. The improved biological realism of our benchmark leads to conclusions about the relative accuracies of reconstruction algorithms that are significantly different from those obtained with A-BIOCHEM, an established in silico benchmark.

Availability: The synthetic benchmark utility and the specific benchmark networks that were used in our analyses are available at http://mblab.wustl.edu/software/grendel/

Contact:  brent@cse.wustl.edu