bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of electron doping on thermoelectric properties for narrow-bandgap intermetallic compound RuGa2
Authors: Takagiwa Y. , Kitahara K. , Kimura K.
Published: January 2013

The maximum dimensionless figure of merit, ZTmax, as a function of the chemical potential of the narrow-bandgap intermetallic compound RuGa2 was calculated by using the Boltzmann transport equation with a simple rigid band approach under the constant relaxation time assumption. The calculation, including the effect of the group velocity, indicates that ZTmax over unity would be achieved by electron doping rather than hole doping. Based on this calculation, the effects of Ir substitution for Ru on the thermoelectric properties for RuGa2 have been investigated in the temperature range from 373 K to 973 K. Indeed, a relatively large ZT value of 0.31 for n-type material was obtained in the nominal composition of Ir3.0Ru30.4Ga66.6. The discussion includes the validity of the rigid band approximation and further enhancement of ZT from theoretical and experimental aspects.
Effect of Fe–O distance on magnetocrystalline anisotropy energy at the Fe/MgO(001) interface
Authors: Lee Sung-Chul , Kim Kwang-Seok , Lee Sung-Hoon , Pi Ung-Hwan , Kim Keewon , Jang Youngman , Chung U-In
Published: January 2013

We report first-principles calculations on the magnetocrystalline anisotropy energy (MAE) of an Fe monolayer sandwiched by MgO. We found that by increasing the interlayer distance between Fe and O by about 8% from its equilibrium value, the perpendicular interfacial magnetic anisotropy can be enhanced as high as 2.75 erg/cm2, which is three times larger than that at the equilibrium distance. The analysis of MAE based on the second-order interactions of the spin-orbit coupling shows that the energy position of the majority-spin dz2 orbital is of central importance in determining MAE. Our results suggest that increasing the Fe–O distance in the Fe/MgO system is an important material-design direction for high-performance magnetic memories.
Band offset determination of mixed As/Sb type-II staggered gap heterostructure for n-channel tunnel field effect transistor application
Authors: Zhu Y. , Jain N. , Mohata D. K. , Datta S. , Lubyshev D. , Fastenau J. M. , Liu A. K. , Hudait M. K.
Published: January 2013

The experimental study of the valence band offset (ΔEv) of a mixed As/Sb type-II staggered gap GaAs0.35Sb0.65/In0.7Ga0.3As heterostructure used as source/channel junction of n-channel tunnel field effect transistor (TFET) grown by molecular beam epitaxy was investigated by x-ray photoelectron spectroscopy (XPS). Cross-sectional transmission electron micrograph shows high crystalline quality at the source/channel heterointerface. XPS results demonstrate a ΔEv of 0.39 ± 0.05 eV at the GaAs0.35Sb0.65/In0.7Ga0.3As heterointerface. The conduction band offset was calculated to be ∼0.49 eV using the band gap values of source and channel materials and the measured valence band offset. An effective tunneling barrier height of 0.21 eV was extracted, suggesting a great promise for designing a metamorphic mixed As/Sb type-II staggered gap TFET device structure for low-power logic applications.
From circular to triangular alumina nanopore arrays via simple replication
Authors: Yu Guiduk , Shin Kyusoon
Published: January 2013

We found inverse-hexagonal packing pattern from self-assembled anodic aluminum oxide and exploited the pattern to obtain triangular pore array. By replicating the curved interface between aluminum and porous alumina, we fabricated a pattern with the opposite packing structure as well as the inversed pattern curvature. Anodization from the replicated structure formed triangular pores in inverse-hexagonal packing, whereas that from the original pattern produces circular pores in hexagonal packing. Our finding highlights the importance of the curvature as well as packing structure of pre-patterns in pore formation and achievement in the control via a simple replication process.
Two-path solid-state interferometry using ultra-subwavelength two-dimensional plasmonic waves
Authors: Yeung Kitty Y. M. , Yoon Hosang , Andress William , West Ken , Pfeiffer Loren , Ham Donhee
Published: January 2013

We report an on-chip solid-state Mach-Zehnder interferometer operating on two-dimensional (2D) plasmonic waves at microwave frequencies. Two plasmonic paths are defined with GaAs/AlGaAs 2D electron gas 80 nm below a metallic gate. The gated 2D plasmonic waves achieve a velocity of ∼c/300 (c: free-space light speed). Due to this ultra-subwavelength confinement, the resolution of the 2D plasmonic interferometer is two orders of magnitude higher than that of its electromagnetic counterpart at a given frequency. This gigahertz proof-of-concept at cryogenic temperatures can be scaled to the terahertz–infrared range for room temperature operation, while maintaining the benefits of ultra-subwavelength confinement.
Electrohydrodynamic printing under applied pole-type nozzle configuration
Authors: Xu Lei , Sun Daoheng
Published: January 2013

A pole-type nozzle has an inserted pole that jams a contraction flow into capillary in electrohydrodynamic deposition. The jammed solution improves Taylor cone formation by shortening the hysteresis time so that pole-type nozzle is suitable for high-resolution electrohydrodynamic printing. Experimental results demonstrate a governed frequency-dividing relationship with an integral ratio of applied voltage frequency to droplet deposition frequency. It is observed that low integral frequency ratio is in favor of low voltage amplitude and duty cycle, and high voltage frequency, since polymer solution jets in a small fluidic volume per droplet under low electric force and short pulse duration.
Spin pumping by nonreciprocal spin waves under local excitation
Authors: Iguchi R. , Ando K. , Qiu Z. , An T. , Saitoh E. , Sato T.
Published: January 2013

We measured spatial distribution of spin pumping by nonreciprocal magnetostatic surface waves (MSSWs) using inverse spin Hall effect (ISHE) in a YIG/Pt system under local excitation. The local intensity of spin pumping by MSSWs shows center displacement of ± 0.1 mm from the center of a waveguide according to the reversal of a bias field, which is due to the nonreciprocal propagation of MSSWs over a macroscopic distance. The combination of spin pumping and ISHE enables electrical investigation of local spin dynamics in a magnetic insulator.
X-ray diffraction analysis and Monte Carlo simulations of CoFeB-MgO based magnetic tunnel junctions
Authors: Kanak J. , Wiśniowski P. , Stobiecki T. , Zaleski A. , Powroźnik W. , Cardoso S. , Freitas P. P.
Published: January 2013

Here, we present the x-ray diffraction (XRD) analysis of a pseudo spin valve (P-SV): CoFeB/MgO/CoFeB and an exchange bias spin valve (EB-SV): PtMn/CoFe/Ru/CoFeB/MgO/CoFeB magnetic tunnel junctions where the composition of CoFeB was (Co52Fe48)75B25. In the P-SV, CoFeB layers crystallized into a highly bcc (001)-oriented CoFe texture while in the EB-SV, CoFeB crystallized into both (001)-oriented and (110)-oriented textures. Moreover, CoFeB crystallized better into the (001)-oriented texture when deposited on MgO than on a Ru layer. The P-SV and EB-SV devices with layer structures equivalent to the XRD samples, showed tunneling magnetoresistance of 240% and 180%, respectively. The Ru and Ta buffer layers annealed at 340 °C mixed at the interface. The simulated crystalline structure and calculated θ-2θ profiles, using kinematical theory of x-ray scattering, correlated very well with the experimental profiles and confirmed Ta-Ru intermixing.
Epitaxial MgO/Fe(001) and Fe/MgO(001): Structures of the interfaces
Authors: Młyńczak E. , Freindl K. , Spiridis N. , Korecki J.
Published: January 2013

The chemical, electronic and magnetic structures of the interfaces between Fe(001) and MgO(001) thin films were studied using conversion electron Mössbauer spectroscopy (CEMS). A 1 ML thick 57Fe probe located at either of the interfaces in the MgO/56Fe/MgO epitaxial structure enabled precise measurements of the interfacial hyperfine interactions. Analysis of the CEMS spectra showed that both the “MgO/Fe” and “Fe/MgO” interfaces are partially oxidized (63% and 86%, respectively), although, despite good crystallinity, no well-defined iron oxide phases were detected. At the “MgO/Fe” interface, 14% of the oxidized Fe sites were found to be defective (located at steps, corners or kinks). The “Fe/MgO” interface, from which the formation of 57Fe islands of at least 3 ML in height was inferred, was found to be almost defect-free. No modification of the hyperfine parameters of Fe atoms located away from the interface was detected for “Fe/MgO,” in contrast with the “MgO/Fe” interface. Approximately 6% of the probe layer diffused into the MgO films at both interfaces.
A hemodynamics model to study the collective behavior of the ventricular-arterial system
Authors: Lin Wang Yuh-Ying , Wang Wei-Kung
Published: January 2013

Applying principles from complex systems to study the efficacy of integrative therapies has become a new interest in medical research. We aimed to construct a concise model for the ventricular-arterial (VA) system and to provide a systematic method for exploring its overall behavior. The transportation of blood from the heart to the peripheral arterioles via hydraulic pressure forces was described by a multi-rank model. Parts of the VA system that have strong mutual interactions were combined into a single sub system. Sub systems of four different ranks were characterized. We then applied the multi-rank model to analyze the aortic pressure wave generated by the periodic ventricular blood ejection, the renal pressure in response to the input from the VA system, and the blood flowing from the renal artery to its arterioles. Maintaining the pressure distribution along the main arteries and in all of the organs with the lowest possible ventricular input turned out to be the first principle for the operation of an efficient VA system. By this principle, we pointed out the benefit of some arterial structures in mammals, derived specific regulation rules and deduced some fundamental concepts for healing. The justification of the biomechanics in our model that differed greatly from those in the prevailing models was given. We concluded that the oscillatory motion and the pressure pulse of the arterial system can be analyzed as steady states with resonance behaviors and suggested utilizing this model to construct integrative therapies for diseases correlated with abnormality in blood circulation.
Stand-alone micro-hydro power plant with induction generator supplying single phase loads
Authors: Ion C. P. , Marinescu C.
Published: January 2013

Micro-hydro power plants less than 10 kW usually supply isolated networks. This paper presents a new control method for a stand-alone three-phase induction generator supplying single-phase loads. Besides voltage and frequency regulation, the phase balancing should be ensured for this particular operating regime. The proposed control topology relies on a combination between a voltage source inverter (VSI) and a dump load (DL). The VSI imposes the system frequency and performs the unbalances compensation, while the DL deals with the voltage regulation. Through simulations and experiments, the reliability of such a configuration is tested when supplying varying loads. The results show a stable operation for a wide range of loads, during both steady-state and transitory regimes; moreover, the maximum obtained power in single-phase mode of operation is close to the generator rating in three-phase mode of operation.
Experimental investigation of the effect of using closed-loop pulsating heat pipe on the performance of a flat plate solar collector
Authors: Kargarsharifabad H. , Mamouri S. Jahangiri , Shafii M. B. , Rahni M. Taeibi
Published: January 2013

In this study, performance of a flat plate solar collector operating in conjunction with a closed-loop pulsating heat pipe is investigated experimentally. The experiments were carried out in Yazd, Iran. The experimental setup consisted of a flat plate solar collector, pulsating heat pipe, and a tank. The pulsating heat pipe's evaporator is located inside the flat plate collector. In order to investigate the effect of the evaporator length on the efficiency of the system, three different length collectors are manufactured in the evaporating section. In addition, the effects of the pulsating heat pipe filling ratio, inclination angle, and flow rate are investigated for each collector separately. Although the increase in the length of the evaporator adversely affects the convectional heat transfer, the results do not show a noticeable deterioration in the performance of the flat plate solar collector. The optimum value of the filling ratio of the pulsating heat pipe in all three devices was measured at 30%, regardless of the length of the evaporator. Finally by varying the inclination angle to maximize the value of solar radiation, the study determined that the optimal tilt angle occurred at 20°.
A biomass briquetting fuel machine and its large-scale operation system
Authors: Lei Tingzhou , Wang Zhiwei , Li Zaifeng , Xu Jiufeng , He Xiaofeng , Zhu Jinling
Published: January 2013

Biomass such as agricultural and forestry residues is an important resource for energy. Biomass can be converted into densified solid biofuel by briquetting fuel technology to increase the number of applications and enhance its utilization efficiency. In this study, a flat die press machine was designed and studied to realize characteristics of a broad range of feedstock, variable briquetting diameter and length, high briquetting efficiency, easy process control, low processing noise, and low energy consumption. Different experiments were conducted to ensure suitability for large-scale operations while reducing energy consumption, enhancing yield, and lowering product costs. The biomass briquetting fuel system equipment was integrated, and the system could adjust its overall running conditions automatically according to the feed rate, chopping rate, heat supply, output, and feedstock moisture content, allowing for continuous integrated operation. In addition, a biomass hot-blast furnace was used as a drying machine and burned biomass material rather than fossil fuels. This study of biomass briquetting technology supports the large-scale production of densified solid biofuel through the use of biomass resources.
A first-principles investigation of the optical spectra of oxidized graphene
Authors: Singh N. , Kaloni T. P. , Schwingenschlögl U.
Published: January 2013

The electronic and optical properties of mono, di, tri, and tetravacancies in graphene are studied in comparison to each other, using density functional theory. In addition, oxidized monovacancies are considered for different oxygen concentrations. Pristine graphene is found to be more absorptive than any defect configuration at low energy. We demonstrate characteristic differences in the optical spectra of the various defects for energies up to 3 eV. This makes it possible to quantify by optical spectroscopy the ratios of the defect species present in a sample.
Convenient Ambient Temperature Generation of Sulfonyl Radicals
Authors: Gilmore Kerry , Gold Brian , Clark Ronald J. , Alabugin Igor V.
Published: January 2013

Presented herein is a novel method for the efficient, ambient temperature generation of sulfonyl radicals from aryl and alkyl sulfonylbromides upon autoxidation of triethylborane (Et3B). The resultant radicals were regioselectively trapped via addition to terminal alkynes, generating a secondary vinyl radical that selectively abstracts a Br atom from RSO2Br, yielding the (E)-bromo vinylsulfones. Sensitivity towards Lewis basic groups was observed, presumably due to the disruptive coordination to Et3B before atom-transfer.
Role of poly(ADP-ribose) polymerase-1 in the removal of UV-induced DNA lesions by nucleotide excision repair
Authors: Robu Mihaela , Shah Rashmi G. , Petitclerc Nancy , Brind’Amour Julie , Kandan-Kulangara Febitha , Shah Girish M.
Published: January 2013

Among the earliest responses of mammalian cells to DNA damage is catalytic activation of a nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1). Activated PARP-1 forms the polymers of ADP-ribose (pADPr or PAR) that posttranslationally modify its target proteins, such as PARP-1 and DNA repair–related proteins. Although this metabolism is known to be implicated in other repair pathways, here we show its role in the versatile nucleotide excision repair pathway (NER) that removes a variety of DNA damages including those induced by UV. We show that PARP inhibition or specific depletion of PARP-1 decreases the efficiency of removal of UV-induced DNA damage from human skin fibroblasts or mouse epidermis. Using NER-proficient and -deficient cells and in vitro PARP-1 assays, we show that damaged DNA-binding protein 2 (DDB2), a key lesion recognition protein of the global genomic subpathway of NER (GG-NER), associates with PARP-1 in the vicinity of UV-damaged chromatin, stimulates its catalytic activity, and is modified by pADPr. PARP inhibition abolishes UV-induced interaction of DDB2 with PARP-1 or xeroderma pigmentosum group C (XPC) and also decreases localization of XPC to UV-damaged DNA, which is a key step that leads to downstream events in GG-NER. Thus, PARP-1 collaborates with DDB2 to increase the efficiency of the lesion recognition step of GG-NER.
Antibodies are necessary for rVSV/ZEBOV-GP–mediated protection against lethal Ebola virus challenge in nonhuman primates
Authors: Marzi Andrea , Engelmann Flora , Feldmann Friederike , Haberthur Kristen , Shupert W. Lesley , Brining Douglas , Scott Dana P. , Geisbert Thomas W. , Kawaoka Yoshihiro , Katze Michael G. , Feldmann Heinz , Messaoudi Ilhem
Published: January 2013

Ebola viruses cause hemorrhagic disease in humans and nonhuman primates with high fatality rates. These viruses pose a significant health concern worldwide due to the lack of approved therapeutics and vaccines as well as their potential misuse as bioterrorism agents. Although not licensed for human use, recombinant vesicular stomatitis virus (rVSV) expressing the filovirus glycoprotein (GP) has been shown to protect macaques from Ebola virus and Marburg virus infections, both prophylactically and postexposure in a homologous challenge setting. However, the immune mechanisms of protection conferred by this vaccine platform remain poorly understood. In this study, we set out to investigate the role of humoral versus cellular immunity in rVSV vaccine-mediated protection against lethal
Zaire ebolavirus
(ZEBOV) challenge. Groups of cynomolgus macaques were depleted of CD4+ T, CD8+ T, or CD20+ B cells before and during vaccination with rVSV/ZEBOV-GP. Unfortunately, CD20-depleted animals generated a robust IgG response. Therefore, an additional group of vaccinated animals were depleted of CD4+ T cells during challenge. All animals were subsequently challenged with a lethal dose of ZEBOV. Animals depleted of CD8+ T cells survived, suggesting a minimal role for CD8+ T cells in vaccine-mediated protection. Depletion of CD4+ T cells during vaccination caused a complete loss of glycoprotein-specific antibodies and abrogated vaccine protection. In contrast, depletion of CD4+ T cells during challenge resulted in survival of the animals, indicating a minimal role for CD4+ T-cell immunity in rVSV-mediated protection. Our results suggest that antibodies play a critical role in rVSV-mediated protection against ZEBOV.
RNF2/Ring1b negatively regulates p53 expression in selective cancer cell types to promote tumor development
Authors: Su Wen-jing , Fang Jun-shun , Cheng Feng , Liu Chao , Zhou Fang , Zhang Jian
Published: January 2013

Large numbers of studies have focused on the posttranslational regulation of p53 activity. One of the best-known negative regulators for p53 is MDM2, an E3 ubiquitin ligase that promotes p53 degradation through proteasome degradation pathways. Additional E3 ligases have also been reported to negatively regulate p53. However, whether these E3 ligases have distinct/overlapping roles in the regulation of p53 is largely unknown. In this study, we identify RNF2 (ring finger protein 2) as an E3 ligase that targets p53 for degradation. The E3 ligase activity of RNF2 requires Bmi1 protein, a component of the polycomb group (PcG) complex. The up-regulation of p53 does not affect RNF2 expression. Unlike Mdm2, RNF2 only degrades p53 in selective cell lines, such as those from germ-cell tumors. The knockdown of
RNF2
induces apoptosis, which can be rescued through the reduction of p53 expression. Moreover, the down-regulation of RNF2 expression in germ-cell tumors significantly reduces tumor cell growth, while the simultaneous down-regulation of both genes restores tumor cell growth in vitro and in tumor xenograft models. Furthermore, a reverse correlation between RNF2 and p53 expression was detected in human ovarian cancer tissues. Together, these results indicate that RNF2 is an E3 ligase for p53 degradation in selective cells, implicating RNF2 as a therapeutic target to restore tumor suppression through p53 in certain tumor cells.
Genome-wide data substantiate Holocene gene flow from India to Australia
Authors: Pugach Irina , Delfin Frederick , Gunnarsdóttir Ellen , Kayser Manfred , Stoneking Mark
Published: January 2013

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.
Nerve growth factor scales endocannabinoid signaling by regulating monoacylglycerol lipase turnover in developing cholinergic neurons
Authors: Keimpema Erik , Tortoriello Giuseppe , Alpár Alán , Capsoni Simona , Arisi Ivan , Calvigioni Daniela , Hu Sherry Shu-Jung , Cattaneo Antonino , Doherty Patrick , Mackie Kenneth , Harkany Tibor
Published: January 2013

Endocannabinoid, particularly 2-arachidonoyl glycerol (2-AG), signaling has recently emerged as a molecular determinant of neuronal migration and synapse formation during cortical development. However, the cell type specificity and molecular regulation of spatially and temporally confined morphogenic 2-AG signals remain unexplored. Here, we demonstrate that genetic and pharmacological manipulation of CB
1
cannabinoid receptors permanently alters cholinergic projection neuron identity and hippocampal innervation. We show that nerve growth factor (NGF), implicated in the morphogenesis and survival of cholinergic projection neurons, dose-dependently and coordinately regulates the molecular machinery for 2-AG signaling via tropomyosine kinase A receptors in vitro. In doing so, NGF limits the sorting of monoacylglycerol lipase (MGL), rate limiting 2-AG bioavailability, to proximal neurites, allowing cell-autonomous 2-AG signaling at CB
1
cannabinoid receptors to persist at atypical locations to induce superfluous neurite extension. We find that NGF controls MGL degradation in vitro and in vivo and identify the E3 ubiquitin ligase activity of breast cancer type 1 susceptibility protein (BRCA1) as a candidate facilitating MGL’s elimination from motile neurite segments, including growth cones. BRCA1 inactivation by cisplatin or genetically can rescue and reposition MGL, arresting NGF-induced growth responses. These data indicate that NGF can orchestrate endocannabinoid signaling to promote cholinergic differentiation and implicate BRCA1 in determining neuronal morphology.
High throughput kinase inhibitor screens reveal TRB3 and MAPK-ERK/TGFβ pathways as fundamental Notch regulators in breast cancer
Authors: Izrailit Julia , Berman Hal K. , Datti Alessandro , Wrana Jeffrey L. , Reedijk Michael
Published: January 2013

Expression of the Notch ligand Jagged 1 (JAG1) and Notch activation promote poor-prognosis in breast cancer. We used high throughput screens to identify elements responsible for Notch activation in this context. Chemical kinase inhibitor and kinase-specific small interfering RNA libraries were screened in a breast cancer cell line engineered to report Notch. Pathway analyses revealed MAPK-ERK signaling to be the predominant JAG1/Notch regulator and this was supported by gene set enrichment analyses in 51 breast cancer cell lines. In accordance with the chemical screen, kinome small interfering RNA high throughput screens identified Tribbles homolog 3 (TRB3), a known regulator of MAPK-ERK, among the most significant hits. We demonstrate that TRB3 is a master regulator of Notch through the MAPK-ERK and TGFβ pathways. Complementary in vitro and in vivo studies underscore the importance of TRB3 for tumor growth. These data demonstrate a dominant role for TRB3 and MAPK-ERK/TGFβ pathways as Notch regulators in breast cancer, establishing TRB3 as a potential therapeutic target.
Coupling of functional connectivity and regional cerebral blood flow reveals a physiological basis for network hubs of the human brain
Authors: Liang Xia , Zou Qihong , He Yong , Yang Yihong
Published: January 2013

Human brain functional networks contain a few densely connected hubs that play a vital role in transferring information across regions during resting and task states. However, the relationship of these functional hubs to measures of brain physiology, such as regional cerebral blood flow (rCBF), remains incompletely understood. Here, we used functional MRI data of blood-oxygenation-level–dependent and arterial-spin–labeling perfusion contrasts to investigate the relationship between functional connectivity strength (FCS) and rCBF during resting and an
N
-back working-memory task. During resting state, functional brain hubs with higher FCS were identified, primarily in the default-mode, insula, and visual regions. The FCS showed a striking spatial correlation with rCBF, and the correlation was stronger in the default-mode network (DMN; including medial frontal-parietal cortices) and executive control network (ECN; including lateral frontal-parietal cortices) compared with visual and sensorimotor networks. Moreover, the relationship was connection–distance dependent; i.e., rCBF correlated stronger with long-range hubs than short-range ones. It is notable that several DMN and ECN regions exhibited higher rCBF per unit connectivity strength (rCBF/FCS ratio); whereas, this index was lower in posterior visual areas. During the working-memory experiment, both FCS–rCBF coupling and rCBF/FCS ratio were modulated by task load in the ECN and/or DMN regions. Finally, task-induced changes of FCS and rCBF in the lateral-parietal lobe positively correlated with behavioral performance. Together, our results indicate a tight coupling between blood supply and brain functional topology during rest and its modulation in response to task demands, which may shed light on the physiological basis of human brain functional connectome.
Structure of the trypanosome haptoglobin–hemoglobin receptor and implications for nutrient uptake and innate immunity
Authors: Higgins Matthew K. , Tkachenko Olga , Brown Alan , Reed Jenny , Raper Jayne , Carrington Mark
Published: January 2013

African trypanosomes are protected by a densely packed surface monolayer of variant surface glycoprotein (VSG). A haptoglobin–hemoglobin receptor (HpHbR) within this VSG coat mediates heme acquisition. HpHbR is also exploited by the human host to mediate endocytosis of trypanolytic factor (TLF)1 from serum, contributing to innate immunity. Here, the crystal structure of HpHbR from
Trypanosoma congolense
has been solved, revealing an elongated three α-helical bundle with a small membrane distal head. To understand the receptor in the context of the VSG layer, the dimensions of
Trypanosoma brucei
HpHbR and VSG have been determined by small-angle X-ray scattering, revealing the receptor to be more elongated than VSG. It is, therefore, likely that the receptor protrudes above the VSG layer and unlikely that the VSG coat can prevent immunoglobulin binding to the receptor. The HpHb-binding site has been mapped by single-residue mutagenesis and surface plasmon resonance. This site is located where it is readily accessible above the VSG layer. A single HbHpR polymorphism unique to human infective
T. brucei gambiense
has been shown to be sufficient to reduce binding of both HpHb and TLF1, modulating ligand affinity in a delicate balancing act that allows nutrient acquisition but avoids TLF1 uptake.
Transmembrane helix orientation influences membrane binding of the intracellular juxtamembrane domain in
Neu
receptor peptides
Authors: Matsushita Chihiro , Tamagaki Hiroko , Miyazawa Yudai , Aimoto Saburo , Smith Steven O. , Sato Takeshi
Published: January 2013

The transmembrane (TM) and juxtamembrane (JM) regions of the ErbB family receptor tyrosine kinases connect the extracellular ligand-binding domain to the intracellular kinase domain. Evidence for the role of these regions in the mechanism of receptor dimerization and activation is provided by TM–JM peptides corresponding to the
Neu
(or rat ErbB2) receptor. Solid-state NMR and fluorescence spectroscopy show that there are tight interactions of the JM sequence with negatively charged lipids, including phosphatidylinositol 4,5-bisphosphate, in TM–JM peptides corresponding to the wild-type receptor sequence. We observe a release of the JM sequence from the negatively charged membrane surface using peptides containing an activating V664E mutation within the TM domain or in peptides engineered to form TM helix dimers with Val664 in the interface. These results provide the basis of a mechanism for coupling ligand binding to kinase activation in the full-length receptor.
Gene body methylation is conserved between plant orthologs and is of evolutionary consequence
Authors: Takuno Shohei , Gaut Brandon S.
Published: January 2013

DNA methylation is a common feature of eukaryotic genomes and is especially common in noncoding regions of plants. Protein coding regions of plants are often methylated also, but the extent, function, and evolutionary consequences of gene body methylation remain unclear. Here we investigate gene body methylation using an explicit comparative evolutionary approach. We generated bisulfite sequencing data from two tissues of
Brachypodium distachyon
and compared genic methylation patterns to those of rice (
Oryza sativa
ssp.
japonica
). Gene body methylation was strongly conserved between orthologs of the two species and affected a biased subset of long, slowly evolving genes. Because gene body methylation is conserved over evolutionary time, it shapes important features of plant genome evolution, such as the bimodality of G+C content among grass genes. Our results superficially contradict previous observations of high cytosine methylation polymorphism within
Arabidopsis thaliana
genes, but reanalyses of these data are consistent with conservation of methylation within gene regions. Overall, our results indicate that the methylation level is a long-term property of individual genes and therefore of evolutionary consequence.
Buried lysine, but not arginine, titrates and alters transmembrane helix tilt
Authors: Gleason Nicholas J. , Vostrikov Vitaly V. , Greathouse Denise V. , Koeppe Roger E.
Published: January 2013

The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid–bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK
a
values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.
Crystal structure of glycoprotein C from Rift Valley fever virus
Authors: Dessau Moshe , Modis Yorgo
Published: January 2013

Rift Valley fever virus (RVFV), like many other
Bunyaviridae
family members, is an emerging human and animal pathogen. Bunyaviruses have an outer lipid envelope bearing two glycoproteins, G
N
and G
C
, required for cell entry. Bunyaviruses deliver their genome into the host-cell cytoplasm by fusing their envelope with an endosomal membrane. The molecular mechanism of this key entry step is unknown. The crystal structure of RVFV G
C
reveals a class II fusion protein architecture found previously in flaviviruses and alphaviruses. The structure identifies G
C
as the effector of membrane fusion and provides a direct view of the membrane anchor that initiates fusion. A structure of nonglycosylated G
C
reveals an extended conformation that may represent a fusion intermediate. Unanticipated similarities between G
C
and flavivirus envelope proteins reveal an evolutionary link between the two virus families and provide insights into the organization of G
C
in the outer shell of RVFV.
Chimpanzees play the ultimatum game
Authors: Proctor Darby , Williamson Rebecca A. , de Waal Frans B. M. , Brosnan Sarah F.
Published: January 2013

Is the sense of fairness uniquely human? Human reactions to reward division are often studied by means of the ultimatum game, in which both partners need to agree on a distribution for both to receive rewards. Humans typically offer generous portions of the reward to their partner, a tendency our close primate relatives have thus far failed to show in experiments. Here we tested chimpanzees (Pan troglodytes) and human children on a modified ultimatum game. One individual chose between two tokens that, with their partner’s cooperation, could be exchanged for rewards. One token offered equal rewards to both players, whereas the other token favored the chooser. Both apes and children responded like humans typically do. If their partner’s cooperation was required, they split the rewards equally. However, with passive partners—a situation akin to the so-called dictator game—they preferred the selfish option. Thus, humans and chimpanzees show similar preferences regarding reward division, suggesting a long evolutionary history to the human sense of fairness.
Biogeochemistry of beetle-killed forests: Explaining a weak nitrate response
Authors: Rhoades Charles C. , McCutchan James H. , Cooper Leigh A. , Clow David , Detmer Thomas M. , Briggs Jennifer S. , Stednick John D. , Veblen Thomas T. , Ertz Rachel M. , Likens Gene E. , Lewis William M.
Published: January 2013

A current pine beetle infestation has caused extensive mortality of lodgepole pine (
Pinus contorta
) in forests of Colorado and Wyoming; it is part of an unprecedented multispecies beetle outbreak extending from Mexico to Canada. In United States and European watersheds, where atmospheric deposition of inorganic N is moderate to low (<10 kg⋅ha⋅y), disturbance of forests by timber harvest or violent storms causes an increase in stream nitrate concentration that typically is close to 400% of predisturbance concentrations. In contrast, no significant increase in streamwater nitrate concentrations has occurred following extensive tree mortality caused by the mountain pine beetle in Colorado. A model of nitrate release from Colorado watersheds calibrated with field data indicates that stimulation of nitrate uptake by vegetation components unaffected by beetles accounts for significant nitrate retention in beetle-infested watersheds. The combination of low atmospheric N deposition (<10 kg⋅ha⋅y), tree mortality spread over multiple years, and high compensatory capacity associated with undisturbed residual vegetation and soils explains the ability of these beetle-infested watersheds to retain nitrate despite catastrophic mortality of the dominant canopy tree species.
Analysis of naïve lung CD4 T cells provides evidence of functional lung to lymph node migration
Authors: Caucheteux Stephane M. , Torabi-Parizi Parizad , Paul William E.
Published: January 2013

The proportion of CD4 T cells with phenotypic and functional properties of naïve cells out of total CD4 T cells is similar in the lung parenchyma and lymph nodes. On treatment with a sphingosine-1-phosphate agonist, the frequency of these cells falls precipitously, but with a delay of ∼14 h compared with blood CD4 T cells; neither anti-CD62L nor pertussis toxin prevents entry of naïve CD4 T cells into the lung. Based on treatment with anti-CD62L and the use of CCR7−/−cells, lung naïve CD4 T cells appear to migrate to the mediastinal lymph nodes along a CD62L-independent, CCR7-dependent pathway. Cells that have entered the node in this manner are competent to respond to antigen. Thus, a portion (approximately one-half) of naïve CD4 T cells appears to enter the mediastinal lymph nodes through a blood-to-lung-to-lymph node route.
A kinase interacting protein (AKIP1) is a key regulator of cardiac stress
Authors: Sastri Mira , Haushalter Kristofer J. , Panneerselvam Mathivadhani , Chang Philip , Fridolfsson Heidi , Finley J. Cameron , Ng Daniel , Schilling Jan M. , Miyanohara Atsushi , Day Michele E. , Hakozaki Hiro , Petrosyan Susanna , Koller Antonius , King Charles C. , Darshi Manjula , Blumenthal Donald K. , Ali Sameh Saad , Roth David M. , Patel Hemal H. , Taylor Susan S.
Published: January 2013

Significance

Early signaling events leading to protection in the heart under cardiac injury are poorly understood. We identified one such protein, A kinase interacting protein (AKIP1), as a modulator that responds to oxidative stress; up-regulation of AKIP1 showed protection to ischemic injury through enhanced mitochondrial integrity. We show AKIP1 functions as a molecular scaffold via interaction with mitochondrial apoptosis inducing factor and increases protein kinase A activity. These mitochondrial signaling complexes assembled by AKIP1 alter the physiological response of the heart under ischemic stress. Understanding molecular activity and regulation of AKIP1 could lead to novel therapeutic approaches to limit myocardial injury.
Long-term in vivo monitoring of mouse and human hematopoietic stem cell engraftment with a human positron emission tomography reporter gene
Authors: McCracken Melissa N. , Gschweng Eric H. , Nair-Gill Evan , McLaughlin Jami , Cooper Aaron R. , Riedinger Mireille , Cheng Donghui , Nosala Christopher , Kohn Donald B. , Witte Owen N.
Published: January 2013

Positron emission tomography (PET) reporter genes allow noninvasive whole-body imaging of transplanted cells by detection with radiolabeled probes. We used a human deoxycytidine kinase containing three amino acid substitutions within the active site (hdCK3mut) as a reporter gene in combination with the PET probe [
18
F]-L-FMAU (1-(2-deoxy-2-
18
fluoro-β-L-arabinofuranosyl)-5-methyluracil) to monitor models of mouse and human hematopoietic stem cell (HSC) transplantation. These mutations in hdCK3mut expanded the substrate capacity allowing for reporter-specific detection with a thymidine analog probe. Measurements of long-term engrafted cells (up to 32 wk) demonstrated that hdCK3mut expression is maintained in vivo with no counter selection against reporter-labeled cells. Reporter cells retained equivalent engraftment and differentiation capacity being detected in all major hematopoietic lineages and tissues. This reporter gene and probe should be applicable to noninvasively monitor therapeutic cell transplants in multiple tissues.
Transcriptional responses of
Pseudomonas syringae
to growth in epiphytic versus apoplastic leaf sites
Authors: Yu Xilan , Lund Steven P. , Scott Russell A. , Greenwald Jessica W. , Records Angela H. , Nettleton Dan , Lindow Steven E. , Gross Dennis C. , Beattie Gwyn A.
Published: January 2013

Significance

Plant leaves are heavily colonized by microorganisms, but the extent to which the surface sites differ from interior sites in selecting for microbial colonization traits is poorly understood. Global gene-expression studies of the foliar pathogen
Pseudomonas syringae
reveal that leaf surface sites specifically favor active exploration using flagellar motility, chemosensing, and chemotaxis. In contrast, interior sites favor production of enzymes and secondary compounds that modulate bacterial interactions with the plant and its defense system. Water limitation is a dominating force in both surface and interior sites. These findings provide a rich understanding of the leaf habitats encountered by bacteria.
Antitumor activity of a pyrrole-imidazole polyamide
Authors: Yang Fei , Nickols Nicholas G. , Li Benjamin C. , Marinov Georgi K. , Said Jonathan W. , Dervan Peter B.
Published: January 2013

Many cancer therapeutics target DNA and exert cytotoxicity through the induction of DNA damage and inhibition of transcription. We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) polyamide interferes with RNA polymerase II (RNAP2) activity in cell culture. Polyamide treatment activates p53 signaling in LNCaP prostate cancer cells without detectable DNA damage. Genome-wide mapping of RNAP2 binding shows reduction of occupancy, preferentially at transcription start sites, but occupancy at enhancer sites is unchanged. Polyamide treatment results in a time- and dose-dependent depletion of the RNAP2 large subunit RPB1 that is preventable with proteasome inhibition. This polyamide demonstrates antitumor activity in a prostate tumor xenograft model with limited host toxicity.
Frustration in the energy landscapes of multidomain protein misfolding
Authors: Zheng Weihua , Schafer Nicholas P. , Wolynes Peter G.
Published: January 2013

Frustration from strong interdomain interactions can make misfolding a more severe problem in multidomain proteins than in single-domain proteins. On the basis of bioinformatic surveys, it has been suggested that lowering the sequence identity between neighboring domains is one of nature’s solutions to the multidomain misfolding problem. We investigate folding of multidomain proteins using the associative-memory, water-mediated, structure and energy model (AWSEM), a predictive coarse-grained protein force field. We find that reducing sequence identity not only decreases the formation of domain-swapped contacts but also decreases the formation of strong self-recognition contacts between β-strands with high hydrophobic content. The ensembles of misfolded structures that result from forming these amyloid-like interactions are energetically disfavored compared with the native state, but entropically favored. Therefore, these ensembles are more stable than the native ensemble under denaturing conditions, such as high temperature. Domain-swapped contacts compete with self-recognition contacts in forming various trapped states, and point mutations can shift the balance between the two types of interaction. We predict that multidomain proteins that lack these specific strong interdomain interactions should fold reliably.
Global maternal mortality decline and the role of development factors - Mini Review.
Authors: Hussein J.
Published: January 2013

Maternal mortality has declined over the last 20 years. Specific technical interventions are known to work in reducing maternal mortality, but it is likely that improvements in development across all the Millennium Development Goals have played a part. Better understanding of how these intersectoral factors work is needed.
Leaving the godfather to follow God the father: successor generation conversion in a mob family
Authors: Litz Reginald A.
Published: January 2013

How does conversion happen when one is part of a family involved in organized crime? We consider this question through in-depth study of the Christian conversion of the “Yuppie Don”, Michael Franzese. The paper begins with a review of religion, spirituality, and conversion literatures and the emerging area of family business research. Drawing on the posthumous published testament of a former member of the Bonanno crime Family, a brief overview of the history of “La Cosa Nostra” is then presented. Next, we review the life history of former Colombo Family “made man” Michael Franzese with special focus on his conversion experience. Using Lewin’s three-stage process model of change, we reflect on Franzese’s conversion experience. The paper concludes with discussion of the limitations of this effort and also identifies avenues for further research on spiritual individuation in family enterprises.
Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies
Authors: Muellenbeck Matthias F. , Ueberheide Beatrix , Amulic Borko , Epp Alexandra , Fenyo David , Busse Christian E. , Esen Meral , Theisen Michael , Mordmüller Benjamin , Wardemann Hedda
Published: January 2013

Antibodies can protect from Plasmodium falciparum (Pf) infection and clinical malaria disease. However, in the absence of constant reexposure, serum immunoglobulin (Ig) levels rapidly decline and full protection from clinical symptoms is lost, suggesting that B cell memory is functionally impaired. We show at the single cell level that natural Pf infection induces the development of classical memory B cells (CM) and atypical memory B cells (AtM) that produce broadly neutralizing antibodies against blood stage Pf parasites. CM and AtM contribute to anti-Pf serum IgG production, but only AtM show signs of active antibody secretion. AtM and CM were also different in their IgG gene repertoire, suggesting that they develop from different precursors. The findings provide direct evidence that natural Pf infection leads to the development of protective memory B cell antibody responses and suggest that constant immune activation rather than impaired memory function leads to the accumulation of AtM in malaria. Understanding the memory B cell response to natural Pf infection may be key to the development of a malaria vaccine that induces long-lived protection.