bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal conductivity of III-V semiconductor superlattices
Authors: Mei S. , Knezevic I.
Published: November 2015

This paper presents a semiclassical model for the anisotropic thermal transport in III-V semiconductor superlattices (SLs). An effective interface rms roughness is the only adjustable parameter. Thermal transport inside a layer is described by the Boltzmann transport equation in the relaxation time approximation and is affected by the relevant scattering mechanisms (three-phonon, mass-difference, and dopant and electron scattering of phonons), as well as by diffuse scattering from the interfaces captured via an effective interface scattering rate. The in-plane thermal conductivity is obtained from the layer conductivities connected in parallel. The cross-plane thermal conductivity is calculated from the layer thermal conductivities in series with one another and with thermal boundary resistances (TBRs) associated with each interface; the TBRs dominate cross-plane transport. The TBR of each interface is calculated from the transmission coefficient obtained by interpolating between the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM), where the weight of the AMM transmission coefficient is the same wavelength-dependent specularity parameter related to the effective interface rms roughness that is commonly used to describe diffuse interface scattering. The model is applied to multiple III-arsenide superlattices, and the results are in very good agreement with experimental findings. The method is both simple and accurate, easy to implement, and applicable to complicated SL systems, such as the active regions of quantum cascade lasers. It is also valid for other SL material systems with high-quality interfaces and predominantly incoherent phonon transport.
Thermal phonon boundary scattering in anisotropic thin films
Authors: Minnich A. J.
Published: November 2015

Boundary scattering of thermal phonons in thin solid films is typically analyzed using Fuchs-Sondheimer theory, which provides a simple equation to calculate the reduction of thermal conductivity as a function of the film thickness. However, this widely used equation is not applicable to highly anisotropic solids like graphite because it assumes the phonon dispersion is isotropic. Here, we derive a generalization of the Fuchs-Sondheimer equation for solids with arbitrary dispersion relations and examine its predictions for graphite. We find that the isotropic equation vastly overestimates the boundary scattering that occurs in thin graphite films due to the highly anisotropic group velocity, and that graphite can maintain its high in-plane thermal conductivity even in thin films with thicknesses as small as 10 nm.
Low-temperature formation of high-quality gate oxide by ultraviolet irradiation on spin-on-glass
Authors: Usuda R. , Uchida K. , Nozaki S.
Published: November 2015

Although a UV cure was found to effectively convert a perhydropolysilazane (PHPS) spin-on-glass film into a dense SiOx film at low temperature, the electrical characteristics were never reported in order to recommend the use of PHPS as a gate-oxide material that can be formed at low temperature. We have formed a high-quality gate oxide by UV irradiation on the PHPS film, and obtained an interface midgap trap density of 3.4 × 1011 cm−2 eV−1 by the UV wet oxidation and UV post-metallization annealing (PMA), at a temperature as low as 160 °C. In contrast to the UV irradiation using short-wavelength UV light, which is well known to enhance oxidation by the production of the excited states of oxygen, the UV irradiation was carried out using longer-wavelength UV light from a metal halide lamp. The UV irradiation during the wet oxidation of the PHPS film generates electron-hole pairs. The electrons ionize the H2O molecules and facilitate dissociation of the molecules into H and OH−. The OH− ions are highly reactive with Si and improve the stoichiometry of the oxide. The UV irradiation during the PMA excites the electrons from the accumulation layer, and the built-in electric field makes the electron injection into the oxide much easier. The electrons injected into the oxide recombine with the trapped holes, which have caused a large negative flat band voltage shift after the UV wet oxidation, and also ionize the H2O molecules. The ionization results in the electron stimulated dissociation of H2O molecules and the decreased interface trap density.
Combining liquid inertia with pressure recovery from bubble expansion for enhanced flow boiling
Authors: Kalani A. , Kandlikar S. G.
Published: November 2015

In this paper, we demonstrate using liquid inertia force in a taper gap microchannel geometry to provide a high level of heat dissipation capacity accompanied by a high heat transfer coefficient and low pressure drop during flow boiling. The high mass flux increases liquid inertia force and promotes vapor removal from the manifold, thereby increasing critical heat flux (CHF) and heat transfer coefficient. The tapered gap above the microchannels provides an increasing cross-sectional area in the flow direction. This gap allows bubbles to emerge from microchannels and expand within the gap along the flow direction. The bubble evaporation and expansion in tapered gap causes pressure recovery and reduces the total pressure drop. The pressure recovery increases with the increased evaporation rate at higher heat fluxes. Using a 6% taper and a moderately high inlet liquid flow Reynolds number of 1095, we have reached a CHF of 1.07 kW/cm2 with a heat transfer coefficient of 295 kW/m2 °C and a pressure drop of 30 kPa.
Multicaloric effect in bi-layer multiferroic composites
Authors: Vopson M. M. , Zhou D. , Caruntu G.
Published: November 2015

The multicaloric effect was theoretically proposed in 2012 and, despite numerous follow up studies, the effect still awaits experimental confirmation. The main limitation is the fact that the multicaloric effect is only observed at a temperature equal to the transition temperature of the magnetic and electric phases coexisting within a multiferroic (MF) (i.e., T ≈ Tcm ≈ Tce). Such condition is hard to fulfill in single phase MFs and a solution is to develop suitable composite MF materials. Here, we examine the multicaloric effect in a bi-layer laminated composite MF in order to determine the optimal design parameters for best caloric response. We show that magnetically induced multicaloric effect requires magnetic component of heat capacity smaller than that of the electric phase, while the layer thickness of the magnetic phase must be at least 5 times the thickness of the electric phase. The electrically induced multicaloric effect requires the magnetic layer to be 10% of the electric phase thickness, while its heat capacity must be larger than that of the electric phase. These selection rules are generally applicable to bulk as well as thin film MF composites for optimal multicaloric effect.
Pulsed-N2 assisted growth of 5-20 nm thick β-W films
Authors: Narasimham Avyaya J. , Green Avery , Matyi Richard J. , Khare Prasanna , Vo Tuan , Diebold Alain , LaBella Vincent P.
Published: November 2015

A technique to deposit 5-20 nm thick β-phase W using a 2-second periodic pulse of 1 sccm-N2 gas on Si(001) and SiN(5 nm)/Si(001) substrates is reported. Resistivity, X-ray photoelectron spectroscopy and X-ray reflectivity were utilized to determine phase, bonding and thickness, respectively. X-ray diffraction patterns were utilized to determine the crystal structure, lattice constant and crystal size using the LeBail method. The flow rate of Nitrogen gas (continuous vs. pulsing) had significant impact upon the crystallinity and formation of β-phase W.
Fat, weather, and date affect migratory songbirds’ departure decisions, routes, and time it takes to cross the Gulf of Mexico
Authors: Deppe Jill L. , Ward Michael P. , Bolus Rachel T. , Diehl Robert H. , Celis-Murillo Antonio , Zenzal Theodore J. , Moore Frank R. , Benson Thomas J. , Smolinsky Jaclyn A. , Schofield Lynn N. , Enstrom David A. , Paxton Eben H. , Bohrer Gil , Beveroth Tara A. , Raim Arlo , Obringer Renee L. , Delaney David , Cochran William W.
Published: November 2015

Significance

Bird migration has captivated the attention of scientists and lay people for centuries, but many unanswered questions remain about how birds negotiate large geographic features during migration. We tracked songbirds across the Gulf of Mexico to investigate the factors associated with birds’ departure decisions, arrival at the Yucatan Peninsula (YP), and crossing times. Our findings suggest that a bird’s fat reserves and low humidity, indicative of favorable synoptic weather patterns, shape departure decisions. Fat, date, and wind conditions predict birds’ detection in the YP. This study highlights the complex decision-making process involved in crossing the Gulf and its effects on migratory routes and speeds. A better understanding of the factors influencing migration across these features will inform conservation of migratory animals.
Seasonal fluxes of carbonyl sulfide in a midlatitude forest
Authors: Commane Róisín , Meredith Laura K. , Baker Ian T. , Berry Joseph A. , Munger J. William , Montzka Stephen A. , Templer Pamela H. , Juice Stephanie M. , Zahniser Mark S. , Wofsy Steven C.
Published: November 2015

Significance

The flux of carbonyl sulfide (OCS) provides a quantitative, independent measure of biospheric activity, especially stomatal conductance and carbon uptake, at the ecosystem scale. We describe the factors controlling the hourly, daily, and seasonal fluxes of OCS based on 1 year of observations in a forest ecosystem. Vegetation dominated uptake of OCS, with daytime fluxes accounting for 72% of the total uptake for the year. Nighttime fluxes had contributions from both incompletely closed stomata and soils. Net OCS emission was observed at high temperature in summer. Diurnal and seasonal variations in OCS flux show variable stoichiometry relative to photosynthetic uptake of CO2. An effective model framework is shown, using an explicit representation of ecosystem processing of OCS.
High-temperature in situ crystallographic observation of reversible gas sorption in impermeable organic cages
Authors: Baek Seung Bin , Moon Dohyun , Graf Robert , Cho Woo Jong , Park Sung Woo , Yoon Tae-Ung , Cho Seung Joo , Hwang In-Chul , Bae Youn-Sang , Spiess Hans W. , Lee Hee Cheon , Kim Kwang S.
Published: November 2015

Significance

Crystallographic observation of adsorbed gas molecules at high temperatures is a highly challenging task due to their rapid motion. We provide evidence of restrained motions in a self-assembled organic crystal with small isolated cages, inside which the confined CO
2
molecules can be identified with in situ X-ray diffraction technique at the high temperature. Although the crystal is nonporous, the CO
2
molecules can permeate into the crystal because of thermally activated transient pathways between the cages. We show that the flexible nature of the transient pathways leads to the temperature-driven reversible CO
2
sorption, understanding of which can contribute to the design of a system with controlled capture/release of gas molecules.
Automatic classification of prostate cancer Gleason scores from multiparametric magnetic resonance images
Authors: Fehr Duc , Veeraraghavan Harini , Wibmer Andreas , Gondo Tatsuo , Matsumoto Kazuhiro , Vargas Herbert Alberto , Sala Evis , Hricak Hedvig , Deasy Joseph O.
Published: November 2015

Significance

Gleason scores and ultimately the aggressiveness of prostate cancers determined using transrectal ultrasound (TRUS)-guided biopsy procedures could result in incorrect diagnosis in addition to patient discomfort. The Gleason scores determined from TRUS-guided biopsies often differ from immediate repeat biopsies and the biopsies determined following whole excision of the prostate. Our approach presents a highly accurate and automated method for differentiating between the high ≥7 and low Gleason score 6(3+3), as well as between 7(3+4) and 7(4+3) Gleason score cancers through multiparametric MRI combined with texture features computed on the same images. Noninvasive and accurate techniques such as ours can benefit patient care without subjecting them to unnecessary interventions.
Ultrasensitive gas detection of large-area boron-doped graphene
Authors: Lv Ruitao , Chen Gugang , Li Qing , McCreary Amber , Botello-Méndez Andrés , Morozov S. V. , Liang Liangbo , Declerck Xavier , Perea-López Nestor , Cullen David A. , Feng Simin , Elías Ana Laura , Cruz-Silva Rodolfo , Fujisawa Kazunori , Endo Morinobu , Kang Feiyu , Charlier Jean-Christophe , Meunier Vincent , Pan Minghu , Harutyunyan Avetik R. , Novoselov Konstantin S. , Terrones Mauricio
Published: November 2015

Significance

The gas-sensing performance of graphene could be remarkably enhanced by incorporating dopants into its lattice based on theoretical calculations. However, to date, experimental progress on boron-doped graphene (BG) is still very scarce. Here, we achieved the controlled growth of large-area, high-crystallinity BG sheets and shed light on their electronic features associated with boron dopants at the atomic scale. As a proof-of-concept, it is demonstrated that boron doping in graphene could lead to a much enhanced sensitivity when detecting toxic gases (e.g. NO2). Our results will open up new avenues for developing high-performance sensors able to detect trace amount of molecules. In addition, other new fascinating properties can be exploited based on as-synthesized large-area BG sheets.
Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair
Authors: Liao Yi , Schroeder Jeremy W. , Gao Burke , Simmons Lyle A. , Biteen Julie S.
Published: November 2015

Significance

We integrated single-molecule superresolution imaging with biochemical and genomic approaches to understand how the mismatch repair protein MutS efficiently identifies DNA mismatches during real time in living cells. We show that MutS molecules move fast, exploring the entire nucleoid, but can transition to a slow-moving population that is localized at the replisome even before a mismatch is produced. We show that bacterial MutS must initiate mismatch binding in very close proximity to the replisome. We also show that mismatch detection increases MutS speed, supporting the model for MutS sliding clamp formation after mismatch recognition. Our results provide fundamental insight into the searching behavior of single MutS molecules during DNA replication in live cells.
Maternal testosterone exposure increases anxiety-like behavior and impacts the limbic system in the offspring
Authors: Hu Min , Richard Jennifer Elise , Maliqueo Manuel , Kokosar Milana , Fornes Romina , Benrick Anna , Jansson Thomas , Ohlsson Claes , Wu Xiaoke , Skibicka Karolina Patrycja , Stener-Victorin Elisabet
Published: November 2015

Significance

Polycystic ovary syndrome (PCOS) is the leading cause of anovulatory infertility characterized by excessive androgen secretion. PCOS women are at an increased risk of developing depression and anxiety disorders. Although the etiology of PCOS is unclear, it is proposed to originate during fetal development because of maternal androgen excess. We describe here, in rodent models reflecting the anxiety phenotype of PCOS, evidence for disordered androgen receptor function in the amygdala, together with changes in estrogen receptor-α, serotonergic and GABAergic genes in the amygdala, and hippocampus. These findings define a previously unknown mechanism that may be critical in understanding how maternal androgen excess has the potential to increase the risk of developing anxiety disorders in daughters and sons of PCOS mothers.
Persistent impacts of West Nile virus on North American bird populations
Authors: George T. Luke , Harrigan Ryan J. , LaManna Joseph A. , DeSante David F. , Saracco James F. , Smith Thomas B.
Published: November 2015

Significance

Since its introduction to North America, West Nile virus (WNV) has impacted the health of both human and wildlife populations, but the extent of the burden across host species remains poorly understood. Using extensive mark-recapture data from 49 species spanning nearly two decades, combined with recently developed models of WNV risk, we estimated the impacts of this emergent disease on avian populations. We show that WNV has had significant negative effects on survival of 47% of bird species examined. We provide the first in-depth picture of the extent, duration, and phylogenetic signal of WNV impacts on bird populations. Our results suggest that introduced infectious diseases can have significant persistent effects on populations long after initial concerns have waned.
Deciphering tissue-induced
Klebsiella pneumoniae
lipid A structure
Authors: Llobet Enrique , Martínez-Moliner Verónica , Moranta David , Dahlström Käthe M. , Regueiro Verónica , Tomás Anna , Cano Victoria , Pérez-Gutiérrez Camino , Frank Christian G. , Fernández-Carrasco Helena , Insua José Luis , Salminen Tiina A. , Garmendia Junkal , Bengoechea José A.
Published: November 2015

Significance

The host launches an antimicrobial defense program upon infection. A long-held belief is that pathogens prevent host recognition by remodeling their surface in response to different host microenvironments. Yet direct evidence that this happens in vivo is lacking. Here we report that the pathogen
Klebsiella pneumoniae
modifies one of its surface molecules, the lipopolysaccharide, in the lungs of mice to evade immune surveillance. These in vivo-induced changes are lost in bacteria grown after isolation from the tissues. These lipopolysaccharide modifications contribute to survival in vivo and mediate resistance to colistin, one of the last options to treat multidrug-resistant
Klebsiella
. This work opens the possibility of designing novel therapeutics targeting the enzymes responsible for the in vivo lipid A pattern.
An analysis of ozone damage to historical maize and soybean yields in the United States
Authors: McGrath Justin M. , Betzelberger Amy M. , Wang Shaowen , Shook Eric , Zhu Xin-Guang , Long Stephen P. , Ainsworth Elizabeth A.
Published: November 2015

Significance

Although it has long been known that ground-level ozone (O3) damages crops and reduces yield, there has never been an estimate of the total loss attributed to ambient O3for field-grown maize and soybean in the United States. Knowing the loss caused by this pollutant would be useful for projecting food supply and setting regulatory standards for pollutant emissions. Here we show that ambient O3has reduced maize and soybean yields in rain-fed fields by ∼10% and 5%, respectively, based on historical observations from the past 31 y. Results suggest that air-quality regulations in the United States have been effective in reducing crop production losses to O3, and indicate that further reductions in ground-level [O3] would be beneficial in the United States and globally.
Community rescue in experimental metacommunities
Authors: Low-Décarie Etienne , Kolber Marcus , Homme Paige , Lofano Andrea , Dumbrell Alex , Gonzalez Andrew , Bell Graham
Published: November 2015

Significance

Global environmental change is challenging the adaptive capacity of entire ecological communities. Community rescue occurs when populations within a community evolve in response to an environmental stress that was initially lethal to all the constituent organisms. We studied how communities of soil microbes can extend the area they occupy to include conditions that were initially lethal, and how these communities can persist despite the degradation of environmental conditions. Our results suggest that entire communities have the potential to adapt to severe environmental stress. Community rescue is promoted by the initial diversity in the community, is more frequent among communities that have previously experienced intermediate sublethal levels of stress, and is facilitated by the dispersal of organisms across the landscape.
The human hippocampus contributes to both the recollection and familiarity components of recognition memory
Authors: Merkow Maxwell B. , Burke John F. , Kahana Michael J.
Published: November 2015

Significance

Recognition memory is thought to be composed of recollection, accompanied by vivid details, and familiarity or a general sense of knowing. A fundamental and long-standing question remains: Which of these processes does the hippocampus support? We measured high-frequency activity (HFA), a spatiotemporally precise signal of neural activation, in subjects undergoing direct brain recordings and found that hippocampal HFA dissociated based on both the stimulus evidence presented and the response choice. Hippocampal HFA predicted overall memory performance as well as individual differences in both recollection and familiarity estimates. Our findings reject the hypothesis that the hippocampus exclusively supports the recollection component of recognition memory and, instead, indicate that this structure is functionally relevant to both processes thought to support recognition.
Filming the formation and fluctuation of skyrmion domains by cryo-Lorentz transmission electron microscopy
Authors: Rajeswari Jayaraman , Huang Ping , Mancini Giulia Fulvia , Murooka Yoshie , Latychevskaia Tatiana , McGrouther Damien , Cantoni Marco , Baldini Edoardo , White Jonathan Stuart , Magrez Arnaud , Giamarchi Thierry , Rønnow Henrik Moodysson , Carbone Fabrizio
Published: November 2015

Significance

The need for denser storage devices calls for new materials and nanostructures capable of confining single bits of information in a few nanometers. A new topological distribution of spins termed skyrmions is emerging, which promises to robustly confine a small magnetization in a few-nanometers-wide circular domain. A great deal of attention is being devoted to the understanding of these magnetic patterns and their manipulation. We manufactured a large nanoslice supporting over 70,000 skyrmions, and film their evolution in direct-space via cryo-Lorentz transmission electron microscopy. We reveal the octagonal distortion of the skyrmion lattice and show how these distortions and other defects impact its long-range order. These results pave the way to the control of a large two-dimensional array of skyrmions.
An anticomplement agent that homes to the damaged brain and promotes recovery after traumatic brain injury in mice
Authors: Ruseva Marieta M. , Ramaglia Valeria , Morgan B. Paul , Harris Claire L.
Published: November 2015

Significance

Traumatic brain injury (TBI) is the leading cause of death in young adults. We describe an inhibitor of complement membrane attack complex (MAC), which homes to sites of complement deposition in the injured brain, inhibits local inflammation and inflammasome activation, and is neuroprotective in experimental TBI, raising the prospect that such agents may provide effective treatment of TBI in man. Targeting anti-MAC therapy to pathology minimizes systemic effects and maintains upstream opsonization pathways essential to fight infections, a major cause of death post-TBI. Critically, we show a significant therapeutic window in the mouse model, raising the prospect that such a homing agent, administered postinjury, would be neuroprotective. We provide a rational basis for developing novel future therapeutic strategies for TBI.
Role of HIV-1 matrix protein p17 variants in lymphoma pathogenesis
Authors: Dolcetti Riccardo , Giagulli Cinzia , He Wangxiao , Selleri Marina , Caccuri Francesca , Eyzaguirre Lindsay M. , Mazzuca Pietro , Corbellini Silvia , Campilongo Federica , Marsico Stefania , Giombini Emanuela , Muraro Elena , Rozera Gabriella , De Paoli Paolo , Carbone Antonino , Capobianchi Maria Rosaria , Ippolito Giuseppe , Fiorentini Simona , Blattner William A. , Lu Wuyuan , Gallo Robert C. , Caruso Arnaldo
Published: November 2015

Significance

Non-Hodgkin lymphomas (NHLs) are associated with HIV-1 infection, but the HIV1 genome is not detectable in malignant B cells. Here we show that variants of the HIV-1 matrix protein p17 (vp17s) are detected in the NHL specimens of HIV+ patients. These vp17s are more frequently detected in HIV+ patients with NHL than in patients without NHL. These vp17s display a potent B-cell growth-promoting activity, which is exerted by activating the Akt signaling pathway. Results obtained by CD spectroscopy and thermal denaturation suggest that mutation-induced protein destabilization may lead to a conformational change potentially responsible for the viral protein to promote B-cell growth. Our results suggest that vp17s may have a role in sustaining lymphomagenesis, thus offering new opportunities to prevent and/or treat HIV-associated NHLs.
Direct real-time detection of the structural and biochemical events in the myosin power stroke
Authors: Muretta Joseph M. , Rohde John A. , Johnsrud Daniel O. , Cornea Sinziana , Thomas David D.
Published: November 2015

Significance

Myosins use ATP hydrolysis to power movement, but how they do this remains enigmatic. If we understood exactly how ATP’s chemical energy is coupled to force generation, we would gain insight into the fundamental biophysics of these fascinating and medically important proteins. We combined subnanosecond time-resolved FRET with millisecond-resolved transient kinetics to monitor subnanometer structural transitions in myosin during the actin-activated myosin power stroke. Our results show that the power stroke precedes phosphate release, thus contradicting the dominant model of myosin function, which argues that phosphate release should precede the power stroke. Our work prompts future studies investigating how this coordination is altered by disease-causing mutations and therapies designed to treat these diseases.
JAK inhibition alleviates the cellular senescence-associated secretory phenotype and frailty in old age
Authors: Xu Ming , Tchkonia Tamara , Ding Husheng , Ogrodnik Mikolaj , Lubbers Ellen R. , Pirtskhalava Tamar , White Thomas A. , Johnson Kurt O. , Stout Michael B. , Mezera Vojtech , Giorgadze Nino , Jensen Michael D. , LeBrasseur Nathan K. , Kirkland James L.
Published: November 2015

Significance

A hallmark of aging is chronic sterile inflammation, which is closely associated with frailty and age-related diseases. We found that senescent fat progenitor cells accumulate in adipose tissue with aging and acquire a senescence-associated secretory phenotype (SASP), with increased production of proinflammatory cytokines compared with nonsenescent cells. These cells provoked inflammation in adipose tissue and induced macrophage migration. The JAK pathway is activated in adipose tissue with aging, and the SASP can be suppressed by inhibiting the JAK pathway in senescent cells. JAK1/2 inhibitors reduced inflammation and alleviated frailty in aged mice. One possible mechanism contributing to reduced frailty is SASP inhibition. Our study points to the JAK pathway as a potential target for countering age-related dysfunction.
Life and extinction of megafauna in the ice-age Arctic
Authors: Mann Daniel H. , Groves Pamela , Reanier Richard E. , Gaglioti Benjamin V. , Kunz Michael L. , Shapiro Beth
Published: November 2015

Significance

Understanding species extinction is a major concern today, and past extinctions provide valuable lessons. Numerous mammal species became extinct in the Arctic at the end of the ice age, but it is unclear why. By comparing numbers of dated bones with climate records, we find that megafaunal species, like mammoth, horse, and bison, experienced boom and bust cycles during the ice age as they tracked rapid climate changes. For these species to persist, long-distance dispersal was necessary. Their extinction on the North Slope occurred as the ice age ended, because rising sea level severed dispersal routes and spreading peat simultaneously degraded range quality. This finding suggests that arctic mammals can be resilient to environmental changes but only if their habitats remain widely interconnected.
Evolutionary origins of hepatitis A virus in small mammals
Authors: Drexler Jan Felix , Corman Victor M. , Lukashev Alexander N. , van den Brand Judith M. A. , Gmyl Anatoly P. , Brünink Sebastian , Rasche Andrea , Seggewiβ Nicole , Feng Hui , Leijten Lonneke M. , Vallo Peter , Kuiken Thijs , Dotzauer Andreas , Ulrich Rainer G. , Lemon Stanley M. , Drosten Christian ,   the Hepatovirus Ecology Consortium, Akoua-Koffi Chantal G. , Ameneiros Ramón Seage , Goodman Steven M. , Godlevska Elena V. , Tungaluna Guy-Crispin Gembu , Görföl Tamás , Hassanin Alexandre , Koivogui Lamine , Krüger Detlev H. , Lakim Maklarin B. , Lavrenchenko Leonid , Leroy Eric M. , Matthee Sonja , ter Meulen Jan , Adu-Sarkodie Yaw , Oppong Samuel , Preiser Wolfgang , Pereira Maria João Ramos , Reusken Chantal B. E. M. , Schneider Julia , Schmidt-Chanasit Jonas , Fichet-Calvet Elisabeth , Seebens-Hoyer Antje , Gloza-Rausch Florian , Setién Alvaro Aguilar , Tschapka Marco , Wells Konstans , Wegner Tom , Wilkinson David A.
Published: November 2015

Significance

The origins of human hepatitis A virus (HAV) are unknown. We conducted a targeted search for HAV-related viruses in small mammals sampled globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews. We demonstrate that these viruses share unique biological features with HAV, including structural, genomic, antigenic, and pathogenic properties. We found evidence of major shifts of HAV-related viruses between mammalian hosts in the past, suggesting both an origin of this viral genus in small mammals and a zoonotic origin of human HAV. Our data show that risk assessments for emerging viruses can benefit greatly from the analysis of viral infection patterns that evolved within animal reservoirs.
Twisted photon entanglement through turbulent air across Vienna
Authors: Krenn Mario , Handsteiner Johannes , Fink Matthias , Fickler Robert , Zeilinger Anton
Published: November 2015

Significance

The spatial structure of photons provides access to a very large state space. It enables the encoding of more information per photon, useful for (quantum) communication with large alphabets and fundamental studies of high-dimensional entanglement. However, the question of the distribution of such photons has not been settled yet, as they are significantly influenced by atmospheric turbulence in free-space transmissions. In the present paper we show that it is possible to distribute quantum entanglement of spatially structured photons over a free-space intracity link. We demonstrate the access to four orthogonal quantum channels in which entanglement can be distributed over large distances. Furthermore, already available technology could provide access to even larger quantum state spaces.
Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells
Authors: Tanne Antoine , Muniz Luciana R. , Puzio-Kuter Anna , Leonova Katerina I. , Gudkov Andrei V. , Ting David T. , Monasson Rémi , Cocco Simona , Levine Arnold J. , Bhardwaj Nina , Greenbaum Benjamin D.
Published: November 2015

Significance

Using an approach derived from statistical physics, we quantify transcriptome-wide motif usage in human and murine noncoding RNAs (ncRNAs), determining that most have motif usage consistent with the coding genome. However, an outlier subset of tumor-associated ncRNAs comprises repetitive elements whose motif usage patterns are more typically associated with the genomes of inflammatory pathogens. We demonstrate that a key subset of these elements directly activates the cellular innate immune response. We propose that the innate response in tumors partially originates from direct interaction of immunogenic ncRNAs preferentially expressed in cancer cells with innate pattern recognition receptors.
Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer
Authors: Bersani Francesca , Lee Eunjung , Kharchenko Peter V. , Xu Andrew W. , Liu Mingzhu , Xega Kristina , MacKenzie Olivia C. , Brannigan Brian W. , Wittner Ben S. , Jung Hyunchul , Ramaswamy Sridhar , Park Peter J. , Maheswaran Shyamala , Ting David T. , Haber Daniel A.
Published: November 2015

Significance

Unique among the large number of noncoding RNA species, the pericentromeric human satellite II (HSATII) repeat is massively expressed in a broad set of epithelial cancers but is nearly undetectable in normal tissues. Here, we show that deregulation of HSATII expression is tightly linked to growth under nonadherent conditions, and we uncover an unexpected mechanism by which HSATII RNA-derived DNA (rdDNA) leads to progressive elongation of pericentromeric regions in tumors. The remarkable specificity of HSATII overexpression in cancers, together with the consequences of targeting its RT, points to a potential novel vulnerability of cancer cells.
Rising morbidity and mortality in midlife among white non-Hispanic Americans in the 21st century
Authors: Case Anne , Deaton Angus
Published: November 2015

Significance

Midlife increases in suicides and drug poisonings have been previously noted. However, that these upward trends were persistent and large enough to drive up all-cause midlife mortality has, to our knowledge, been overlooked. If the white mortality rate for ages 45−54 had held at their 1998 value, 96,000 deaths would have been avoided from 1999–2013, 7,000 in 2013 alone. If it had continued to decline at its previous (1979‒1998) rate, half a million deaths would have been avoided in the period 1999‒2013, comparable to lives lost in the US AIDS epidemic through mid-2015. Concurrent declines in self-reported health, mental health, and ability to work, increased reports of pain, and deteriorating measures of liver function all point to increasing midlife distress.
Beneficial effects of growth hormone-releasing hormone agonists on rat INS-1 cells and on streptozotocin-induced NOD/SCID mice
Authors: Zhang Xianyang , Cui Tengjiao , He Jinlin , Wang Haibo , Cai Renzhi , Popovics Petra , Vidaurre Irving , Sha Wei , Schmid Janine , Ludwig Barbara , Block Norman L. , Bornstein Stefan R. , Schally Andrew V.
Published: November 2015

Significance

Improved therapeutic strategies for transplantation of pancreatic islet cells to selected patients with type-1 diabetes are urgently needed. Growth hormone-releasing hormone (GHRH) agonists to influence growth, function, and engraftment of islet cells were previously reported by us. This study demonstrates greater stimulation by improved GHRH agonists, on proliferation, gene expressions, and the signaling pathways in pancreatic β cells. Agonist MR-409 in vivo reduced the severity of streptozotocin-induced diabetes in nonobese diabetic severe combined immunodeficiency mice. Transplantation of rat islets preconditioned in vitro with MR-409 and its administration in vivo promoted growth, function, and engraftment of exogenous islets, supporting the use of GHRH agonists in type-1 diabetes. The beneficial effects of GHRH agonists on the functions of β cells may also provide approaches to their application in type-2 diabetes.
Electron cryotomography reveals ultrastructure alterations in platelets from patients with ovarian cancer
Authors: Wang Rui , Stone Rebecca L. , Kaelber Jason T. , Rochat Ryan H. , Nick Alpa M. , Vijayan K. Vinod , Afshar-Kharghan Vahid , Schmid Michael F. , Dong Jing-Fei , Sood Anil K. , Chiu Wah
Published: November 2015

Significance

Platelets are known to be both numerically and functionally altered in some patients with cancer. However, structural differences in the platelets from these patients have not been studied. Here we use electron cryotomography to reveal that, compared with control donors, the microtubule system and the mitochondria of platelets from patients diagnosed with ovarian cancer are significantly different. This finding suggests the potential of electron cryotomography as a technology to detect structural biomarkers of diseases affecting platelets.
Role of vascular density and normalization in response to neoadjuvant bevacizumab and chemotherapy in breast cancer patients
Authors: Tolaney Sara M. , Boucher Yves , Duda Dan G. , Martin John D. , Seano Giorgio , Ancukiewicz Marek , Barry William T. , Goel Shom , Lahdenrata Johanna , Isakoff Steven J. , Yeh Eren D. , Jain Saloni R. , Golshan Mehra , Brock Jane , Snuderl Matija , Winer Eric P. , Krop Ian E. , Jain Rakesh K.
Published: November 2015

Significance

Emerging evidence indicates patients who benefit from antiangiogenic therapies have improved vessel function. To determine how bevacizumab modulates vessel morphology to improve vessel function we conducted a phase II trial of preoperative bevacizumab followed by bevacizumab combined with chemotherapy in HER2-negative breast cancer patients. Our results suggest that the clinical response to bevacizumab may occur through an increase in the extent of vascular normalization primarily in patients with a high baseline tumor microvessel density. If validated, these observations suggest approaches to improve antiangiogenic therapy and to identify patients likely to benefit.
Unique COPII component AtSar1a/AtSec23a pair is required for the distinct function of protein ER export in
Arabidopsis thaliana
Authors: Zeng Yonglun , Chung Kin Pan , Li Baiying , Lai Ching Man , Lam Sheung Kwan , Wang Xiangfeng , Cui Yong , Gao Caiji , Luo Ming , Wong Kam-Bo , Schekman Randy , Jiang Liwen
Published: November 2015

Significance

The underlying mechanisms causing the functional diversity of small GTPase Sar1 paralogs in coat protein complex II-mediated protein endoplasmic reticulum (ER) export remain elusive in higher organisms.
Arabidopsis
contains five Sar1 homologs. In this study, we show that AtSar1a exhibits a distinct localization and effects on ER cargo export in plants through a unique interaction with the COPII coat protein AtSec23a. This specific pairing is required for the distinct function in ER export under ER stress in
Arabidopsis
. Our results point to a mechanism underlying the functional diversity of COPII paralogs in eukaryotes.
Elp3 drives Wnt-dependent tumor initiation and regeneration in the intestine
Authors: Ladang Aurélie , Rapino Francesca , Heukamp Lukas C. , Tharun Lars , Shostak Kateryna , Hermand Damien , Delaunay Sylvain , Klevernic Iva , Jiang Zheshen , Jacques Nicolas , Jamart Diane , Migeot Valérie , Florin Alexandra , Göktuna Serkan , Malgrange Brigitte , Sansom Owen J. , Nguyen Laurent , Büttner Reinhard , Close Pierre , Chariot Alain
Published: November 2015

Tumor initiation in the intestine can rapidly occur from Lgr5+ crypt columnar stem cells. Dclk1 is a marker of differentiated Tuft cells and, when coexpressed with Lgr5, also marks intestinal cancer stem cells. Here, we show that Elp3, the catalytic subunit of the Elongator complex, is required for Wnt-driven intestinal tumor initiation and radiation-induced regeneration by maintaining a subpool of Lgr5+/Dclk1+/Sox9+ cells. Elp3 deficiency dramatically delayed tumor appearance in Apc-mutated intestinal epithelia and greatly prolonged mice survival without affecting the normal epithelium. Specific ablation of Elp3 in Lgr5+ cells resulted in marked reduction of polyp formation upon Apc inactivation, in part due to a decreased number of Lgr5+/Dclk1+/Sox9+ cells. Mechanistically, Elp3 is induced by Wnt signaling and promotes Sox9 translation, which is needed to maintain the subpool of Lgr5+/Dclk1+ cancer stem cells. Consequently, Elp3 or Sox9 depletion led to similar defects in Dclk1+ cancer stem cells in ex vivo organoids. Finally, Elp3 deficiency strongly impaired radiation-induced intestinal regeneration, in part because of decreased Sox9 protein levels. Together, our data demonstrate the crucial role of Elp3 in maintaining a subpopulation of Lgr5-derived and Sox9-expressing cells needed to trigger Wnt-driven tumor initiation in the intestine.
Identification of a novel cis-regulatory element essential for immune tolerance
Authors: LaFlam Taylor N. , Seumois Grégory , Miller Corey N. , Lwin Wint , Fasano Kayla J. , Waterfield Michael , Proekt Irina , Vijayanand Pandurangan , Anderson Mark S.
Published: November 2015

Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tolerize self-reactive thymocytes. Interestingly, Aire has a highly tissue-restricted pattern of expression, with only mTECs and peripheral extrathymic Aire-expressing cells (eTACs) known to express detectable levels in adults. Despite this high level of tissue specificity, the cis-regulatory elements that control Aire expression have remained obscure. Here, we identify a highly conserved noncoding DNA element that is essential for Aire expression. This element shows enrichment of enhancer-associated histone marks in mTECs and also has characteristics of being an NF-κB-responsive element. Finally, we find that this element is essential for Aire expression in vivo and necessary to prevent spontaneous autoimmunity, reflecting the importance of this regulatory DNA element in promoting immune tolerance.
Incorporating historical data into aquaculture planning
Authors: Alleway Heidi K. , Thurstan Ruth H. , Lauer Peter R. , Connell Sean D.
Published: November 2015

Marine historical research has made progress in bridging the gap between science and policy, but examples in which it has been effectively applied remain few. In particular, its application to aquaculture remains unexplored. Using actual examples of natural resource management in the state of South Australia, we illustrate how historical data of varying resolution can be incorporated into aquaculture planning. Historical fisheries records were reviewed to identify data on the now extinct native oyster Ostrea angasi fishery throughout the 1800 and early-1900s. Records of catch, number of boats fishing, and catch per unit effort (cpue) were used to test fishing rates and estimate the total quantity of oysters taken from select locations across periods of time. Catch quantities enabled calculation of the minimum number of oysters per hectare for two locations. These data were presented to government scientists, managers, and industry. As a result, interest in growing O. angasi increased and new areas for oyster aquaculture were included in regulatory zoning (spatial planning). Records of introductions of the non-native oyster Saccostrea glomerata, Sydney rock oysters, from 1866 through 1959, were also identified and used to evaluate the biosecurity risk of aquaculture for this species through semi-quantitative risk assessment. Although applications to culture S. glomerata in South Australia had previously been declined, the inclusion of historical data in risk assessment led to the conclusion that applications to culture this species would be accepted. The examples presented here have been effectively incorporated into management processes and represent an important opportunity for the aquaculture industry in South Australia to diversify. This demonstrates that historical data can be used to inform planning and support industry, government, and societies in addressing challenges associated with aquaculture, as well as natural resource management more broadly.
Big Cypress fox squirrel ( Sciurus niger avicennia ) ecology and habitat use in a cypress dome swamp-pine forest mosaic
Authors: Kellam John O. , Jansen Deborah K. , Johnson Annette T. , Arwood Ralph W. , Merrick Melissa J. , Koprowski John L.
Published: November 2015

Forested wetlands are in decline, as are many species that are obligate residents. Big Cypress fox squirrels (BCFS; Sciurus niger avicennia ) are a threatened endemic to wet pine and cypress forests in southwestern Florida. The region is characterized by development resulting in habitat loss, habitat fragmentation, and hydrological change that influence the quality of these wet forests. Through radiotelemetry and field observations, we examined the ecology and habitat use of BCFS in a natural cypress dome-pine forest mosaic. BCFS selected cypress domes for food and nests throughout the year. Cypress dome habitats were the only habitat type to be used more than available; however, the availability of nearby pine forest was also important. Home ranges were large relative to other tree squirrels, with male home ranges exceeding female ranges. Males overlapped more females than males, while sharing similar food preferences and use patterns with females, suggesting that the sexual dimorphism in home range size is related to mate searching. Roads and oil extraction pads were used less frequently than expected and were incorporated into home ranges less than randomly generated features. The importance of cypress domes within the wet forests and grasslands of Big Cypress National Preserve demonstrates the value of maintaining this delicate mosaic.
Comparison of Epidural or Regional Analgesia and Patient-controlled Analgesia
Authors: van Boekel Regina L. M. , Vissers Kris C. P. , van de Vossenberg Glenn , de Baat-Ananta Mira , van der Sande Rob , Scheffer Gert Jan , Steegers Monique A. H.
Published: November 2015

Objectives:

A large number of patients still experience pain after surgery. This study investigates if epidural or regional analgesia (continuous infusion peripheral nerve blocks [CPNB]) provide superior pain relief compared with patient-controlled analgesia (PCIA) and identifies the incidence of minor and major adverse effects or complications of these techniques.

Materials and Methods:

Prospectively collected data of postoperative patients from an online data registration system of a special dedicated nurse-based acute pain service were analyzed. The acute pain service consultations were documented from January 2008 to August 2013 in a university hospital in The Netherlands.

Results:

An analysis was applied on data of 12,399 consecutive patients. Results showed that patients who received epidural analgesia and CPNB reported lower pain scores than those who received PCIA, after undergoing the same procedures. In addition, pain scores at rest were significantly lower than movement-evoked pain scores, in abdominal surgery. Severe nausea was mostly observed in patients with PCIA and itching was most common in patients with epidural analgesia. Opioid-induced respiratory depression was found in 5 patients with PCIA.

Discussion:

Epidural analgesia and CPNB provide better pain relief to patients than PCIA, especially in dynamic pain scores of patients. Evaluating real patient data on every patient visit is important for further improvement of the quality of postoperative pain management. Pain scores may vary widely between patients with similar surgical procedures. Therefore, we recommend that future research focuses on personalized pain measurement and pain management, to improve clinical practice more intensely.
Weighting dissimilarities to detect communities in networks
Authors: Alvarez Alejandro J. , Sanz-Rodríguez Carlos E. , Cabrera Juan Luis
Published: November 2015

Many complex systems can be described as networks exhibiting inner organization as communities of nodes. The identification of communities is a key factor to understand community-based functionality. We propose a family of measures based on the weighted sum of two dissimilarity quantifiers that facilitates efficient classification of communities by tuning the quantifiers’ relative weight to the network’s particularities. Additionally, two new dissimilarities are introduced and incorporated in our analysis. The effectiveness of our approach is tested by examining the Zachary’s Karate Club Network and the
Caenorhabditis elegans
reactions network. The analysis reveals the method’s classification power as confirmed by the efficient detection of intrapathway metabolic functions in
C. elegans
.
Transition from non-periodic to periodic explosions
Authors: Cartes Carlos , Descalzi Orazio
Published: November 2015

We show the existence of periodic exploding dissipative solitons. These non-chaotic explosions appear when higher-order nonlinear and dispersive effects are added to the complex cubic–quintic Ginzburg–Landau equation modelling soliton transmission lines. This counterintuitive phenomenon is the result of period-halving bifurcations leading to order (periodic explosions), followed by period-doubling bifurcations (or intermittency) leading to chaos (non-periodic explosions).