bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-Debye heat capacity formula refined and applied to GaP, GaAs, GaSb, InP, InAs, and InSb
Authors: Pässler R.
Published: August 2013

Characteristic non-Debye behaviors of low-temperature heat capacities of GaP, GaAs, GaSb, InP, InAs, and InSb, which are manifested above all in form of non-monotonic behaviors (local maxima) of the respective Cp(T)/T3 curves in the cryogenic region, are described by means of a refined version of a recently proposed low-to-high-temperature interpolation formula of non-Debye type. Least-mean-square fittings of representative Cp(T) data sets available for these materials from several sources show excellent agreements, from the liquid-helium region up to room temperature. The results of detailed calculations of the respective material-specific Debye temperature curves, ΘD(T), are represented in graphical form. The strong, non-monotonic variations of ΘD(T) values confirm that it is impossible to provide reasonable numerical simulations of measured Cp(T) dependences in terms of fixed Debye temperatures. We show that it is possible to describe in good approximation the complete Debye temperature curves, from the cryogenic region up to their definitive disappearance (dropping to 0) in the high temperature region, by a couple of unprecedented algebraic formulas. The task of constructing physically adequate prolongations of the low-temperature Cp(T) curves up to melting points was strongly impeded by partly rather large differences (up to an order of 10 J/(K·mol)) between the high-temperature data sets presented in different research papers and/or data reviews. Physically plausible criteria are invoked, which enabled an a priori rejection of a series of obviously unrealistic high-temperature data sets. Residual uncertainties for GaAs and InAs could be overcome by re-evaluations of former enthalpy data on the basis of a novel set of properly specified four-parameter polynomial expressions applying to large regions, from moderately low temperatures up to melting points. Detailed analytical and numerical descriptions are given for the anharmonicity-related differences of isobaric vs. isochoric (harmonic) parts of heat capacities. Relevant sets of empirical parameters and representative collections of heat capacity and Debye temperature values for all materials under study are presented in tabulated form.
Optical bistability in side-mode injection locked dual-mode Fabry-Pérot laser diode
Authors: Wu Jian Wei , Nakarmi Bikash , Hoai Tran Quoc , Won Yong Hyub
Published: August 2013

In this paper, optical bistability characteristics are demonstrated experimentally based on a dual-mode laser system comprising a multi-mode Fabry-Pérot laser diode (MMFP-LD) and a built-in feedback cavity formed by a fiber facet. The results show that two lasing modes with frequency separation of ∼0.58 THz and comparable peak powers can be achieved by judicious adjustment of the bias current and the operating temperature of the laser chip, which has a peak fluctuation of less than ∼1 dBm over a measurement period of one hour. A combination of appropriate external injection power and wavelength detuning can result in remarkable optical bistability in two oscillation modes, in which the resulting contrast ratio between the unlocked and locked states can be up to 30 dB, and the corresponding hysteresis loop width can be changed by controlling the side-mode injection power and the wavelength detuning.
A novel mode of current switching dependent on activated charge transport
Authors: Britton David T. , Walton Stanley D. , Zambou Serges , Magunje Batsirai , Jonah Emmanuel O. , Härting Margit
Published: August 2013

We demonstrate a fully printed transistor with a planar triode geometry, using nanoparticulate silicon as the semiconductor material, which has a unique mode of operation as an electrically controlled two-way (double throw) switch. A signal applied to the base changes the direction of the current from between the collector and base to between the base and emitter. We further show that the switching characteristic results from the activated charge transport in the semiconductor material, and that it is independent of the dominant carrier type in the semiconductor and the nature of the junction between the semiconductor and the three contacts. The same equivalent circuit, and hence similar device characteristics, can be produced using any other material combination with non-linear current-voltage characteristics, such as a suitable combination of semiconducting and conducting materials, such that a Schottky junction is present at all three contacts.
Multidisciplinary collaboration in primary care: through the eyes of patients
Authors: Cheong Lynn H. , Armour Carol L. , Bosnic-Anticevich Sinthia Z.
Published: August 2013

Managing chronic illness is highly complex and the pathways to access health care for the patient are unpredictable and often unknown. While multidisciplinary care (MDC) arrangements are promoted in the Australian primary health care system, there is a paucity of research on multidisciplinary collaboration from patients’ perspectives. This exploratory study is the first to gain an understanding of the experiences, perceptions, attitudes and potential role of people with chronic illness (asthma) on the delivery of MDC in the Australian primary health care setting. In-depth semi-structured interviews were conducted with asthma patients from Sydney, Australia. Qualitative analysis of data indicates that patients are significant players in MDC and their perceptions of their chronic condition, perceived roles of health care professionals, and expectations of health care delivery, influence their participation and attitudes towards multidisciplinary services. Our research shows the challenges presented by patients in the delivery and establishment of multidisciplinary health care teams, and highlights the need to consider patients’ perspectives in the development of MDC models in primary care.
Conditionals by inversion provide a universal method for the generation of conditional alleles
Authors: Economides Aris N. , Frendewey David , Yang Peter , Dominguez Melissa G. , Dore Anthony T. , Lobov Ivan B. , Persaud Trikaldarshi , Rojas Jose , McClain Joyce , Lengyel Peter , Droguett Gustavo , Chernomorsky Rostislav , Stevens Sean , Auerbach Wojtek , DeChiara Thomas M. , Pouyemirou William , Cruz Joseph M. , Feeley Kieran , Mellis Ian A. , Yasenchack Jason , Hatsell Sarah J. , Xie LiQin , Latres Esther , Huang Lily , Zhang Yuhong , Pefanis Evangelos , Skokos Dimitris , Deckelbaum Ron A. , Croll Susan D. , Davis Samuel , Valenzuela David M. , Gale Nicholas W. , Murphy Andrew J. , Yancopoulos George D.
Published: August 2013

Significance

We describe conditional by inversion (COIN), a new design for conditional alleles that uses an optimized conditional gene trap module (COIN module) inserted into the target gene in an orientation opposite to the gene’s direction of transcription. Activation by Cre recombinase inverts the COIN module, resulting in expression of a reporter and termination of transcription, thereby inactivating the target gene while marking the cells where the conditional event has occurred. Creation of COIN alleles for more than 20 genes showed that it is a robust and universal method—applicable to any gene regardless of exon–intron structure—that overcomes the limitations of previous conditional approaches.
Auditory ganglion source of Sonic hedgehog regulates timing of cell cycle exit and differentiation of mammalian cochlear hair cells
Authors: Bok Jinwoong , Zenczak Colleen , Hwang Chan Ho , Wu Doris K.
Published: August 2013

Neural precursor cells of the central nervous system undergo successive temporal waves of terminal division, each of which is soon followed by the onset of cell differentiation. The organ of Corti in the mammalian cochlea develops differently, such that precursors at the apex are the first to exit from the cell cycle but the last to begin differentiating as mechanosensory hair cells. Using a tissue-specific knockout approach in mice, we show that this unique temporal pattern of sensory cell development requires that the adjacent auditory (spiral) ganglion serve as a source of the signaling molecule Sonic hedgehog (Shh). In the absence of this signaling, the cochlear duct is shortened, sensory hair cell precursors exit from the cell cycle prematurely, and hair cell differentiation closely follows cell cycle exit in a similar apical-to-basal direction. The dynamic relationship between the restriction of
Shh
expression in the developing spiral ganglion and its proximity to regions of the growing cochlear duct dictates the timing of terminal mitosis of hair cell precursors and their subsequent differentiation.
Host-related metabolic cues affect colonization strategies of a root endophyte
Authors: Lahrmann Urs , Ding Yi , Banhara Aline , Rath Magnus , Hajirezaei Mohammad R. , Döhlemann Stefanie , von Wirén Nicolaus , Parniske Martin , Zuccaro Alga
Published: August 2013

The mechanisms underpinning broad compatibility in root symbiosis are largely unexplored. The generalist root endophyte
Piriformospora indica
establishes long-lasting interactions with morphologically and biochemically different hosts, stimulating their growth, alleviating salt stress, and inducing local and systemic resistance to pathogens. Cytological studies and global investigations of fungal transcriptional responses to colonization of barley and
Arabidopsis
at different symbiotic stages identified host-dependent colonization strategies and host-specifically induced effector candidates. Here, we show that in
Arabidopsis
,
P. indica
establishes and maintains biotrophic nutrition within living epidermal cells, whereas in barley the symbiont undergoes a nutritional switch to saprotrophy that is associated with the production of secondary thinner hyphae in dead cortex cells. Consistent with a diversified trophic behavior and with the occurrence of nitrogen deficiency at the onset of saprotrophy in barley, fungal genes encoding hydrolytic enzymes and nutrient transporters were highly induced in this host but not in
Arabidopsis
. Silencing of the high-affinity ammonium transporter
PiAMT1
gene, whose transcripts are accumulating during nitrogen starvation and in barley, resulted in enhanced colonization of this host, whereas it had no effect on the colonization of
Arabidopsis
. Increased levels of free amino acids and reduced enzymatic activity for the cell-death marker VPE (vacuolar-processing enzyme) in colonized barley roots coincided with an extended biotrophic lifestyle of
P. indica
upon silencing of
PiAMT1
. This suggests that PiAmt1 functions as a nitrogen sensor mediating the signal that triggers the
in planta
activation of the saprotrophic program. Thus, host-related metabolic cues affect the expression of
P. indica
’s alternative lifestyles.
Influence of early-life nutrition on mortality and reproductive success during a subsequent famine in a preindustrial population
Authors: Hayward Adam D. , Rickard Ian J. , Lummaa Virpi
Published: August 2013

Individuals with insufficient nutrition during development often experience poorer later-life health and evolutionary fitness. The Predictive Adaptive Response (PAR) hypothesis proposes that poor early-life nutrition induces physiological changes that maximize fitness in similar environments in adulthood and that metabolic diseases result when individuals experiencing poor nutrition during development subsequently encounter good nutrition in adulthood. However, although cohort studies have shown that famine exposure in utero reduces health in favorable later-life conditions, no study on humans has demonstrated the predicted fitness benefit under low later-life nutrition, leaving the evolutionary origins of such plasticity unexplored. Taking advantage of a well-documented famine and unique datasets of individual life histories and crop yields from two preindustrial Finnish populations, we provide a test of key predictions of the PAR hypothesis. Known individuals from fifty cohorts were followed from birth until the famine, where we analyzed their survival and reproductive success in relation to the crop yields around birth. We were also able to test whether the long-term effects of early-life nutrition differed between individuals of varying socioeconomic status. We found that, contrary to predictions of the PAR hypothesis, individuals experiencing low early-life crop yields showed lower survival and fertility during the famine than individuals experiencing high early-life crop yields. These effects were more pronounced among young individuals and those of low socioeconomic status. Our results do not support the hypothesis that PARs should have been favored by natural selection and suggest that alternative models may need to be invoked to explain the epidemiology of metabolic diseases.
State-dependent climate sensitivity in past warm climates and its implications for future climate projections
Authors: Caballero Rodrigo , Huber Matthew
Published: August 2013

Projections of future climate depend critically on refined estimates of climate sensitivity. Recent progress in temperature proxies dramatically increases the magnitude of warming reconstructed from early Paleogene greenhouse climates and demands a close examination of the forcing and feedback mechanisms that maintained this warmth and the broad dynamic range that these paleoclimate records attest to. Here, we show that several complementary resolutions to these questions are possible in the context of model simulations using modern and early Paleogene configurations. We find that (
i
) changes in boundary conditions representative of slow “Earth system” feedbacks play an important role in maintaining elevated early Paleogene temperatures, (
ii
) radiative forcing by carbon dioxide deviates significantly from pure logarithmic behavior at concentrations relevant for simulation of the early Paleogene, and (
iii
) fast or “Charney” climate sensitivity in this model increases sharply as the climate warms. Thus, increased forcing and increased slow and fast sensitivity can all play a substantial role in maintaining early Paleogene warmth. This poses an equifinality problem: The same climate can be maintained by a different mix of these ingredients; however, at present, the mix cannot be constrained directly from climate proxy data. The implications of strongly state-dependent fast sensitivity reach far beyond the early Paleogene. The study of past warm climates may not narrow uncertainty in future climate projections in coming centuries because fast climate sensitivity may itself be state-dependent, but proxies and models are both consistent with significant increases in fast sensitivity with increasing temperature.
ETV4
promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer
Authors: Aytes Alvaro , Mitrofanova Antonina , Kinkade Carolyn Waugh , Lefebvre Celine , Lei Ming , Phelan Vanessa , LeKaye H. Carl , Koutcher Jason A. , Cardiff Robert D. , Califano Andrea , Shen Michael M. , Abate-Shen Cory
Published: August 2013

Significance

Although locally invasive prostate cancer is nearly always curable, metastatic prostate cancer usually results in lethality. Our study investigates the temporal progression and molecular mechanisms underlying prostate cancer metastasis using a new genetically engineered mouse model. Using lineage-tracing analyses, we show that dissemination of tumor cells occurs early in cancer progression, and well before the occurrence of metastases. We further show that metastasis is temporally coincident with expression of the oncogenic
ETS
gene
Etv4
, and that
Etv4
promotes prostate cancer metastasis in vivo. Our findings suggest that
Etv4
may be a target for therapeutic intervention in metastatic prostate cancer.
Inhibition of pluripotent stem cell-derived teratoma formation by small molecules
Authors: Lee Mi-Ok , Moon Sung Hwan , Jeong Ho-Chang , Yi Ji-Yeon , Lee Tae-Hee , Shim Sung Han , Rhee Yong-Hee , Lee Sang-Hun , Oh Seok-Jeong , Lee Moo-Yeol , Han Min-Joon , Cho Yee Sook , Chung Hyung-Min , Kim Kwang-Soo , Cha Hyuk-Jin
Published: August 2013

Significance

We found that quercetin/YM155-induced selective cell death is sufficient to completely inhibit teratoma formation after transplantation of human pluripotent stem cell (hPSC)-derived cells. These data provide the first “proof of concept” that small-molecule targeting of hPSC-specific antiapoptotic pathway(s) is a viable strategy to prevent tumor formation by selectively eliminating remaining undifferentiated pluripotent cells for safe hPSC-based therapy.
Convergent Ca
2+
and Zn
2+
signaling regulates apoptotic Kv2.1 K
+
currents
Authors: McCord Meghan C. , Aizenman Elias
Published: August 2013

A simultaneous increase in cytosolic Zn
2+
and Ca
2+
accompanies the initiation of neuronal cell death signaling cascades. However, the molecular convergence points of cellular processes activated by these cations are poorly understood. Here, we show that Ca
2+
-dependent activation of Ca
2+
/calmodulin-dependent protein kinase II (CaMKII) is required for a cell death-enabling process previously shown to also depend on Zn
2+
. We have reported that oxidant-induced intraneuronal Zn
2+
liberation triggers a syntaxin-dependent incorporation of Kv2.1 voltage-gated potassium channels into the plasma membrane. This channel insertion can be detected as a marked enhancement of delayed rectifier K
+
currents in voltage clamp measurements observed at least 3 h following a short exposure to an apoptogenic stimulus. This current increase is the process responsible for the cytoplasmic loss of K
+
that enables protease and nuclease activation during apoptosis. In the present study, we demonstrate that an oxidative stimulus also promotes intracellular Ca
2+
release and activation of CaMKII, which, in turn, modulates the ability of syntaxin to interact with Kv2.1. Pharmacological or molecular inhibition of CaMKII prevents the K
+
current enhancement observed following oxidative injury and, importantly, significantly increases neuronal viability. These findings reveal a previously unrecognized cooperative convergence of Ca
2+
- and Zn
2+
-mediated injurious signaling pathways, providing a potentially unique target for therapeutic intervention in neurodegenerative conditions associated with oxidative stress.
Understanding metropolitan patterns of daily encounters
Authors: Sun Lijun , Axhausen Kay W. , Lee Der-Horng , Huang Xianfeng
Published: August 2013

Understanding of the mechanisms driving our daily face-to-face encounters is still limited; the field lacks large-scale datasets describing both individual behaviors and their collective interactions. However, here, with the help of travel smart card data, we uncover such encounter mechanisms and structures by constructing a time-resolved in-vehicle social encounter network on public buses in a city (about 5 million residents). Using a population scale dataset, we find physical encounters display reproducible temporal patterns, indicating that repeated encounters are regular and identical. On an individual scale, we find that collective regularities dominate distinct encounters’ bounded nature. An individual’s encounter capability is rooted in his/her daily behavioral regularity, explaining the emergence of “familiar strangers” in daily life. Strikingly, we find individuals with repeated encounters are not grouped into small communities, but become strongly connected over time, resulting in a large, but imperceptible, small-world contact network or “structure of co-presence” across the whole metropolitan area. Revealing the encounter pattern and identifying this large-scale contact network are crucial to understanding the dynamics in patterns of social acquaintances, collective human behaviors, and—particularly—disclosing the impact of human behavior on various diffusion/spreading processes.
Neutralization of terminal differentiation in gliomagenesis
Authors: Hu Jian , Ho Allen L. , Yuan Liang , Hu Baoli , Hua Sujun , Hwang Soyoon Sarah , Zhang Jianhua , Hu Tianyi , Zheng Hongwu , Gan Boyi , Wu Gongxiong , Wang Yaoqi Alan , Chin Lynda , DePinho Ronald A.
Published: August 2013

An immature state of cellular differentiation—characterized by stem cell–like tendencies and impaired differentiation—is a hallmark of cancer. Using glioblastoma multiforme (GBM) as a model system, we sought to determine whether molecular determinants that drive cells toward terminal differentiation are also genetically targeted in carcinogenesis and whether neutralizing such genes also plays an active role to reinforce the impaired differentiation state and promote malignancy. To that end, we screened 71 genes with known roles in promoting nervous system development that also sustain copy number loss in GBM through antineoplastic assay and identified A2BP1 (ataxin 2 binding protein 1, Rbfox1), an RNA-binding and splicing regulator that is deleted in 10% of GBM cases. Integrated in silico analysis of GBM profiles to elucidate the A2BP1 pathway and its role in glioma identified myelin transcription factor 1-like (Myt1L) as a direct transcriptional regulator of A2BP1. Reintroduction of A2BP1 or Myt1L in GBM cell lines and glioma stem cells profoundly inhibited tumorigenesis in multiple assays, and conversely, shRNA-mediated knockdown of A2BP1 or Myt1L in premalignant neural stem cells compromised neuronal lineage differentiation and promoted orthotopic tumor formation. On the mechanistic level, with the top-represented downstream target TPM1 as an illustrative example, we demonstrated that, among its multiple functions, A2BP1 serves to regulate TPM1’s alternative splicing to promote cytoskeletal organization and terminal differentiation and suppress malignancy. Thus, in addition to the activation of self-renewal pathways, the neutralization of genetic programs that drive cells toward terminal differentiation may also promote immature and highly plastic developmental states that contribute to the aggressive malignant properties of GBM.
Vascular endothelial growth factor-dependent spatiotemporal dual roles of placental growth factor in modulation of angiogenesis and tumor growth
Authors: Yang Xiaojuan , Zhang Yin , Yang Yunlong , Lim Sharon , Cao Ziquan , Rak Janusz , Cao Yihai
Published: August 2013

Placental growth factor (PlGF) remodels tumor vasculatures toward a normalized phenotype, which affects tumor growth, invasion and drug responses. However, the coordinative and spatiotemporal relation between PlGF and VEGF in modulation of tumor angiogenesis and vascular remodeling is less understood. Here we report that PlGF positively and negatively modulate tumor growth, angiogenesis, and vascular remodeling through a VEGF-dependent mechanism. In two independent tumor models, we show that PlGF inhibited tumor growth and angiogenesis and displayed a marked vascular remodeling effect, leading to normalized microvessels with infrequent vascular branches and increased perivascular cell coverage. Surprisingly, elimination of VEGF gene (i.e., VEGF-null) in PlGF-expressing tumors resulted in (
i
) accelerated tumor growth rates and angiogenesis and (
ii
) complete attenuation of PlGF-induced vascular normalization. Thus, PlGF positively and negatively modulates tumor growth, angiogenesis, and vascular remodeling through VEGF-dependent spatiotemporal mechanisms. Our data uncover molecular mechanisms underlying the complex interplay between PlGF and VEGF in modulation of tumor growth and angiogenesis, and have conceptual implication for antiangiogenic cancer therapy.
An allele of the
crm
gene blocks cyanobacterial circadian rhythms
Authors: Boyd Joseph S. , Bordowitz Juliana R. , Bree Anna C. , Golden Susan S.
Published: August 2013

The SasA-RpaA two-component system constitutes a key output pathway of the cyanobacterial Kai circadian oscillator. To date, rhythm of phycobilisome associated (
rpaA
) is the only gene other than
kaiA
,
kaiB
, and
kaiC
, which encode the oscillator itself, whose mutation causes completely arrhythmic gene expression. Here we report a unique transposon insertion allele in a small ORF located immediately upstream of
rpaA
in
Synechococcus elongatus
PCC 7942 termed
crm
(for circadian rhythmicity modulator), which results in arrhythmic promoter activity but does not affect steady-state levels of RpaA. The
crm
ORF complements the defect when expressed in
trans,
but only if it can be translated, suggesting that
crm
encodes a small protein. The
crm1
insertion allele phenotypes are distinct from those of an
rpaA
null;
crm1
mutants are able to grow in a light:dark cycle and have no detectable oscillations of KaiC phosphorylation, whereas low-amplitude KaiC phosphorylation rhythms persist in the absence of RpaA. Levels of phosphorylated RpaA in vivo measured over time are significantly altered compared with WT in the
crm1
mutant as well as in the absence of KaiC. Taken together, these results are consistent with the hypothesis that the Crm polypeptide modulates a circadian-specific activity of RpaA.
Structure of N-linked oligosaccharides attached to chlorovirus PBCV-1 major capsid protein reveals unusual class of complex N-glycans
Authors: De Castro Cristina , Molinaro Antonio , Piacente Francesco , Gurnon James R. , Sturiale Luisa , Palmigiano Angelo , Lanzetta Rosa , Parrilli Michelangelo , Garozzo Domenico , Tonetti Michela G. , Van Etten James L.
Published: August 2013

The major capsid protein Vp54 from the prototype chlorovirus
Paramecium bursaria
chlorella virus 1 (PBCV-1) contains four Asn-linked glycans. The structure of the four N-linked oligosaccharides and the type of substitution at each glycosylation site was determined by chemical, spectroscopic, and spectrometric analyses. Vp54 glycosylation is unusual in many ways, including: (
i
) unlike most viruses, PBCV-1 encodes most, if not all, of the machinery to glycosylate its major capsid protein; (
ii
) the glycans are attached to the protein by a β-glucose linkage; (
iii
) the Asn-linked glycans are not located in a typical N-X-(T/S) consensus site; and (
iv
) the process probably occurs in the cytoplasm. The four glycoforms share a common core structure, and the differences are related to the nonstoichiometric presence of two monosaccharides. The most abundant glycoform consists of nine neutral monosaccharide residues, organized in a highly branched fashion. Among the most distinctive features of the glycoforms are (
i
) a dimethylated rhamnose as the capping residue of the main chain, (
ii
) a hyperbranched fucose unit, and (
iii
) two rhamnose residues with opposite absolute configurations. These glycoforms differ from what has been reported so far in the three domains of life. Considering that chloroviruses and other members of the family
Phycodnaviridae
may have a long evolutionary history, we suggest that the chlorovirus glycosylation pathway is ancient, possibly existing before the development of the endoplasmic reticulum and Golgi pathway, and involves still unexplored mechanisms.
Statistically accurate low-order models for uncertainty quantification in turbulent dynamical systems
Authors: Sapsis Themistoklis P. , Majda Andrew J.
Published: August 2013

A framework for low-order predictive statistical modeling and uncertainty quantification in turbulent dynamical systems is developed here. These reduced-order, modified quasilinear Gaussian (ROMQG) algorithms apply to turbulent dynamical systems in which there is significant linear instability or linear nonnormal dynamics in the unperturbed system and energy-conserving nonlinear interactions that transfer energy from the unstable modes to the stable modes where dissipation occurs, resulting in a statistical steady state; such turbulent dynamical systems are ubiquitous in geophysical and engineering turbulence. The ROMQG method involves constructing a low-order, nonlinear, dynamical system for the mean and covariance statistics in the reduced subspace that has the unperturbed statistics as a stable fixed point and optimally incorporates the indirect effect of non-Gaussian third-order statistics for the unperturbed system in a systematic calibration stage. This calibration procedure is achieved through information involving only the mean and covariance statistics for the unperturbed equilibrium. The performance of the ROMQG algorithm is assessed on two stringent test cases: the 40-mode Lorenz 96 model mimicking midlatitude atmospheric turbulence and two-layer baroclinic models for high-latitude ocean turbulence with over 125,000 degrees of freedom. In the Lorenz 96 model, the ROMQG algorithm with just a single mode captures the transient response to random or deterministic forcing. For the baroclinic ocean turbulence models, the inexpensive ROMQG algorithm with 252 modes, less than 0.2% of the total, captures the nonlinear response of the energy, the heat flux, and even the one-dimensional energy and heat flux spectra.
Adjectival valency as valency constructions
Authors: Haugen Tor Arne
Published: August 2013

The article offers new data to the debate on lexical vs. constructional approaches to valency. Research on valency has mainly been concerned with verbs, and in this article it is argued that the neglected area of adjectival valency can shed some new light on this fundamental question. Among the evidence in favour of a constructional approach are the considerable differences in the possibilities of valency realisation between adjectives in attributive and in predicative function. It is also argued that a constructional approach allows for a more principled treatment of polysemy between valency variants.
Evaluation of Aging Structures for Silver Carp from Midwestern U.S. Rivers
Authors: Seibert Justin R. , Phelps Quinton E.
Published: August 2013

To combat the potential deleterious effects that Silver Carp Hypophthalmichthys molitrix have on native populations, management of this species is essential. Before developing population-level models, a determination of which aging structure for estimating the age of Silver Carp is needed. To our knowledge, no consensus has been reached on which structure should be used for estimating Silver Carp ages. We collected 120 Silver Carp from the Illinois, Mississippi, Missouri, and Ohio rivers via electrofishing to evaluate aging structures. Removal time, processing time, and discernible annuli were evaluated for scales, opercles, vertebrae, pectoral fin rays, postcleithra, and asterisci and lapilli otoliths. Asteriscus otolith, opercle and scale annuli were difficult to discern and not evaluated further. Total processing times for postcleithra (246.1 s) and lapilli (251.2 s) were the most time-efficient; pectoral fin rays and vertebrae were more time intensive. Between-reader precision and agreement rates resulted in lapilli being the most precise, followed by postcleithra, pectoral fin rays, and vertebrae. Comparisons of structures with lapilli revealed that pectoral fin rays exhibited 78% agreement, 49% agreement with postcleithra, and 53% agreement for vertebrae. In terms of agreement ±1 year to lapilli, pectoral fin ray, postcleithrum, and vertebra resulted in high agreement (>85%). Age bias plots revealed that these discrepancies consistently underestimated ages compared with lapilli. Discrepancies may be attributed to erosion of the central lumen of fin rays and postcleithra, while locating the first annulus on vertebrae may have led to this disparity. Based on previous studies, evaluation of overall processing times, assessment of between-reader precision, between-reader agreement rates, and bias that may be involved with alternative structures, we recommend lapilli otoliths be used for estimating age of Silver Carp. Future efforts should focus on validating accuracy of lapilli for estimating Silver Carp ages.

Received March 1, 2013; accepted June 5, 2013
Origin, trafficking, and intraepithelial fate of gut-tropic T cells
Authors: Guy-Grand Delphine , Vassalli Pierre , Eberl Gerard , Pereira Pablo , Burlen-Defranoux Odile , Lemaitre Fabrice , Di Santo James P. , Freitas Antonio A. , Cumano Ana , Bandeira Antonio
Published: August 2013

The small intestine epithelium (SI-Ep) harbors millions of unconventional (γδ and CD4− CD8− NK1.1− TCRαβ) and conventional (CD8αβ and CD4) T cells, designated intraepithelial lymphocytes (IELs). Here, we identified the circulating pool of SI-Ep–tropic T cells and studied their capacity to colonize the SI-Ep under steady-state conditions in SPF mice. Developmentally regulated levels of α4β7 endowed recent thymic emigrants (RTEs) of unconventional types with higher SI-Ep tropism than their conventional homologues. SI-Ep–tropic RTEs, which in all lineages emerged naive, homed to the SI-Ep, but this environment was inadequate to stimulate them to cycle. In contrast, conventional and, unexpectedly, unconventional T cells, particularly Vγ7+ (hallmark of γδ IELs), previously stimulated to cycle in the gut-associated lymphoid tissue (GALT), proliferated in the SI-Ep. Cycling unconventional SI-Ep immigrants divided far more efficiently than their conventional homologues, thereby becoming predominant. This difference impacted on acquisition of high Granzyme B content, which required extensive proliferation. In conclusion, SI-Ep–tropic T cells follow a thymus–SI-Ep or a GALT–SI-Ep pathway, the latter generating highly competitive immigrants that are the sole precursors of cytotoxic IELs. These events occur continuously as part of the normal IEL dynamics.
Pclust: protein network visualization highlighting experimental data
Authors: Li Wenlin , Kinch Lisa N. , Grishin Nick V.
Published: August 2013

Summary: One approach to infer functions of new proteins from their homologs utilizes visualization of an all-against-all pairwise similarity network (A2ApsN) that exploits the speed of BLAST and avoids the complexity of multiple sequence alignment. However, identifying functions of the protein clusters in A2ApsN is never trivial, due to a lack of linking characterized proteins to their relevant information in current software packages. Given the database errors introduced by automatic annotation transfer, functional deduction should be made from proteins with experimental studies, i.e. ‘reference proteins’. Here, we present a web server, termed Pclust, which provides a user-friendly interface to visualize the A2ApsN, placing emphasis on such ‘reference proteins’ and providing access to their full information in source databases, e.g. articles in PubMed. The identification of ‘reference proteins’ and the ease of cross-database linkage will facilitate understanding the functions of protein clusters in the network, thus promoting interpretation of proteins of interest.

Availability: The Pclust server is freely available at http://prodata.swmed.edu/pclust

Contact:  grishin@chop.swmed.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Failure to eliminate overfishing and attain optimum yield in the New England groundfish fishery
Authors: Rothschild Brian J. , Keiley Emily F. , Jiao Yue
Published: August 2013

Rothschild, B. J., Keiley, E. F., and Jiao, Y. 2014. Failure to eliminate overfishing and attain optimum yield in the New England groundfish fishery. – ICES Journal of Marine Science, 71: 226–233. Under US law, fishery management is required to eliminate overfishing and attain optimum yield (OY). In New England, many groundfish stocks continue to be overfished, and the fishery continues to harvest less than OY. The reasons for the shortfalls are rooted in the socio-economic structure of the management regime, and technical and scientific issues that constrain the management system. The most recent change in the management regime (days-at-sea to catch shares) and performance relative to OY and the prevention of overfishing are analyzed along with metrics used to gauge performance. The commonly used age-based production model gives a problematic perception of stock abundance. Structural issues that seem to impair achieving OY are the adherence to the single-species interpretation of multiple-species yield and the use of the Fx% proxy. Simpler approaches to stock assessment are discussed. A management system that creates feasible goals and uses improved and simpler metrics to measure performance is needed to facilitate attainment of management goals.
Nuclear spin isomers of guest molecules in H
2
@C
60
, H
2
O@C
60
and other endofullerenes
Authors: Chen Judy Y.-C. , Li Yongjun , Frunzi Michael , Lei Xuegong , Murata Yasujiro , Lawler Ronald G. , Turro Nicholas J.
Published: August 2013

Spectroscopic studies of recently synthesized endofullerenes, in which H
2
, H
2
O and other atoms and small molecules are trapped in cages of carbon atoms, have shown that although the trapped molecules interact relatively weakly with the internal environment they are nevertheless susceptible to appropriately applied external perturbations. These properties have been exploited to isolate and study samples of H
2
in C
60
and other fullerenes that are highly enriched in the
para
spin isomer. Several strategies for spin-isomer enrichment, potential extensions to other endofullerenes and possible applications of these materials are discussed.
Predicting the paramagnet-enhanced NMR relaxation of H2encapsulated in endofullerene nitroxides by density-functional theory calculations
Authors: Rastrelli Federico , Frezzato Diego , Lawler Ronald G. , Li Yongjun , Turro Nicholas J. , Bagno Alessandro
Published: August 2013

We have investigated the structure and nuclear magnetic resonance (NMR) spectroscopic properties of some dihydrogen endofullerene nitroxides by means of density-functional theory (DFT) calculations. Quantum versus classical roto-translational dynamics of H2have been characterized and compared. Geometrical parameters and hyperfine couplings calculated by DFT have been input to the Solomon–Bloembergen equations to predict the enhancement of the NMR longitudinal relaxation of H2due to coupling with the unpaired electron. Estimating the rotational correlation time via computed molecular volumes leads to a fair agreement with experiment for the simplest derivative; the estimate is considerably improved by recourse to the calculation of the diffusion tensor. For the other more flexible congeners, the agreement is less good, which may be due to an insufficient sampling of the conformational space. In all cases, relaxation by Fermi contact and Curie mechanisms is predicted to be negligible.
Anisotropic nuclear spin interactions in H
2
O@C
60
determined by solid-state NMR
Authors: Concistrè M. , Mamone S. , Denning M. , Pileio G. , Lei X. , Li Y. , Carravetta M. , Turro N. J. , Levitt M. H.
Published: August 2013

We report a solid-state NMR study of the anisotropic nuclear spin interactions in H
2
O@C
60
at room temperature. We find evidence of significant dipole–dipole interactions between the water protons, and also a proton chemical shift anisotropy (CSA) interaction. The principal axes of these interaction tensors are found to be perpendicular. The magnitude of the CSA is too large to be explained by a model in which the water molecules are partially aligned with respect to an external axis. The evidence indicates that the observed CSA is caused by a distortion of the geometry or electronic structure of the fullerene cages, in response to the presence of the endohedral water.
Spectroscopy of light-molecule endofullerenes
Authors: Levitt Malcolm H.
Published: August 2013

Molecular endofullerenes are supramolecular systems consisting of fullerene cages encapsulating small molecules. Although most early examples consist of encapsulated metal clusters, recently developed synthetic routes have provided endofullerenes with non-metallic guest molecules in high purity and macroscopic quantities. The encapsulated light molecule behaves as a confined quantum rotor, displaying rotational quantization as well as translational quantization, and a rich coupling between the translational and rotational degrees of freedom. Furthermore, many encapsulated molecules display spin isomerism. Spectroscopies such as inelastic neutron scattering, nuclear magnetic resonance and infrared spectroscopy may be used to obtain information on the quantized energy level structure and spin isomerism of the guest molecules. It is also possible to study the influence of the guest molecules on the cages, and to explore the communication between the guest molecules and the molecular environment outside the cage.
Rates and energetics of intramolecular electron transfer processes in conjugated metallofullerenes
Authors: Schubert Christina , Rudolf Marc , Guldi Dirk M. , Takano Yuta , Mizorogi Naomi , Herranz M. Ángeles , Martín Nazario , Nagase Shigeru , Akasaka Takeshi
Published: August 2013

In this paper, we report on the design, redox potentials, excited state energies and radical ion pair state energies in electron donor–acceptor conjugates comprising the electron-donating
π
-extended tetrathia- fulvalene and several electron-accepting fullerenes. To this end, we contrast an empty fullerene, that is, C
60
, with two endohedral metallofullerenes, that is, open-shell La@C
82
and closed-shell La
2
@C
80
, in terms of charge separation and charge recombination dynamics.
Pseudomonas
guangdongensis sp. nov., isolated from an electroactive biofilm, and emended description of the genus Pseudomonas Migula 1894
Authors: Yang Guiqin , Han Luchao , Wen Junlin , Zhou Shungui
Published: August 2013

A Gram-negative, straight to slightly curved rod-shaped bacterium, motile with peritrichous flagella, designated SgZ-6T, was isolated from an electroactive biofilm and was characterized by means of a polyphasic approach. Growth occurred with 0–5.0 % (w/v) NaCl (optimum 1 %), at pH 6.0–10.0 (optimum pH 7.0) and at 10–42 °C (optimum 30 °C) in trypticase soya broth. Phylogenetic analyses based on the 16S rRNA and gyrB genes identified the isolate as a member of a novel species of the genus

Pseudomonas

. Strain SgZ-6T exhibited the highest 16S rRNA gene sequence similarity to ‘

Pseudomonas

linyingensis’ CGMCC 1.10701 (97.5 %), followed by

Pseudomonas sagittaria

JCM 18195T (97.4 %),

P. oleovorans subsp. lubricantis

DSM 21016T (96.6 %),

P. tuomuerensis

JCM 14085T (96.5 %) and

P. alcaliphila

JCM 10630T (96.4 %). Strain SgZ-6T showed the highest gyrB gene sequence similarity of 93.7 % to ‘P. linyingensis’ CGMCC 1.10701 among all type strains of genus

Pseudomonas

. DNA–DNA pairing studies showed that strain SgZ-6T displayed 47.1 and 40.3 % relatedness to ‘P. linyingensis’ CGMCC 1.10701 and

P. sagittaria

JCM 18195T, respectively. The major isoprenoid quinone was ubiquinone 9 (Q-9). The whole-cell fatty acids consisted mainly of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of the genomic DNA was 68.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SgZ-6T is proposed to represent a novel species of the genus

Pseudomonas

, for which the name

Pseudomonas

guangdongensis sp. nov. is proposed. The type strain is SgZ-6T ( = CCTCC AB 2012022T = KACC 16606T). An emended description of the genus

Pseudomonas

is also proposed.
Identification and characterization of a novel paramyxovirus, porcine parainfluenza virus 1, from deceased pigs
Authors: Lau Susanna K. P. , Woo Patrick C. Y. , Wu Ying , Wong Annette Y. P. , Wong Beatrice H. L. , Lau Candy C. Y. , Fan Rachel Y. Y. , Cai Jian-Piao , Tsoi Hoi-Wah , Chan Kwok-Hung , Yuen Kwok-Yung
Published: August 2013

We describe the discovery and characterization of a novel paramyxovirus, porcine parainfluenza virus 1 (PPIV-1), from swine. The virus was detected in 12 (3.1 %) of 386 nasopharyngeal and two (0.7 %) of 303 rectal swab samples from 386 deceased pigs by reverse transcription-PCR, with viral loads of up to 106 copies ml−1. Complete genome sequencing and phylogenetic analysis showed that PPIV-1 represented a novel paramyxovirus within the genus Respirovirus, being most closely related to human parainfluenza virus 1 (HPIV-1) and Sendai virus (SeV). In contrast to HPIV-1, PPIV-1 possessed a mRNA editing function in the phosphoprotein gene. Moreover, PPIV-1 was unique among respiroviruses in having two G residues instead of three to five G residues following the A6 run at the editing site. Nevertheless, PPIV-1, HPIV-1 and SeV share common genomic features and may belong to a separate group within the genus Respirovirus. The presence of PPIV-1 in mainly respiratory samples suggests a possible association with respiratory disease, similar to HPIV-1 and SeV.
A new structure of a serotonin salt: comparison and conformational analysis of all known serotonin complexes
Authors: Rychkov Denis , Boldyreva Elena V. , Tumanov Nikolay A.
Published: August 2013

Four serotonin salt structures (serotonin adipate, C10H13N2O+·C6H9O4−, is a previously unknown structure) were analysed to understand the influence of the anion on serotonin conformation. Hydrogen bonding alone favours a flat conformation, whereas additional stacking interactions between ions may possibly account for the nonplanar conformation. Since molecular conformation, stability and biological activity are interrelated, one can consider influencing the chemical and biological properties of serotonin by selecting an appropriate counter-ion for salt formation.
Is subjective hyperhidrosis assessment sufficient enough? Prevalence of hyperhidrosis among young Polish adults
Authors: Stefaniak Tomasz , Tomaszewski Krzysztof A. , Proczko‐Markuszewska Monika , Idestal Anette , Royton Anders , Abi‐Khalil Christian
Published: August 2013

The aim of this work was to assess the prevalence of palmar and axillary hyperhidrosis among young Polish adults. Additionally, this work aimed at comparing the subjective and objective (gravimetric) method of hyperhidrosis assessment. Healthy medical students, volunteering to take part in this study, were included. The participants filled out a questionnaire assessing the occurrence and subjective intensity of hyperhidrosis in different areas of the body. Additionally, the students were subjected to gravimetric assessment in four localizations: the face, palms, axillae and abdomino‐lumbar area. Two hundred and fifty‐three students (102 males and 151 females, mean age 24.3 ± 3.21 years) were included in the study. Forty‐two (16.7%) participants declared that they suffer from hyperhidrosis. Out of the 42 students declaring any type of hyperhidrosis, only 20 (47.6%) exceeded the gravimetric reference values. From among the students that exceeded the normative values for palmar hyperhidrosis, only 10 (55.6%) were aware of their hyperhidrosis. In the group of students that exceeded the normative values for axillary hyperhidrosis, 16 (39%) were aware of their hyperhidrosis. Subjectively declared hyperhidrosis incidence may significantly exceed the real‐life occurrence of this disease. Basing studies solely on data gathered from questionnaires, may lead to false results. It is imperative, when assessing patients suffering from hyperhidrosis, to use both objective and subjective methods of evaluation.