bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-state thermodynamics of the ST2 model for supercooled water
Authors: Holten Vincent , Palmer Jeremy C. , Poole Peter H. , Debenedetti Pablo G. , Anisimov Mikhail A.
Published: March 2014

Thermodynamic properties of the ST2 model for supercooled liquid water exhibit anomalies similar to those observed in real water. A possible explanation of these anomalies is the existence of a metastable, liquid–liquid transition terminated by a critical point. This phenomenon, whose possible existence in real water is the subject of much current experimental work, has been unambiguously demonstrated for this particular model by most recent simulations. In this work, we reproduce the anomalies of two versions of the ST2 model with an equation of state describing water as a non-ideal “mixture” of two different types of local molecular order. We show that the liquid–liquid transition in the ST2 water is energy-driven. This is in contrast to another popular model, mW, in which non-ideality in mixing of two alternative local molecular orders is entropy-driven, and is not sufficiently strong to induce a liquid–liquid transition.
Detection and localization of a defect in a reverberant plate using acoustic field correlation
Authors: Chehami Lynda , Moulin Emmanuel , de Rosny Julien , Prada Claire , Bou Matar Olivier , Benmeddour Farouk , Assaad Jamal
Published: March 2014

Green's function can be retrieved from cross-correlation of a diffuse field generated by noise sources. Today, this important result is the fundamental of several passive imaging techniques. The aim of this paper is to establish the suitability of these methods to detect and locate a defect in a reverberant elastic plate. The relations between the noise cross-correlation function over a few number of noise sources and the imaginary part of the Green's function are derived and numerically validated. Then we show through numerical experiments that this technique is exploitable for defect detection and localization in a differential mode, despite a non-perfect estimation of the Green's functions. Finally, a filtering technique based on the singular value decomposition is shown to improve the detection.
Spin precession by pulsed inductive magnetometry in thin amorphous plates
Authors: Magni Alessandro , Bottauscio Oriano , Caprile Ambra , Celegato Federica , Ferrara Enzo , Fiorillo Fausto
Published: March 2014

Broadband magnetic loss and damping behavior of Co-based amorphous ribbons and thin films have been investigated. The permeability and loss response of the transverse anisotropy ribbon samples in the frequency range DC to 1 GHz is interpreted in terms of combined and distinguishable contributions to the magnetization process by domain wall displacements and magnetization rotations. The latter alone are shown to survive at the highest frequencies, where the losses are calculated via coupled Maxwell and Landau–Lifshitz–Gilbert (LLG) equations. Remarkably high values of the LLG damping coefficient α = 0.1–0.2 are invoked in this theoretical prediction. Direct measurements of α by pulsed inductive microwave magnetometry are thus performed, both in these laminae and in amorphous films of identical composition, obtaining about one order of magnitude increase of the α value upon the 100 nm÷10 μm thickness range. This confirms that dissipation by eddy currents enters the LLG equation via large increase of the damping coefficient.
Cold-cavity measurement of optical loss from oxide-confined vertical-cavity surface-emitting lasers
Authors: Fryslie Stewart T. M. , Siriani Dominic F. , Choquette Kent D.
Published: March 2014

Microcavity laser design and performance optimization requires a quantitative knowledge of the cavity optical losses. A generalized method using sub-threshold spectral measurements matched to model calculations is demonstrated to determine optical loss in microcavity lasers. Cold-cavity spectral characteristics are used to extract the size-dependent optical loss for small diameter oxide-confined vertical-cavity surface emitting lasers. For oxide aperture diameters less than 4 μm, the oxide scattering loss can be greater than 10 cm−1, similar to the typical values of free carrier absorption loss.
Phase structure and magnetic properties of Mn3Ga2 alloy
Authors: Lu Q. M. , Yu F. , Yue M. , Zhang H. G. , Li Y. Q. , Yan X. L. , Liu Y. Q. , Zhang J. X.
Published: March 2014

In this paper, Mn3Ga2 alloys with high saturation magnetization and high Curie temperatures were prepared by levitation melting high pure Mn and Ga elements followed by annealing. The effect of annealing temperature on phase structure and magnetic properties was investigated by means of x-ray diffraction and a vibrating sample magnetometer. A single phase alloy Mn3Ga2, which has tetragonal P4/mmm structure, was obtained with an annealing temperature of 773 K and annealing time of 24 h. The hysteresis curve of its easy axis for this single phase alloy shows that the room temperature coercivity and saturation magnetization are 4.18 kOe and 50.81 emu/g, respectively. The thermomagnetic curves indicate that the Curie temperature is about 650 K and a phase transformation occurs above 823 K.
Fast-scale network dynamics in human cortex have specific spectral covariance patterns
Authors: Freudenburg Zachary V. , Gaona Charles M. , Sharma Mohit , Bundy David T. , Breshears Jonathan D. , Pless Robert B. , Leuthardt Eric C.
Published: March 2014

Significance

How different cortical regions are coordinated during a cognitive task is fundamentally important to understanding brain function. At rest, the brain is subdivided into different functional networks that are bound together at very slow oscillating time scales. Less is understood about how this networked behavior operates during the brief moments of a cognitive operation. By recording brain signals directly from the surface of the human brain, we find that, when performing a simple speech task, broad cortical regions are transiently bound together by shared patterns of brain oscillations that are frequency specific. In addition to demonstrating that cortical areas are broadly networked, these findings provide a new analytic tool for understanding fast-scale dynamics in the brain.
High throughput 3D super-resolution microscopy reveals
Caulobacter crescentus
in vivo Z-ring organization
Authors: Holden Seamus J. , Pengo Thomas , Meibom Karin L. , Fernandez Fernandez Carmen , Collier Justine , Manley Suliana
Published: March 2014

Significance

The bacterial cytoskeletal protein FtsZ, which forms a constricting “Z-ring” during cell division, is the major cytoskeletal protein involved in cell division in almost all prokaryotes, and is a key next-generation antibiotic target. However, the small size of the Z-ring, approximately 500 nm in diameter, makes it difficult to observe in vivo. We provide a quantitative nanoscale picture of Z-ring organization in live cells; these results improve our understanding of the structural and force-generating roles of FtsZ in bacterial cell division. To achieve this, we created an automated modality of superresolution fluorescence microscopy, allowing high-throughput live cell microscopy at nanoscale resolution; this technique should be broadly useful in prokaryotic and eukaryotic systems.
Plate tectonic controls on atmospheric CO2levels since the Triassic
Authors: Van Der Meer Douwe G. , Zeebe Richard E. , van Hinsbergen Douwe J. J. , Sluijs Appy , Spakman Wim , Torsvik Trond H.
Published: March 2014

Significance

Although plate tectonics is generally considered to be the main contributor of CO2production, despite decades of paleoproxy and solid-earth research, this very first-order assumption remains unproven. Based on estimates of total subduction-zone lengths, from a combined analysis of seismic tomography models and plate tectonic reconstructions, we have bridged a major gap between solid-earth sciences and the atmosphere and biosphere sciences by providing understanding of one of the most fundamental controls of climate: variation of plate tectonic activity of our planet. By using the subduction zone length input into the GEOCARBSULF climate model, we obtain a better fit with atmospheric CO2proxies compared with previously used plate tectonic assumptions.
Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands
Authors: Hu Bao-lan , Shen Li-dong , Lian Xu , Zhu Qun , Liu Shuai , Huang Qian , He Zhan-fei , Geng Sha , Cheng Dong-qing , Lou Li-ping , Xu Xiang-yang , Zheng Ping , He Yun-feng
Published: March 2014

Significance

Given the current pressing need to more fully understand the methane cycle on Earth, in particular, unidentified sinks for methane, identifying and quantifying novel sinks for methane is fundamental importance. Here, we provide previously unidentified direct evidence for the nitrite-dependent anaerobic methane oxidation (n-damo) process as a previously overlooked microbial methane sink in wetlands by stable isotope measurements, quantitative PCR assays, and 16S rRNA and particulate methane monooxygenase gene clone library analyses. It is estimated that n-damo could consume 4.1–6.1 Tg of CH
4
m
−2
per year in wetlands under anaerobic conditions, which is roughly 2–6% of current worldwide CH
4
flux estimates for wetlands. Given the worldwide increase in nitrogen pollution, this methane sink may become more important in the future.
Emergence of stable interfaces under extreme plastic deformation
Authors: Beyerlein Irene J. , Mayeur Jason R. , Zheng Shijian , Mara Nathan A. , Wang Jian , Misra Amit
Published: March 2014

Significance

Many processing techniques, such as solid-state phase transformation, epitaxial growth, or solidification, can make nanocomposite materials with preferred crystallographic orientation relationships at internal interfaces. On the other hand, metal-working techniques can make composites in bulk quantities for structural applications but typically the resulting bimetal interfaces lack crystallographic order and are unstable with respect to heating. Using a metal-working roll-bonding technique, we find that at extreme plastic strains, the bimetal interfaces develop a remarkably ordered, preferred atomic structure. Using atomic-scale and crystal-plasticity simulations, we study the dynamical stability conditions responsible for this counterintuitive phenomenon. We show that the emergent interface corresponds to a unique stable state, which leads to exceptional mechanical, thermal, and irradiation stability of the nanocomposite.
Shorter telomeres with high telomerase activity are associated with raised allostatic load and impoverished psychosocial resources
Authors: Zalli Argita , Carvalho Livia A. , Lin Jue , Hamer Mark , Erusalimsky Jorge D. , Blackburn Elizabeth H. , Steptoe Andrew
Published: March 2014

Significance

These findings indicate that the combination of shorter leukocyte telomeres with high telomerase activity is associated with stress-related impairment of function at both the biological and psychological levels. Slow poststress recovery in cardiovascular activity in inflammatory responses and reduced stress responsivity in blood pressure and cortisol are indicative of a state of heightened allostatic load. Older men with the shorter telomere/high telomerase phenotype also show impoverished resources for dealing with stress, including low levels of social support and optimism and higher levels of hostility. The integrated approach taken in this study advances our understanding of the cellular substrate of stress-related processes and documents the dynamic interplay between social environmental exposures and the mechanisms underlying chromosomal integrity.
In vivo chemical exchange saturation transfer imaging allows early detection of a therapeutic response in glioblastoma
Authors: Sagiyama Koji , Mashimo Tomoyuki , Togao Osamu , Vemireddy Vamsidhara , Hatanpaa Kimmo J. , Maher Elizabeth A. , Mickey Bruce E. , Pan Edward , Sherry A. Dean , Bachoo Robert M. , Takahashi Masaya
Published: March 2014

Significance

The prognosis and management of patients with glioma is vastly different depending on whether one detects tumor progression or treatment effects. Although the gold standard in the evaluation of treatment efficacy involves MRI, the currently available imaging methods often do not suffice to make the final decision. Our study demonstrated that amide proton transfer (APT) imaging, one subset of chemical exchange saturation transfer imaging, can detect molecular signals in glioma induced by short-term chemotherapy with temozolomide. These molecular events precede morphologic changes. The APT signal did not decrease in tumors resistant to chemotherapy. APT imaging may provide a useful prognostic biomarker of treatment response or tumor progression in glioma.
Assessing the homogenization of urban land management with an application to US residential lawn care
Authors: Polsky Colin , Grove J. Morgan , Knudson Chris , Groffman Peter M. , Bettez Neil , Cavender-Bares Jeannine , Hall Sharon J. , Heffernan James B. , Hobbie Sarah E. , Larson Kelli L. , Morse Jennifer L. , Neill Christopher , Nelson Kristen C. , Ogden Laura A. , O’Neil-Dunne Jarlath , Pataki Diane E. , Roy Chowdhury Rinku , Steele Meredith K.
Published: March 2014

Significance

This paper offers conceptual and empirical contributions to sustainability science in general and urban-ecological studies in particular. We present a new analytical framework for classifying socioecological measures along a homogenization–differentiation spectrum. This simple 2 × 2 matrix highlights the multiscale nature of the processes and outcomes of interest. Our application of the conceptual framework produces needed empirical insights into the extent to which land management appears to be homogenizing in differing biophysical settings. Results suggest that US lawn care behaviors are more differentiated in practice than in theory. Thus even if the biophysical outcomes of urbanization are homogenizing, managing the associated sustainability implications may require a multiscale, differentiated approach.
Determinants of pore folding in potassium channel biogenesis
Authors: Delaney Erin , Khanna Pooja , Tu LiWei , Robinson John M. , Deutsch Carol
Published: March 2014

Significance

The essential structural feature of canonical K, Na, and Ca channels is a permeation pathway created by four reentrant pore loops. This study provides insights into the biogenic determinants of this reentrant architecture, and therefore potential candidates for folding defects.
Mechanism governing a stem cell-generating
cis
-regulatory element
Authors: Sanalkumar Rajendran , Johnson Kirby D. , Gao Xin , Boyer Meghan E. , Chang Yuan-I , Hewitt Kyle J. , Zhang Jing , Bresnick Emery H.
Published: March 2014

Significance

The continuous replenishment of differentiated cells, for example, those constituting the blood, involves proteins that control the generation and function of stem and progenitor cells. Although “master regulators” are implicated in these processes, many questions remain unanswered regarding how their synthesis and activities are regulated. We describe a mechanism that controls the production of the master regulator GATA binding protein-2 (GATA-2) in the context of blood stem and progenitor cells. Thousands of GATA-2 binding sites exist in the genome, and genetic analyses indicate that they differ greatly and unpredictably in functional importance. The parameters involved in endowing sites with functional activity are not established. We describe unique insights into ascertaining functionally important GATA-2 binding sites within chromosomes.
Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury
Authors: Zhang Ming-Dong , Tortoriello Giuseppe , Hsueh Brian , Tomer Raju , Ye Li , Mitsios Nicholas , Borgius Lotta , Grant Gunnar , Kiehn Ole , Watanabe Masahiko , Uhlén Mathias , Mulder Jan , Deisseroth Karl , Harkany Tibor , Hökfelt Tomas G. M.
Published: March 2014

Significance

Calcium-binding proteins (CaBPs) are key determinants of cellular functions, as well as useful anatomical markers for neural subpopulations. Here, we reveal the distribution and phenotypes of neurons expressing neuronal calcium-binding proteins 1 and 2 (NECAB1/2) in intact mouse dorsal root ganglia (DRGs) and spinal cord and after nerve injury using immunohistochemistry and the CLARITY method. In DRGs, NECAB1/2 are expressed in high numbers (∼70%) of all DRG neurons, including nociceptors. Axonal injury down-regulates NECAB2 in DRGs. In spinal cord, NECAB1/2 show a complementary distribution, mostly in excitatory neurons, and represent unique molecular markers for commissural neurons originally described by Ramón y Cajal. Our characterization of NECABs at the spinal level provides a basis for exploring their role in sensory functions, particularly pain.
Human cytomegalovirus pUL37x1-induced calcium flux activates PKCα, inducing altered cell shape and accumulation of cytoplasmic vesicles
Authors: Sharon-Friling Ronit , Shenk Thomas
Published: March 2014

Significance

The human cytomegalovirus protein, pUL37x1, induces the release of calcium from the endoplasmic reticulum into the cytosol, causing reorganization of the infected cell’s actin network with concomitant cell rounding. This study demonstrates that along with its effects on cell shape, calcium release induces the formation of large cytoplasmic vesicles late after infection. This formation requires the activity of a calcium-dependent kinase, protein kinase Cα, as well as enzymes required for the synthesis of fatty acids and lipids. The failure to produce vesicles is correlated with the reduced production of infectious, enveloped virus particles. This work identifies an additional consequence of pUL37x1 action and links de novo lipid synthesis with a specific morphological change after infection.
Bleb-driven chemotaxis of Dictyostelium cells
Authors: Zatulovskiy Evgeny , Tyson Richard , Bretschneider Till , Kay Robert R.
Published: March 2014

Blebs and F-actin–driven pseudopods are alternative ways of extending the leading edge of migrating cells. We show that Dictyostelium cells switch from using predominantly pseudopods to blebs when migrating under agarose overlays of increasing stiffness. Blebs expand faster than pseudopods leaving behind F-actin scars, but are less persistent. Blebbing cells are strongly chemotactic to cyclic-AMP, producing nearly all of their blebs up-gradient. When cells re-orientate to a needle releasing cyclic-AMP, they stereotypically produce first microspikes, then blebs and pseudopods only later. Genetically, blebbing requires myosin-II and increases when actin polymerization or cortical function is impaired. Cyclic-AMP induces transient blebbing independently of much of the known chemotactic signal transduction machinery, but involving PI3-kinase and downstream PH domain proteins, CRAC and PhdA. Impairment of this PI3-kinase pathway results in slow movement under agarose and cells that produce few blebs, though actin polymerization appears unaffected. We propose that mechanical resistance induces bleb-driven movement in Dictyostelium, which is chemotactic and controlled through PI3-kinase.
The i-AAA protease YME1L and OMA1 cleave OPA1 to balance mitochondrial fusion and fission
Authors: Anand Ruchika , Wai Timothy , Baker Michael J. , Kladt Nikolay , Schauss Astrid C. , Rugarli Elena , Langer Thomas
Published: March 2014

Mitochondrial fusion and structure depend on the dynamin-like GTPase OPA1, whose activity is regulated by proteolytic processing. Constitutive OPA1 cleavage by YME1L and OMA1 at two distinct sites leads to the accumulation of both long and short forms of OPA1 and maintains mitochondrial fusion. Stress-induced OPA1 processing by OMA1 converts OPA1 completely into short isoforms, inhibits fusion, and triggers mitochondrial fragmentation. Here, we have analyzed the function of different OPA1 forms in cells lacking YME1L, OMA1, or both. Unexpectedly, deletion of Oma1 restored mitochondrial tubulation, cristae morphogenesis, and apoptotic resistance in cells lacking YME1L. Long OPA1 forms were sufficient to mediate mitochondrial fusion in these cells. Expression of short OPA1 forms promoted mitochondrial fragmentation, which indicates that they are associated with fission. Consistently, GTPase-inactive, short OPA1 forms partially colocalize with ER–mitochondria contact sites and the mitochondrial fission machinery. Thus, OPA1 processing is dispensable for fusion but coordinates the dynamic behavior of mitochondria and is crucial for mitochondrial integrity and quality control.
Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy
Authors: Ossareh-Nazari Batool , Niño Carlos A. , Bengtson Mario H. , Lee Joong-Won , Joazeiro Claudio A.P. , Dargemont Catherine
Published: March 2014

Autophagy, the process by which proteins or organelles are engulfed by autophagosomes and delivered for vacuolar/lysosomal degradation, is induced to ensure survival under starvation and other stresses. A selective autophagic pathway for 60S ribosomal subunits elicited by nitrogen starvation in yeast—ribophagy—was recently described and requires the Ubp3-Bre5 deubiquitylating enzyme. This discovery implied that an E3 ligases act upstream, whether inhibiting the process or providing an initial required signal. In this paper, we show that Ltn1/Rkr1, a 60S ribosome-associated E3 implicated in translational surveillance, acts as an inhibitor of 60S ribosomal subunit ribophagy and is antagonized by Ubp3. The ribosomal protein Rpl25 is a relevant target. Its ubiquitylation is Ltn1 dependent and Ubp3 reversed, and mutation of its ubiquitylation site rendered ribophagy less dependent on Ubp3. Consistently, the expression of Ltn1—but not Ubp3—rapidly decreased after starvation, presumably to allow ribophagy to proceed. Thus, Ltn1 and Ubp3-Bre5 likely contribute to adapt ribophagy activity to both nutrient supply and protein translation.
A Galactic origin for the fast radio burst FRB010621
Authors: Bannister K. W. , Madsen G. J.
Published: March 2014

The recent detection of fast radio bursts has generated strong interest in identifying the origin of these bright, non-repeating, highly dispersed pulses. The principal limitation in understanding the origin of these bursts is the lack of reliable distance estimates; their high dispersion measures imply that they may be at cosmological distances (0.1 < z < 1.0). Here, we discuss new distance constraints to the FRB010621 (a.k.a J1852−08) first reported by Keane. We use velocity resolved Hα and Hβ observations of diffuse ionized gas towards the burst to calculate an extinction-corrected emission measure along the line of sight. We combine this emission measure with models of Galactic rotation and of electron distribution to derive a 90 per cent probability of the pulse residing in the Galaxy. However, we cannot differentiate between the two Galactic interpretations of Keane: a neutron star with unusual pulse amplitude distribution or Galactic black hole annihilation.
Integrating Patient Safety in the OMFS Curriculum: Survey of 4-Year Residency Programs
Authors: Buhrow Suzanne Morse , Buhrow Jack A.
Published: March 2014

Purpose

In 2003, the Institute of Medicine’s (IOM) Committee on Health Professions Education Summit reported that students in all health professions should demonstrate competency in patient safety and performance improvement strategies to reduce the incidence of preventable medical errors. These recommendations have been adopted in medical, pharmacy, and nursing accreditation standards, yet not required in dental education. The purpose of this study was to explore if 4-year oral and maxillofacial surgery (OMFS) residency programs are aligned with other health professions in following the Institute of Medicine’s recommendations to incorporate evidence-based patient safety training in the postgraduate curricula.

Methods

In October of 2012, a multiple choice questionnaire was sent to 27 four-year oral and maxillofacial surgery residency program directors via a link to Survey Monkey. A descriptive analysis of responses was performed upon achieving a 74% response rate.

Results

Ninety-five percent of the responding 4-year OMFS programs have integrated patient safety training in the residency curriculum. Seventy percent complete between 2 and 10 hours of safety training per academic year. Eighty percent of the programs apply human factors and system engineering theories in morbidity and mortality conferences, and 50% require residents to perform root cause analyses (RCA) of adverse events.

Conclusions

The results of this study indicate that the majority of 4-year OMFS programs include patient safety education in the residency curriculum, although the duration of training and integration of acquired knowledge into practice varied among participants.
Naloxone Triggering the RRT: A Human Antidote?
Authors: Guirgis Faheem W. , Gerdik Cynthia , Wears Robert L. , Kalynych Colleen J. , Sabato Joseph , Godwin Steven A.
Published: March 2014

Objectives

At our institution, we observed an increase in opioid-related adverse events after instituting a new pain treatment protocol. To prevent this, we programmed the Omnicell drug dispensing system to page the RRT whenever naloxone was withdrawn on the general wards.

Methods

Retrospective review of a prospectively collected database with a before and after design.

Results

When comparing the two 12-month periods, there was a decrease in monthly opioid-related cardiac arrests from 0.75 to 0.25 per month (difference = 0.5; 95% CI, 0.04–0.96, P = 0.03) and a nearly significant decrease in code deaths from 0.25 to 0 per month (difference = −0.25; 95% CI, −0.02–0.52, P = 0.07) without a significant decrease in pain satisfaction scores (difference = −2.3; 95% CI, −4.4 to 9.0, P = 0.48) over the study period. There were also decreased RRT interventions from 7.3 to 5.6 per month (difference = −1.7; 95% CI, −0.31 to −3.03, P = 0.02) and decreased inpatient transfers from 2.9 to 1.8 transfers per month (difference = −1.2; 95% CI, −0.38 to −1.96, P = 0.005). When adjusting for inpatient admissions and inpatient days, there was a decrease in opioid-related cardiac arrests from 2.9 to 0.1 per 10,000 admissions (difference = −2.0; 95% CI, −0.2 to −3.8, P = 0.03) and a decrease in cardiac arrests from 0.5 to 0.2 per 10,000 patients (difference = −0.34; 95% CI, −.02 to −0.65, P = 0.04).

Conclusion

Naloxone-triggered activation of the RRT resulted in reduced opioid-related inpatient cardiac arrests without adversely affecting pain satisfaction scores.
Insulin-like growth factor-1 is associated with life-history variation across Mammalia
Authors: Swanson Eli M. , Dantzer Ben
Published: March 2014

Despite the diversity of mammalian life histories, persistent patterns of covariation have been identified, such as the ‘fast–slow’ axis of life-history covariation. Smaller species generally exhibit ‘faster’ life histories, developing and reproducing rapidly, but dying young. Hormonal mechanisms with pleiotropic effects may mediate such broad patterns of life-history variation. Insulin-like growth factor 1 (IGF-1) is one such mechanism because heightened IGF-1 activity is related to traits associated with faster life histories, such as increased growth and reproduction, but decreased lifespan. Using comparative methods, we show that among 41 mammalian species, increased plasma IGF-1 concentrations are associated with fast life histories and altricial reproductive patterns. Interspecific path analyses show that the effects of IGF-1 on these broad patterns of life-history variation are through its direct effects on some individual life-history traits (adult body size, growth rate, basal metabolic rate) and through its indirect effects on the remaining life-history traits. Our results suggest that the role of IGF-1 as a mechanism mediating life-history variation is conserved over the evolutionary time period defining mammalian diversification, that hormone–trait linkages can evolve as a unit, and that suites of life-history traits could be adjusted in response to selection through changes in plasma IGF-1.
Inkjet-printed flexible organic thin-film thermoelectric devices based on p- and n-type poly(metal 1,1,2,2-ethenetetrathiolate)s/polymer composites through ball-milling
Authors: Jiao Fei , Di Chong-an , Sun Yimeng , Sheng Peng , Xu Wei , Zhu Daoben
Published: March 2014

In this article, we put forward a simple method for the synthesis of thermoelectric (TE) composite materials. Both n- and p-type composites were obtained by ball-milling the insoluble and infusible metal coordination polymers with other polymer solutions. The particle size, film morphology and composition were characterized by dynamic light scattering, scanning electron microscopy, transmission electron microscopy and energy-dispersive X-ray spectroscopy. The TE properties of the drop-cast composite film were measured at different temperatures. An inkjet-printed flexible device was fabricated and the output voltage and short-circuit current at various hot-side temperatures (
T
hot
) and temperature gradients (Δ
T
) were tested. The composite material not only highly maintained the TE properties of the pristine material but also greatly improved its processability. This method can be extended to other insoluble and infusible TE materials for solution-processed flexible TE devices.
Description of Lutimonas
halocynthiae sp. nov., isolated from a golden sea squirt (Halocynthia aurantium), reclassification of Aestuariicola saemankumensis as Lutimonas
saemankumensis comb. nov. and emended description of the genus Lutimonas
Authors: Kim Young-Ok , Park Sooyeon , Nam Bo-Hye , Jung Yong-Taek , Kim Dong-Gyun , Bae Kyung Sook , Yoon Jung-Hoon
Published: March 2014

A Gram-stain-negative, non-motile, coccoid, ovoid or rod-shaped bacterial strain, designated RSS3-C1T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS3-C1T was found to grow optimally at 20–25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS3-C1T clustered with the type strains of

Lutimonas vermicola

and

Aestuariicola saemankumensis

. Strain RSS3-C1T exhibited 98.8 % 16S rRNA gene sequence similarity to each type strain. Strain RSS3-C1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain RSS3-C1T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain RSS3-C1T was 39.2 mol%, and DNA–DNA relatedness to the type strains of and was 21±5.3 and 26±7.5 %, respectively. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RSS3-C1T is separated from and . On the basis of the data presented, strain RSS3-C1T is considered to represent a novel species of the genus

Lutimonas

, for which the name Lutimonas halocynthiae sp. nov. is proposed. The type strain is RSS3-C1T ( = KCTC 32537T = CECT 8444T). In this study, it is also proposed that

Aestuariicola saemankumensis

should be reclassified as a member of the genus

Lutimonas

, as
Lutimonas

saemankumensis comb. nov. (type strain SMK-142T = KCTC 22171T = CCUG 55329T), and the description of the genus

Lutimonas

is emended.
Wenxinia saemankumensis sp. nov., isolated from a tidal flat sediment
Authors: Park Sooyeon , Jung Yong-Taek , Yoon Jung-Hoon
Published: March 2014

A Gram-stain-negative, non-motile, ovoid- or rod-shaped bacterial strain, designated S-22T, belonging to the class
Alphaproteobacteria
, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain S-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain S-22T joined
Wenxinia marina
HY34T, with which it exhibited highest 16S rRNA gene sequence similarity (98.0 %). The DNA G+C content was 72.3 mol% and the mean DNA–DNA relatedness value between strain S-22T and the type strain of
W. marina
was 3.7 %. Strain S-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-22T is distinguishable from
W. marina
. On the basis of the data presented, strain S-22T is considered to represent a novel species of the genus

Wenxinia

, for which the name Wenxinia saemankumensis sp. nov. is proposed. The type strain of is S-22T ( = KCTC 32548T = CECT 8456T).
Alignathon: A competitive assessment of whole genome alignment methods
Authors: Earl Dent , Nguyen Ngan , Hickey Glenn , Harris Robert S. , Fitzgerald Stephen , Beal Kathryn , Seledtsov Igor , Molodtsov Vladimir , Raney Brian J. , Clawson Hiram , Kim Jaebum , Kemena Carsten , Chang Jia-Ming , Erb Ionas , Poliakov Alexander , Hou Minmei , Herrero Javier , Solovyev Victor , Darling Aaron E. , Ma Jian , Notredame Cedric , Brudno Michael , Dubchak Inna , Haussler David , Paten Benedict
Published: March 2014

Background

Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark datasets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole genome alignment (WGA).

Results

Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments, and assessments were performed collectively after all the submissions were received. Three datasets were used: two of simulated primate and mammalian phylogenies, and one of 20 real fly genomes. In total 35 submissions were assessed, submitted by ten teams using 12 different alignment pipelines.

Conclusions

We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable difference in the alignment quality of differently annotated regions, and found few tools aligned the duplications analysed. We found many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all datasets, submissions and assessment programs for further study, and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.
Polymerase theta-mediated end joining of replication-associated DNA breaks in C. elegans
Authors: Roerink Sophie F. , van Schendel Robin , Tijsterman Marcel
Published: March 2014

DNA lesions that block replication fork progression are drivers of cancer-associated genome alterations, but the error-prone DNA repair mechanisms acting on collapsed replication are incompletely understood, and their contribution to genome evolution largely unexplored. Here, through whole-genome sequencing of animal populations that were clonally propagated for more than 50 generations, we identify a distinct class of deletions that spontaneously accumulate in C. elegans strains lacking translesion synthesis (TLS) polymerases. Emerging DNA double-strand breaks are repaired via an error-prone mechanism in which the outermost nucleotide of one end serves to prime DNA synthesis on the other end. This pathway critically depends on the A-family polymerase theta, which protects the genome against gross chromosomal rearrangements. By comparing the genomes of isolates of C. elegans from different geographical regions, we found that in fact most spontaneously evolving structural variations match the signature of polymerase theta-mediated end joining (TMEJ), illustrating that this pathway is an important source of genetic diversification.
(4S,5R)-4-Benzyloxy-5-[4-(cyclohexanecarbonyl)phenyl]-1-(4-methoxybenzyl)pyrrolidin-2-one
Authors: Gao Yan-Jiao , Ma Jie , Zheng Xiao
Published: March 2014

The title compound, C32H35NO4, is an unexpected product obtained in the SmI2-mediated radical cross-coupling of a lactam 2-pyridyl sulfone with an arone. The asymmetric unit contains two molecules. In both molecules, the core pyrrolidinone ring adopts an approximate envelope conformation (with the C atom bearling the benzyloxy substituent as the flap) and the cyclohexyl ring has a chair conformation. The relative orientation of the two substitutent groups at the 4- and 5-positions of the pyrrolidinone ring isantiin both molecules, with O(benzyloxy)—C—C—C(benzene) torsion angles of 150.8 (3) and 154.2 (2)°. In the crystal, C—H...O interactions involving carbonyl groups as acceptors lead to the formation of a tape motif propagating parallel to thea-axis direction.
Redetermination of 2-methyl-4-nitropyridineN-oxide
Authors: Peukert Max , Seichter Wilhelm , Weber Edwin
Published: March 2014

An improved crystal structure of the title compound, C6H6N2O3, is reported. The structure, previously solved [Liet al.(1987).Jiegou Huaxue (Chin. J. Struct. Chem.),6, 20–24] in the orthorhombic space groupPca21and refined toR= 0.067, has been solved in the orthorhombic space groupPbcmwith data of enhanced quality, giving an improved structure (R= 0.0485). The molecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of molecular sheets extending parallel to theabplane and connectedviaC—H...O contacts involving ring H atoms and O atoms of theN-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers.
Tetraethylammonium 7,12-dicyano-1-carba-closo-dodecaborate
Authors: Juhasz Marcus A. , Juers Douglas H. , Dwulet Gregory E. , Rosenbaum Aaron J.
Published: March 2014

In the title compound, C8H20N+·C3H10B11N2−, the carborane anion cage displays nearly-perfectCssymmetry, with the two CN groups lying on a noncrystallographic mirror plane that bisects the cage. In the crystal, the anions form extended chains along thea-axis direction, with C—H...N hydrogen bonds linking consecutive anions. The C[triple-bond]N bond lengths (and B—C[triple-bond]N angles) in the nitrile moities are 1.1201 (19) Å, 178.60 (15)° and 1.1433 (17) Å, 179.45 (15)°, similar to those observed in organic nitriles. A hydrogen bond between a methylene H atom of the cation and the N atom in one of the nitrile groups of the anion is the closest contact between the anion and cation, at 2.52 Å.
(1S*,3R*,5S*,7S*)-4,4,8,8-Tetrachloro-1-isopropyl-5-methyltricyclo[5.1.0.03,5]octane
Authors: Turdybekov Koblandy M. , Ryazantsev Oleg G. , Atazhanova Gayane A. , Adekenov Sergazy M.
Published: March 2014

The title compound, C12H16Cl4, is a derivative of the natural product 1-isopropyl-4-methylcyclohexa-1,4-diene, and represents a diastereomer with twotrans-fused cyclopropane rings. Both enantiomers are present in the non-centrosymmetric polar space groupPna21. The central cyclohexane ring is planar within 0.02 (1) Å. The C atoms of dichloromethylene groups deviate from this plane by 1.19 (1) and −1.26 (1) Å, whereas the isopropyl and methyl groups are oriented more equatorially, deviating by 0.71 (1) and −0.87 (1) Å, respectively.
(2-Chloropyrimidin-4-yl)ferrocene
Authors: Shi Guo-Qing , Li Yang , Gao Xiang , Hao Long-Fei , Zhao Wen-en
Published: March 2014

In the title compound, [Fe(C5H5)(C9H6ClN2)], the two cyclopentadienyl rings are almost parallel, subtending a dihedral angle of 3.01 (5)°. The dihedral angle between the substituted cyclopentadienyl ring and the pyrimidinyl ring is 12.02 (1)°. The conformation of the two cyclopentadienyl rings in the ferrocenyl moiety is eclipsed.
X-ray harmonics rejection on third-generation synchrotron sources using compound refractive lenses
Authors: Polikarpov Maxim , Snigireva Irina , Snigirev Anatoly
Published: March 2014

A new method of harmonics rejection based on X-ray refractive optics has been proposed. Taking into account the fact that the focal distance of the refractive lens is energy-dependent, the use of an off-axis illumination of the lens immediately leads to spatial separation of the energy spectrum by focusing the fundamental harmonic at the focal point and suppressing the unfocused high-energy radiation with a screen absorber or slit. The experiment was performed at the ESRF ID06 beamline in the in-line geometry using an X-ray transfocator with compound refractive lenses. Using this technique the presence of the third harmonic has been reduced to 10−3. In total, our method enabled suppression of all higher-order harmonics to five orders of magnitude using monochromator detuning. The method is well suited to third-generation synchrotron radiation sources and is very promising for the future ultimate storage rings.
Performance of a collimating L-shaped laterally graded multilayer mirror for the IXS analyzer system at NSLS-II
Authors: Suvorov Alexey , Coburn David S. , Cunsolo Alessandro , Keister Jeffrey W. , Upton Mary H. , Cai Yong Q.
Published: March 2014

The L-shaped laterally graded multilayer mirror is a vital part of the ultrahigh-energy and momentum-resolution inelastic X-ray scattering spectrometer at the National Synchrotron Light Source II. This mirror was designed and implemented as a two-dimensional collimating optic for the analyzer system. Its performance was characterized using a secondary large-divergence source at the 30-ID beamline of the Advanced Photon Source, which yielded an integrated reflectivity of 47% and a collimated beam divergence of 78 µrad with a source size of 10 µm. Numerical simulations of the mirror performance in tandem with the analyzer crystal optics provided details on the acceptance sample volume in forward scattering and defined the technical requirements on the mirror stability and positioning precision. It was shown that the mirror spatial and angular stability must be in the range <8.4 µm and <21.4 µrad, respectively, for reliable operation of the analyzer.
Applications of direct methods in protein crystallography for dealing with diffraction data down to 5 Å resolution
Authors: Fan Haifu , Gu Yuanxin , He Yao , Lin Zhengjiong , Wang Jiawei , Yao Deqiang , Zhang Tao
Published: March 2014

Apart from solving the heavy-atom substructure in proteins andab initiophasing of protein diffraction data at atomic resolution, direct methods have also been successfully combined with other protein crystallographic methods in dealing with diffraction data far below atomic resolution, leading to significantly improved results. In this respect, direct methods provide phase constraints in reciprocal space within a dual-space iterative framework rather than solve the phase problem independently. Applications of this type of direct methods to difficult SAD phasing, model completion and low-resolution phase extension will be described in detail.
Defining ecologically relevant water quality targets for lakes in Europe
Authors: Poikane Sandra , Portielje Rob , van den Berg Marcel , Phillips Geoff , Brucet Sandra , Carvalho Laurence , Mischke Ute , Ott Ingmar , Soszka Hanna , Van Wichelen Jeroen
Published: March 2014

The implementation of the Water Framework Directive requires EU member states to establish and harmonize ecological status class boundaries for biological quality elements. In this paper, we describe an approach for defining ecological class boundaries that delineates shifts in lake ecosystem functioning and, therefore, provides ecologically meaningful targets for water policy in Europe.

We collected an extensive data set of 810 lake‐years from nine Central European countries, and we used phytoplankton chlorophyll a, a metric widely used to measure the impact of eutrophication in lakes. Our approach establishes chlorophyll a target values in relation to three significant ecological effects of eutrophication: the decline of aquatic macrophytes, the dominance of potentially harmful cyanobacteria and the major functional switch from a clear water to a turbid state.

Ranges of threshold chlorophyll a concentrations are given for the two most common lake types in lowland Central Europe: for moderately deep lakes (mean depth 3–15 m), the greatest ecological shifts occur in the range 10–12 μg L−1 chlorophyll a, and for shallow lakes (<3 m mean depth), in the range 21–23 μg L−1 chlorophyll a.

Synthesis and applications. Our study provides class boundaries for determining the ecological status of lakes, which have robust ecological consequences for lake functioning and which, therefore, provide strong and objective targets for sustainable water management in Europe. The results have been endorsed by all participant member states and adopted in the European Commission legislation, marking the first attempt in international water policy to move from physico‐chemical quality standards to harmonized ecologically based quality targets.
Release thresholds for moss spores: the importance of turbulence and sporophyte length
Authors: Johansson Victor , Lönnell Niklas , Sundberg Sebastian , Hylander Kristoffer
Published: March 2014

Adequately describing the dispersal mechanisms of a species is important for understanding and predicting its distribution dynamics in space and time. For wind‐dispersed species, the transportation of airborne propagules is comparatively well studied, while the mechanisms triggering propagule release are poorly understood, especially for cryptogams.

We investigated the effect of wind speed and turbulence on spore release in the moss Atrichum undulatum in a wind tunnel. Specifically, we measured the amount of spores released from sporophytes when exposed to different wind speeds, in high and low turbulence, using a particle counter. We also related spore release to variation in vibrations of the sporophyte and investigated how the vibrations were affected by wind speed, turbulence and sporophyte length (here including capsule, seta and the top part of the shoot).

We show that in high turbulence, the amount of spores released increased with increasing wind speed, while in low turbulence, it did not, within the wind speed range 0.8–4.3 m s−1. However, there was a threshold in wind speed (˜2.5–3 m s−1) before large amounts of spores started to be released in turbulent flow, which coincided with incipient vibrations of the sporophyte. Thresholds in wind variation, rather than average wind speed, seemed to initiate sporophyte vibrations. The vibration threshold increased with decreasing sporophyte length.

The deposition of spores near the source decreased with increasing wind variation during the time of their release, based on simulated spore deposition from another study of moss dispersal.

Synthesis. We suggest that vibration of moss sporophytes is an important mechanism to regulate spore release and that turbulence and sporophyte length regulate the onset of sporophyte vibration. Spore release thresholds affect dispersal distances and have implications for our understanding and predictions of species distribution patterns, population dynamics and persistence. The mechanisms of this phase of the dispersal process are also important to explore for other species, as there may be a substantial variation depending on the species' different traits.