bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of early EocenePalaeosinopa(Mammalia, Pantolestidae) in the Willwood Formation of the Bighorn Basin, Wyoming
Authors: Dunn Rachel H. , Rose Kenneth D.
Published: November 2015

Species-level diversity and evolution ofPalaeosinopafrom the Willwood Formation of the Bighorn Basin is reassessed based on substantial new material from the Bighorn, Powder River, and Wind River basins. We recognize three species ofPalaeosinopain the Willwood Formation of the Bighorn Basin:P. lutreola,P. incerta, andP. veterrima. The late Wasatchian speciesP. didelphoidesis not present in the Bighorn Basin. The Willwood species can be differentiated based only on size.P. veterrimais the most common and wide-ranging species and is the most variable in size and morphology: the stratigraphically lowest individuals are smaller, with narrower, more crestiform lower molars; whereas the highest are larger, with wider, more bunodont teeth. Although it could be argued that these represent distinct species, we demonstrate that this morphological evolution occurred as the gradual and mosaic accumulation of features, suggesting in situ anagenetic evolution. The two smaller species are present only low in the section (biochrons Wa0–Wa4) and show no discernable evolution in size or morphology. A new skeleton ofPalaeosinopa veterrimafrom the Willwood Formation is described, and other new postcrania are reported. The skeleton is the oldest associated skeleton ofPalaeosinopaknown, yet it is remarkably similar to those of younger, more derived pantolestids, the primary disparities being minor differences in proportions of the innominate, femur, and tibia, and co-ossification of the distal tibia and fibula. EitherP. incertaorP. lutreolawas likely the ancestral population that gave rise to the other WasatchianPalaeosinopa. Alternatively,P. veterrimamay have migrated into the Bighorn Basin from the Powder River Basin.
Introducing a New 3D Dynamical Model for Barred Galaxies
Authors: Jung Christof , Zotos Euaggelos E.
Published: November 2015

The regular or chaotic dynamics of an analytical realistic three dimensional model composed of a spherically symmetric central nucleus, a bar and a flat disk is investigated. For describing the properties of the bar, we introduce a new simple dynamical model and we explore the influence on the character of orbits of all the involved parameters of it, such as the mass and the scale length of the bar, the major semi-axis and the angular velocity of the bar, as well as the energy. Regions of phase space with ordered and chaotic motion are identified in dependence on these parameters and for breaking the rotational symmetry. First, we study in detail the dynamics in the invariant planez = pz= 0 using the Poincaré map as a basic tool and then study the full three-dimensional case using the Smaller Alignment index method as principal tool for distinguishing between order and chaos. We also present strong evidence obtained through the numerical simulations that our new bar model can realistically describe the formation and the evolution of the observed twin spiral structure in barred galaxies.
An embarrassment of professors?
Authors: Fleming Andrew
Published: November 2015

The judgements shaping archaeology and every subject in British universities (see remarks in the Editorial above) are based on certain presumptions about how research and teaching can best be done. Some of these premisses are noted.
Childeish questions
Authors: Sherratt Andrew
Published: November 2015

The criteria used in the British universities' current assessment of research quality prompt the question: how would Gordon Childe have fared, if assessed that way?
Portraits, the cult of relics and the affirmation of hierarchy at an early medieval monastery: San Vincenzo al Volturno
Authors: Mitchell John , Hodges Richard
Published: November 2015

San Vincenzo al Volturno is an early medieval monastery in the high province of Molise, southeast of Rome, and site of most substantial excavations over the last 15 years. The publication of portrait wall-paintings from the crypt of its great church, San Vincenzo Maggiore, is occasion to examine the place of the individual in that religious society.
Bioarchaeological and climatological evidence for the fate of Norse farmers in medieval Greenland
Authors: Buckland P. C. , Amorosi T. , Barlow L. K. , Dugmore A. J. , Mayewski P. A. , McGovern T. H. , Ogilvie A. E. J. , Sadler J. P. , Skidmore P.
Published: November 2015

Greenland, far north land of the Atlantic, has often been beyond the limit of European farming settlement. One of its Norse settlements, colonized just before AD 1000, is — astonishingly — not even at the southern tip, but a way up the west coast, the ‘Western Settlement’. Environmental studies show why its occupation came to an end within five centuries, leaving Greenland once more a place of Arctic-adapted hunters.
Pattern in the Epipalaeolithic of the Levant: debate after Neeley & Barton
Authors: Gorine-Morris Nigel , Henry Donald O. , Phillips James L. , Clark G. A. , Barton C. Michael , Neeley Michael P.
Published: November 2015

The ANTIQUITY paper by Neeley & Barton (1994) — hereafter ‘N&B'— prompted responses published in the June number last year: Fellner (1995) and Kaufman (1995). Here are more (all shorter than the full versions received), together with a response from Barton & Neeley (B&N) that rounds off the present discussion. The debaters have seen others’ contributions, so there is some cross-comment within them. The questions and the issues are old fundamentals of lithic research and analsis, which one cannot expect to end with this debate.
Functional minimalism versus ethnicity in explaining lithic patterns in the Levantine Epipalaeolithic
Authors: Henry Donald O.
Published: November 2015

The relationship between raw material availability, economizing behaviours and technological procedures undoubtedly influenced the configurations of Levantine Epipalaeolithic assemblages, as has been well recognized for over 20 years (Bar-Yosef 1970; Henry 1973). Other 'functional factors' have also been examined — environmental settings, settlement mobility and provisioning strategies. While each factor has been shown to have influenced the specific configurations of Epipalaeolithic assemblages, none (other than broad environmental settings) has been shown to account for the large-scale patterned variability that distinguishes the three major taxa, the Geometric Kebaran, Natufian, and Mushabian complexes. This is why most prehistorians working in the region hold that ethnicity, at some scale, provides the most robust explanation for the patterned variability observed and for the temporal and geographic distributions at the taxonomic level of 'complex'.
Plus français que les Français
Authors: Clark G. A.
Published: November 2015

The reactions to the N&B essay tell more about epistemological concerns (or lack thereof) than they do about construals of pattern and of what pattern might mean in Levantine Epipalaeolithic archaeology.
Prevalence and characteristics of misreporting of energy intake in US children and adolescents: National Health and Nutrition Examination Survey (NHANES) 2003–2012
Authors: Murakami Kentaro , Livingstone M. Barbara E.
Published: November 2015

Using data from the National Health and Nutrition Examination Survey (NHANES) 2003–2012, we investigated the prevalence and characteristics of under- and over-reporting of energy intake (EI) among 14 044 US children and adolescents aged 2–19 years. For the assessment of EI, two 24-h dietary recalls were conducted with the use of the US Department of Agriculture Automated Multiple-Pass Method. Under-, plausible and over-reporters of EI were identified using two methods: based on the 95 % confidence limits (1) for agreement between the ratio of EI:BMR and a physical activity level for sedentary lifestyle (1·55) and (2) of the expected ratio of EI:estimated energy requirement (EER) of 1·0. BMR was calculated using Schofield’s equations. EER was calculated using equations from the US Dietary Reference Intakes, assuming ‘low active’ level of physical activity. The risk of being an under- or over-reporter compared with a plausible reporter was analysed using multiple logistic regression. Percentages of under-, plausible and over-reporters were 13·1, 81·5 and 5·4 %, respectively, based on EI:BMR and 18·8, 72·3 and 8·8 %, respectively, based on EI:EER. Under-reporting was associated with older age, non-Hispanic blacks (compared with non-Hispanic whites) and overweight and obesity (compared with normal weight). Over-reporting was associated with younger age, lower family poverty income ratio, normal weight and the first survey cycle. Similar findings were obtained when analysing only the first 24-h recall data from NHANES 1999–2012 (n 22 949). In conclusion, we found that EI misreporting remains prevalent and differential in US children and adolescents.
X-ray powder diffraction data for drospirenone, C24H30O3
Authors: Wang Qing , Sun Qiao Mei , Li Shan Shan , Guo Liu Qi , Li Hui
Published: November 2015

X-ray powder diffraction data, unit-cell parameters, and space group for drospirenone, C24H30O3, are reported [a = 12.897(1) Å, b = 12.618(1) Å, c = 12.252(1) Å, α = β = γ = 90°, unit-cell volume V = 1994.13 Å3, Z = 4, ρcal = 1.229 g cm−3, and space group P212121]. All measured lines were indexed and are consistent with the P212121 space group. No detectable impurities were observed.
The humanities are scientific: a reply to the defenses of economic neo-institutionalism
Authors: McCLOSKEY DEIRDRE NANSEN
Published: November 2015

I reply to amiable criticisms by Greif, Mokyr, Langlois, Lawson, and Tabellini of my own criticism of neo-institutionalism. They say that ‘culture’ is included in neo-institutionalism – which is mistaken on any serious definition of culture, such as those involving ethics, rhetoric, ideology, and ideas. They also say that neo-institutionalism has advanced beyond Max U and Samuelsonian economics. That's also mistaken. They do not attend to the humanities, which as ‘humanomics’ can indeed acknowledge ‘culture’ and non-Max U. Their particular historical examples show the opposite of what they think is shown. Ideas, rhetoric, ethics changed, and had to change, before institutions mattered.
Noise conversion of Schottky diodes in mm-wave detectors under different nonlinear regimes: modeling and simulation versus measurement
Authors: Gutiérrez Jéssica , Zeljami Kaoutar , Villa Enrique , Aja Beatriz , de la Fuente Maria Luisa , Sancho Sergio , Pascual Juan Pablo
Published: November 2015

This paper presents and discusses several methods for predicting the low-frequency (LF) noise at the output of a mm-wave detector. These methods are based on the extraction of LF noise source parameters from the single diode under a specific set of bias conditions and the transfer or conversion of these noise sources, under different operating conditions including cyclostationary regime, to the quasi-dc output of a mm-wave detector constructed with the same model of diode. The noise analysis is based on a conversion-matrix type formulation, which relates the carrier noisy sidebands of the input signal with the detector output spectrum through a pair of transfer functions obtained in commercial software. Measurements of detectors in individual and differential setups will be presented and compared with predictions.
Wie stark sind Führungskräfte psychisch gefährdet?
Authors: Zimber Andreas , Hentrich Stephan , Bockhoff Katharina , Wissing Carla , Petermann Franz
Published: November 2015

Zusammenfassung. Der Forschungsstand zur psychischen Gesundheit der Führungskräfte wurde bisher nicht systematisch ausgewertet. Die folgende Literaturübersicht fasst Ergebnisse aus 34 klinisch-epidemiologischen sowie arbeitspsychologischen Studien qualitativ und quantitativ zusammen. Ausgewertet wurden Ergebnisse zur Verbreitung psychischer Beeinträchtigungen (Fragestellung 1) sowie zu arbeitsbezogenen Risiko- und Schutzfaktoren (Fragestellung 2). Es liegen Ergebnisse zu fünf unterschiedlichen Gesundheitsrisiken vor: psychische Gesundheit und Wohlbefinden, depressive und psychosomatische Symptome, Burnout, Irritation und psychischer Stress. Die bisherige Befundlage zu Fragestellung 1 ist zu heterogen, um hieraus Trends ableiten zu können. Eindeutiger zu interpretieren sind Ergebnisse zu den Risiko- und Schutzfaktoren: Die quantitative Arbeitsbelastung und Konflikte durch die Führungsrolle wiesen jeweils in mehreren Studien signifikante Zusammenhänge mit den psychischen Risiken auf. Arbeitsplatzsicherheit, soziale Unterstützung und Handlungsspielraum erwiesen sich als protektive Faktoren. Aus den Ergebnissen des Reviews werden der weitere Forschungsbedarf sowie spezifische Präventionsstrategien abgeleitet.
Teaching the Art and Science of Getting Research Funding
Authors: Wood-Charlson Elisha , Bruno Barbara
Published: November 2015

National Science Foundation–funded EDventures program delivers successful training in proposal writing to graduate students and postdocs.
Mechanisms of fate decision and lineage commitment during haematopoiesis
Authors: Cvejic Ana
Published: November 2015

Blood stem cells need to both perpetuate themselves (self‐renew) and differentiate into all mature blood cells to maintain blood formation throughout life. However, it is unclear how the underlying gene regulatory network maintains this population of self‐renewing and differentiating stem cells and how it accommodates the transition from a stem cell to a mature blood cell. Our current knowledge of transcriptomes of various blood cell types has mainly been advanced by population‐level analysis. However, a population of seemingly homogenous blood cells may include many distinct cell types with substantially different transcriptomes and abilities to make diverse fate decisions. Therefore, understanding the cell‐intrinsic differences between individual cells is necessary for a deeper understanding of the molecular basis of their behaviour. Here we review recent single‐cell studies in the haematopoietic system and their contribution to our understanding of the mechanisms governing cell fate choices and lineage commitment.
Dual-channel near-field control by polarizations using isotropic and inhomogeneous metasurface
Authors: Wan Xiang , Cai Ben Geng , Li Yun Bo , Cui Tie Jun
Published: November 2015

We propose a method for dual-channel near-field manipulations by designing isotropic but inhomogeneous metasurfaces. As example, we present a dual-channel near-field focusing metasurface device. When the device is driven by surface waves from different channels on the metasurface, the near fields will be focused at the same spatial point with different polarizations. Conversely, if a linearly polarized source is radiated at the spatial focal point, different channels will be evoked on the metasurface controlled by polarization. We fabricated and measured the metasurface device in the microwave frequency. Well agreements between the simulation and measurement results are observed. The proposed method exhibits great flexibility in controlling the surface waves and spatial waves simultaneously. It is expected that the proposed method and dual-channel device will facilitate the manipulation of near electromagnetic or optical waves in different frequency regimes.
Annexin A2 binds to endosomes and negatively regulates TLR4-triggered inflammatory responses via the TRAM-TRIF pathway
Authors: Zhang Shuang , Yu Min , Guo Qiang , Li Rongpeng , Li Guobo , Tan Shirui , Li Xuefeng , Wei Yuquan , Wu Min
Published: November 2015

Lipopolysaccharide (LPS) derived from Gram-negative bacteria activates plasma membrane signaling via Toll-like receptor 4 (TLR4) on host cells and triggers innate inflammatory responses, but the underlying mechanisms remain to be fully elucidated. Here we reveal a role for annexin A2 (AnxA2) in host defense against infection as anxa2−/− mice were highly susceptible to Gram-negative bacteria-induced sepsis with enhanced inflammatory responses. Computing analysis and biochemical experiments identified that constitutive AnxA2 expression facilitated TLR4 internalization and its subsequent translocation into early endosomal membranes. It activated the TRAM-dependent endosomal signaling, leading to the release of anti-inflammatory cytokines. Importantly, AnxA2 deficiency prolonged TLR4-mediated signaling from the plasma membrane, which was attributable to pro-inflammatory cytokine production (IL-6, TNFα and IL-1β). Thus, AnxA2 directly exerted negative regulation of inflammatory responses through TLR4-initiated TRAM-TRIF pathway occurring on endosomes. This study reveals AnxA2 as a critical regulator in infection-initiated inflammation, which protects the host from excessive inflammatory damage.
Genetic variants of SLC17A1 are associated with cholesterol homeostasis and hyperhomocysteinaemia in Japanese men
Authors: Koyama Teruhide , Matsui Daisuke , Kuriyama Nagato , Ozaki Etsuko , Tanaka Keitaro , Oze Isao , Hamajima Nobuyuki , Wakai Kenji , Okada Rieko , Arisawa Kokichi , Mikami Haruo , Shimatani Keiichi , Hirata Akie , Takashima Naoyuki , Suzuki Sadao , Nagata Chisato , Kubo Michiaki , Tanaka Hideo
Published: November 2015

Hyperuricaemia is an undisputed and highly predictive biomarker for cardiovascular risk. SLC17A1, expressed in the liver and kidneys, harbours potent candidate single nucleotide polymorphisms that decrease uric acid levels. Therefore, we examined SLC17A1 polymorphisms (rs1165196, rs1179086 and rs3757131), which might suppress cardiovascular risk factors and that are involved in liver functioning, via a large-scale pooled analysis of the Japanese general population in a cross-sectional study. Using data from the Japan Multi-Institutional Collaborative Cohort Study, we identified 1842 participants of both sexes, 35–69-years-old, having the requisite data and analysed their SLC17A1 genotypes. In men, logistic regression analyses revealed that minor alleles in SLC17A1 polymorphisms (rs1165196 and rs3757131) were associated with a low-/high-density lipoprotein cholesterol ratio >2.0 (rs1165196: odds ratio [OR], 0.703; 95% confidence interval [CI], 0.536–0.922; rs3757131: OR, 0.658; 95% CI, 0.500–0.866) and with homocysteine levels of >10.0 nmol/mL (rs1165196: OR, 0.544; 95% CI, 0.374–0.792; rs3757131: OR, 0.509; 95% CI, 0.347–0.746). Therefore, these polymorphisms had dominant negative effects on cholesterol homeostasis and hyperhomocysteinaemia, in men, independent of alcohol consumption, physical activity, or daily energy and nutrition intake. Thus, genetic variants of SLC17A1 are potential biomarkers for altered cholesterol homeostasis and hyperhomocysteinaemia in Japanese men.
Effect of traditional Chinese exercise on the quality of life and depression for chronic diseases: a meta-analysis of randomised trials
Authors: Wang Xueqiang , Pi Yanling , Chen Binglin , Chen Peijie , Liu Yu , Wang Ru , Li Xin , Zhu Yi , Yang Yujie , Niu Zhanbin
Published: November 2015

Traditional Chinese exercise (TCE) has many uses in the prevention and treatment of chronic diseases. However, there is no consensus regarding the benefit of TCE for chronic diseases. Our objective is to examine the effect of TCE on the quality of life and depression for chronic diseases by performing a meta-analysis of randomized controlled trials (RCTs). We only cover published RCTs. The outcome measures included quality of life and depression. Sixty articles with a total of 4311 patients were included. The pooling revealed that TCE could improve the SF-36 physical function subscale in the short term [SMD (95% CI) = 0.35 (0.13, 0.56), P = 0.002] and mid-term [SMD (95% CI) = 0.49 (0.12, 0.85), P = 0.009], GHQ [SMD (95% CI) = −0.68 (−1.26, −0.09), P = 0.02], the Center for Epidemiologic Studies depression scale in the short term [SMD (95% CI) = −0.86 (−1.42, −0.31), P = 0.002] and mid-term [SMD (95% CI) = −0.41 (−0.64, −0.18), P < 0.001]. The meta-analysis of RCT demonstrates that TCE can significantly improve the quality of life and depression of patients with chronic diseases. These findings provide useful information for patients with chronic diseases as well as for medical staff.
SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy
Authors: Ball Graeme , Demmerle Justin , Kaufmann Rainer , Davis Ilan , Dobbie Ian M. , Schermelleh Lothar
Published: November 2015

Three-dimensional structured illumination microscopy (3D-SIM) is a versatile and accessible method for super-resolution fluorescence imaging, but generating high-quality data is challenging, particularly for non-specialist users. We present SIMcheck, a suite of ImageJ plugins enabling users to identify and avoid common problems with 3D-SIM data and assess resolution and data quality through objective control parameters. Additionally, SIMcheck provides advanced calibration tools and utilities for common image processing tasks. This open-source software is applicable to all commercial and custom platforms and will promote routine application of super-resolution SIM imaging in cell biology.
Epithelial cell-derived micro RNA-146a generates interleukin-10-producing monocytes to inhibit nasal allergy
Authors: Luo Xi , Han Miaomiao , Liu Jianqi , Wang Yu , Luo Xiangqian , Zheng Jing , Wang Shuai , Liu Zhigang , Liu Dabo , Yang Ping-Chang , Li Huabin
Published: November 2015

The aberrant immunity plays an important role in the pathogenesis of allergic diseases. Micro RNAs (miR) are involved in regulating the immunity in the body. This study aims to test a hypothesis that miR-146a induces the expression of interleukin (IL)-10 in monocytes (Mos). In this study, the levels of miR-146a were determined by real time RT-PCR. The IL-10+ Mos were evaluated by flow cytometry. The miR-146a-laden exosomes were generated with RPMI2650 cells (an airway epithelial cell line). An allergic rhinitis mouse model was developed. The results showed that nasal epithelial cells expressed miR-146a, which was markedly lower in the nasal epithelial cells of patients with nasal allergy than that in healthy controls. Exposure to T helper (Th)2 cytokines suppressed the levels of miR-146a in the nasal epithelial cells. The nasal epithelial cell-derived miR-146a up regulated the expression of IL-10 in Mos. The inducible IL-10+ Mos showed an immune suppressor effect on the activities of CD4+ effector T cells and the Th2 polarization in a mouse model of allergic rhinitis. In summary, nasal epithelial cells express miR-146a, the latter is capable of inducing IL-10 expression in Mos, which suppress allergic reactions in the mouse nasal mucosa.
Mouse adaptation of influenza B virus increases replication in the upper respiratory tract and results in droplet transmissibility in ferrets
Authors: Kim Eun-Ha , Park Su-Jin , Kwon Hyeok-Il , Kim Se Mi , Kim Young-il , Song Min-Suk , Choi Eun-Ji , Pascua Philippe Noriel Q. , Choi Young-Ki
Published: November 2015

To investigate the molecular changes that allow influenza B viruses to adapt to new mammalian hosts, influenza B/Florida/04/2006 was serially passaged in BALB/c mice until highly virulent. The viral factors underlying this transition were then investigated in mice and ferrets. Five viruses, including the wild-type virus (P0), three intermediate viruses (P5, P9 and P12) and a lethal mouse-adapted virus (P17 (MA)), harbored one to five amino acid substitutions in the hemagglutinin, M, NP and PA segments suggesting that these mutations enhance virulence. The P17 (MA) virus replicated significantly more efficiently than the P0 virus both in vitro and in vivo (P < 0.0001) and was highly virulent (MLD50: 105.25TCID50) while the P0, P5 and P9 viruses did not kill any infected mice (MLD50 > 106.0TCID50). Furthermore, the P17 (MA) virus grew to greater titers in the ferret upper respiratory tract compared with the P0 and intermediate viruses and only the P17 (MA) virus was transmissible between ferrets via both direct and aerosol contact. To our knowledge, this is the first study to demonstrate ferret-to-ferret transmission of influenza B virus and to delineate factors that may affect its transmission.
Micro-structural Change During Nucleation: From Nucleus To Bicontinuous Morphology
Authors: Jeong Seongmin , Jho Yongseok , Zhou Xin
Published: November 2015

Although the microstructure of coexistence phase provides direct insights of the nucleation mechanism and their change is substantial in the phase transition, their study is limited due to the lack of suitable tools capturing the thermodynamically unstable transient states. We resolve this problem in computational study by introducing a generalized canonical ensemble simulation and investigate the morphological change of the nucleus during the water evaporation and condensation. We find that at very low pressure, where the transition is first order, classical nucleation theory holds approximately. A main nucleus is formed in the supersaturation near spinodal and the overall shape of the nucleus is finite and compact. On increasing the pressure of the system, more nuclei are formed even before spinodal. They merge into a larger nuclei with a smaller free energy penalty to form ramified shapes. We suggest order parameters to describe the extent of fluctuation and their relation to the free energy profile.
Fast-Response Calmodulin-Based Fluorescent Indicators Reveal Rapid Intracellular Calcium Dynamics
Authors: Helassa Nordine , Zhang Xiao-hua , Conte Ianina , Scaringi John , Esposito Elric , Bradley Jonathan , Carter Thomas , Ogden David , Morad Martin , Török Katalin
Published: November 2015

Faithful reporting of temporal patterns of intracellular Ca2+ dynamics requires the working range of indicators to match the signals. Current genetically encoded calmodulin-based fluorescent indicators are likely to distort fast Ca2+ signals by apparent saturation and integration due to their limiting fluorescence rise and decay kinetics. A series of probes was engineered with a range of Ca2+ affinities and accelerated kinetics by weakening the Ca2+-calmodulin-peptide interactions. At 37 °C, the GCaMP3-derived probe termed GCaMP3fast is 40-fold faster than GCaMP3 with Ca2+ decay and rise times, t1/2, of 3.3 ms and 0.9 ms, respectively, making it the fastest to-date. GCaMP3fast revealed discreet transients with significantly faster Ca2+ dynamics in neonatal cardiac myocytes than GCaMP6f. With 5-fold increased two-photon fluorescence cross-section for Ca2+ at 940 nm, GCaMP3fast is suitable for deep tissue studies. The green fluorescent protein serves as a reporter providing important novel insights into the kinetic mechanism of target recognition by calmodulin. Our strategy to match the probe to the signal by tuning the affinity and hence the Ca2+ kinetics of the indicator is applicable to the emerging new generations of calmodulin-based probes.
Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142
Authors: Bernstein Hans C. , Charania Moiz A. , McClure Ryan S. , Sadler Natalie C. , Melnicki Matthew R. , Hill Eric A. , Markillie Lye Meng , Nicora Carrie D. , Wright Aaron T. , Romine Margaret F. , Beliaev Alexander S.
Published: November 2015

To date, the proposed mechanisms of nitrogenase-driven photosynthetic H2 production by the diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142 have assumed that reductant and ATP requirements are derived solely from glycogen oxidation and cyclic-electron flow around photosystem I. Through genome-scale transcript and protein profiling, this study presents and tests a new hypothesis on the metabolic relationship between oxygenic photosynthesis and nitrogenase-mediated H2 production in Cyanothece 51142. Our results show that net-positive rates of oxygenic photosynthesis and increased expression of photosystem II reaction centers correspond and are synchronized with nitrogenase expression and H2 production. These findings provide a new and more complete view on the metabolic processes contributing to the energy budget of photosynthetic H2 production and highlight the role of concurrent photocatalytic H2O oxidation as a participating process.
Mosaic patterns of diversification dynamics following the colonization of Melanesian islands
Authors: Toussaint Emmanuel F. A. , Hendrich Lars , Shaverdo Helena , Balke Michael
Published: November 2015

The fate of newly settled dispersers on freshly colonized oceanic islands is a central theme of island biogeography. The emergence of increasingly sophisticated methods of macroevolutionary pattern inference paves the way for a deeper understanding of the mechanisms governing these diversification patterns on lineages following their colonization of oceanic islands. Here we infer a comprehensive molecular phylogeny for Melanesian Exocelina diving beetles. Recent methods in historical biogeography and diversification rate inference were then used to investigate the evolution of these insects in space and time. An Australian origin in the mid-Miocene was followed by independent colonization events towards New Guinea and New Caledonia in the late Miocene. One colonization of New Guinea led to a large radiation of >150 species and 3 independent colonizations of New Caledonia gave rise to about 40 species. The comparably late colonizations of Vanuatu, Hawaii and China left only one or two species in each region. The contrasting diversification trajectories of these insects on Melanesian islands are likely accounted for by island size, age and availability of ecological opportunities during the colonization stage.
Identification of the active components in Bone Marrow Soup: a mitigator against irradiation-injury to salivary glands
Authors: Fang Dongdong , Hu Shen , Liu Younan , Quan Vu-Hung , Seuntjens Jan , Tran Simon D.
Published: November 2015

In separate studies, an extract of soluble intracellular contents from whole bone marrow cells, named “Bone Marrow (BM) Soup”, was reported to either improve cardiac or salivary functions post-myocardial infarction or irradiation (IR), respectively. However, the active components in BM Soup are unknown. To demonstrate that proteins were the active ingredients, we devised a method using proteinase K followed by heating to deactivate proteins and for safe injections into mice. BM Soup and “deactivated BM Soup” were injected into mice that had their salivary glands injured with 15Gy IR. Control mice received either injections of saline or were not IR. Results at week 8 post-IR showed the ‘deactivated BM Soup’ was no better than injections of saline, while injections of native BM Soup restored saliva flow, protected salivary cells and blood vessels from IR-damage. Protein arrays detected several angiogenesis-related factors (CD26, FGF, HGF, MMP-8, MMP-9, OPN, PF4, SDF-1) and cytokines (IL-1ra, IL-16) in BM Soup. In conclusion, the native proteins (but not the nucleic acids, lipids or carbohydrates) were the therapeutic ingredients in BM Soup for functional salivary restoration following IR. This molecular therapy approach has clinical potential because it is theoretically less tumorigenic and immunogenic than cell therapies.
Natural transformation occurs independently of the essential actin-like MreB cytoskeleton in Legionella pneumophila
Authors: Juan Pierre-Alexandre , Attaiech Laetitia , Charpentier Xavier
Published: November 2015

Natural transformation is the process by which bacteria can actively take up and integrate exogenous DNA thereby providing a source of genetic diversity. Under specific growth conditions the coordinated expression of several genes – a situation referred to as “competence” – allows bacteria to assemble a highly processive and dedicated system that can import high molecular weight DNA. Within the cell these large imported DNA molecules are protected from degradation and brought to the chromosome for recombination. Here, we report elevated expression of mreB during competence in the Gram-negative pathogen Legionella pneumophila. Interestingly a similar observation had previously been reported in the distantly-related Gram-positive organism Bacillus subtilis. MreB is often viewed as the bacterial actin homolog contributing to bacterial morphogenesis by coordinating peptidoglycan-synthesising complexes. In addition MreB is increasingly found to be involved in a growing number of processes including chromosome segregation and motor-driven motility. Using genetic and pharmacological approaches, we examined the possible role of MreB during natural transformation in L. pneumophila. Our data show that natural transformation does not require MreB dynamics and exclude a direct role of MreB filaments in the transport of foreign DNA and its recombination in the chromosome.
Family history of esophageal cancer increases the risk of esophageal squamous cell carcinoma
Authors: Chen Tiantian , Cheng Hongwei , Chen Xingdong , Yuan Ziyu , Yang Xiaorong , Zhuang Maoqiang , Lu Ming , Jin Li , Ye Weimin
Published: November 2015

A population-based case-control was performed to explore familial aggregation of esophageal squamous cell carcinoma (ESCC). Family history of cancer was assessed by a structured questionnaire and from which 2 cohorts of relatives of cases and controls were reconstructed. Unconditional logistic regression and Cox proportional hazards regression were applied for case-control design and reconstructed cohort design, respectively. We observed a close to doubled risk of ESCC associated with a positive family history of esophageal cancer among first degree relatives (odds ratio [OR] = 1.85, 95% confidence interval [CI]: 1.42–2.41), after adjusting age, sex, family size and other confounders. The excess risks of ESCC increased with the increasing of first-degree relatives affected by esophageal cancer (p < 0.001). In particular, those individuals whose both parents with esophageal cancer had an 8-fold excess risk of ESCC (95% CI: 1.74–36.32). The reconstructed cohort analysis showed that the cumulative risk of esophageal cancer to age 75 was 12.2% in the first-degree relatives of cases and 7.0% in those of controls (hazard ratio = 1.91, 95% CI: 1.54–2.37). Our results suggest family history of esophageal cancer significantly increases the risk for ESCC. Future studies are needed to understand how the shared genetic susceptibility and/or environmental exposures contribute to the observed excess risk.
Transcriptome analysis of genes involved in defence response in Polyporus umbellatus with Armillaria mellea infection
Authors: Liu Meng-Meng , Xing Yong-Mei , Zhang Da-Wei , Guo Shun-Xing
Published: November 2015

Polyporus umbellatus, a species symbiotic with Armillaria mellea and it also exhibits substantial defence response to Armillaria mellea infection. There are no genomics resources databases for understanding the molecular mechanism underlying the infection stress of P. umbellatus. Therefore, we performed a large-scale transcriptome sequencing of this fungus with A. mellea infection using Illumina sequencing technology. The assembly of the clean reads resulted in 120,576 transcripts, including 38,444 unigenes. Additionally, we performed a gene expression profiling analysis upon infection treatment. The results indicated significant differences in the gene expression profiles between the control and the infection group. In total, 10933 genes were identified between the two groups. Based on the differentially expressed genes, a Gene Ontology annotation analysis showed many defence-relevant categories. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways. Furthermore, the expression patterns of 13 putative genes that are involved in defence response resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The sequenced genes covered a considerable proportion of the P. umbellatus transcriptome and the expression results may be useful to strengthen the knowledge on the defence response of this fungus defend against Armillaria mellea invasion.
Coastal sea level projections with improved accounting for vertical land motion
Authors: Han Guoqi , Ma Zhimin , Chen Nan , Yang Jingsong , Chen Nancy
Published: November 2015

Regional and coastal mean sea level projections in the Intergovernmental Panel for Climate Change (IPCC) Fifth Assessment Report (AR5) account only for vertical land motion (VLM) associated with glacial isostatic adjustment (GIA), which may significantly under- or over-estimate sea level rise. Here we adjust AR5-like regional projections with the VLM from Global Positioning Satellite (GPS) measurements and/or from a combination of altimetry and tide-gauge data, which include both GIA and non-GIA VLM. Our results at selected tide-gauge locations on the North American and East Asian coasts show drastically different projections with and without non-GIA VLM being accounted for. The present study points to the importance of correcting IPCC AR5 coastal projections for the non-GIA VLM in making adaptation decisions.
Atomic mapping of Ruddlesden-Popper faults in transparent conducting BaSnO3-based thin films
Authors: Wang W. Y. , Tang Y. L. , Zhu Y. L. , Suriyaprakash J. , Xu Y. B. , Liu Y. , Gao B. , Cheong S-W. , Ma X. L.
Published: November 2015

Doped BaSnO3 has arisen many interests recently as one of the promising transparent conducting oxides for future applications. Understanding the microstructural characteristics are crucial for the exploration of relevant devices. In this paper, we investigated the microstructural features of 0.001% La doped BaSnO3 thin film using both conventional and aberration corrected transmission electron microscopes. Contrast analysis shows high densities of Ruddlesden-Popper faults in the film, which are on {100} planes with translational displacements of 1/2a < 111 > . Atomic EELS element mappings reveal that the Ruddlesden-Popper faults are Ba-O layer terminated and two kinds of kink structures at the Ruddlesden-Popper faults with different element distributions are also demonstrated. Quantitative analysis on lattice distortions of the Ruddlesden-Popper faults illustrates that the local lattice spacing poses a huge increment of 36%, indicating that large strains exist around the Ruddlesden-Popper faults in the film.
Metabolomics Identifies Biomarker Pattern for Early Diagnosis of Hepatocellular Carcinoma: from Diethylnitrosamine Treated Rats to Patients
Authors: Zeng Jun , Huang Xin , Zhou Lina , Tan Yexiong , Hu Chunxiu , Wang Xiaomei , Niu Junqi , Wang Hongyang , Lin Xiaohui , Yin Peiyuan
Published: November 2015

Early diagnosis of hepatocellular carcinoma (HCC) remains challenging to date. Characteristic metabolic deregulations of HCC may enable novel biomarkers discovery for early diagnosis. A capillary electrophoresis-time of flight mass spectrometry (CE-TOF/MS)-based metabolomics approach was performed to discover and validate potential biomarkers for HCC from the diethylnitrosamine-induced rat hepatocarcinogenesis model to human subjects. Time series sera from the animal model were evaluated using multivariate and univariate analyses to reveal dynamic metabolic changes. Two independent human cohorts (populations I and II) containing 122 human serum specimens were enrolled for validations. A novel biomarker pattern of ratio creatine/betaine which reflects the balance of methylation was identified. This biomarker pattern achieved effective classification of pre-HCC and HCC stages in animal model. It was still effective in the diagnosis of HCC from high-risk patients with cirrhotic nodules, achieving AUC values of 0.865 and 0.905 for two validation cohorts, respectively. The diagnosis of small HCC from cirrhosis with an AUC of 0.928 highlighted the potential for early diagnosis. This ratio biomarker can also improve the diagnostic performance of α-fetoprotein (AFP). This study demonstrates the efficacy of present strategy for biomarker discovery and the potential of metabolomics approach to provide novel insights for disease study.
Antinociceptive effects of incarvillateine, a monoterpene alkaloid from Incarvillea sinensis and possible involvement of the adenosine system
Authors: Wang Mei-Liang , Yu Gang , Yi Shou-Pu , Zhang Feng-Ying , Wang Zhi-Tong , Huang Bin , Su Rui-Bin , Jia Yan-Xing , Gong Ze-Hui
Published: November 2015

Incarvillea sinensis is a Bignoniaceae plant used to treat rheumatism and relieve pain in traditional Chinese medicine. As a major component of I. sinensis, incarvillateine has shown analgesic activity in mice formalin tests. Using a series of animal models, this study further evaluated the effects of incarvillateine against acute, inflammatory and neuropathic pain. Incarvillateine (10 or 20 mg/kg, i.p.) dose-dependently attenuated acetic acid-induced writhing, but did not affect thermal threshold in the hot plate test. In a Complete Freund’s Adjuvant model, incarvillateine inhibited both thermal hyperalgesia and paw edema and increased interleukin-1β levels. Additionally, incarvillateine attenuated mechanical allodynia induced by spared nerve injury or paclitaxel, whereas normal mechanical sensation was not affected. Incarvillateine did not affect locomotor activity and time on the rotarod at analgesic doses and no tolerance was observed after 7 consecutive daily doses. Moreover, incarvillateine-induced antinociception was attenuated by theophylline, 1,3-dipropyl-8-cyclopentylxanthine and 3,7-dimethyl-1-propargylxanthine, but not naloxone, indicating that the effects of incarvillateine on chronic pain were related to the adenosine system, but not opioid system. These results indicate that incarvillateine is a novel analgesic compound that is effective against inflammatory and neuropathic pain and that its effects are associated with activation of the adenosine system.
Adrenergic stimulation sensitizes TRPV1 through upregulation of cystathionine β-synthetase in a rat model of visceral hypersensitivity
Authors: Zhu Liyan , Zhao Liting , Qu Ruobing , Zhu Hong-Yan , Wang Yongmeng , Jiang Xinghong , Xu Guang-Yin
Published: November 2015

The pathogenesis of pain in irritable bowel syndrome (IBS) is poorly understood and treatment remains difficult. The present study was designed to investigate roles of adrenergic signaling and the endogenous hydrogen sulfide producing enzyme cystathionine β-synthetase (CBS) in a previously validated rat model of IBS induced by neonatal colonic inflammation (NCI). Here we showed that NCI-induced visceral hypersensitivity (VH) was significantly attenuated by β2 subunit inhibitor but not by β1 or β3 or α subunit inhibitor. NCI markedly elevated plasma norepinephrine (NE) concentration without alteration in expression of β2 subunit receptors in dorsal root ganglion (DRGs) innervating the colon. In addition, NCI markedly enhanced TRPV1 and CBS expression in the colon DRGs. CBS inhibitor AOAA reversed the upregulation of TRPV1 in NCI rats. In vitro experiments showed that incubation of DRG cells with NE markedly enhanced expression of TRPV1, which was reversed by application of AOAA. Incubation of DRG cells with the H2S donor NaHS greatly enhanced TRPV1 expression. Collectively, these data suggest that activation of adrenergic signaling by NCI sensitizes TRPV1 channel activity, which is likely mediated by upregulation of CBS expression in peripheral sensory neurons, thus contributing to chronic visceral hypersensitivity.
Carbon mineralization pathways and bioturbation in coastal Brazilian sediments
Authors: Quintana Cintia O. , Shimabukuro Maurício , Pereira Camila O. , Alves Betina G. R. , Moraes Paula C. , Valdemarsen Thomas , Kristensen Erik , Sumida Paulo Y. G.
Published: November 2015

Carbon mineralization processes and their dependence on environmental conditions (e.g. through macrobenthic bioturbation) have been widely studied in temperate coastal sediments, but almost nothing is known about these processes in subtropical coastal sediments. This study investigated pathways of organic carbon mineralization and associated effects of macrobenthic bioturbation in winter and summer (September 2012 and February 2014) at the SE Brazilian coast. Iron reduction (FeR) was responsible for 73–81% of total microbial carbon mineralization in September 2012 and 32–61% in February 2014. Similar high rates of FeR have only been documented a few times in coastal sediments and can be sustained by the presence of large bioturbators. Denitrification accounted for 5–27% of total microbial carbon mineralization while no SO42−reduction was detected in any season. Redox profiles suggested that conditions were less reduced in February 2014 than in September 2012, probably associated with low reactivity of the organic matter, higher rates of aerobic respiration and bioirrigation by the higher density of small-macrofauna. Bioturbation by small macrofauna may maintain the sediment oxidized in summer, while large-sized species stimulate the reoxidation of reduced compounds throughout the year. Therefore, bioturbation seems to have an important role modulating the pathways of carbon mineralization in the area.
Ailanthone Inhibits Huh7 Cancer Cell Growth via Cell Cycle Arrest and Apoptosis In Vitro and In Vivo
Authors: Zhuo Zhenjian , Hu Jianyang , Yang Xiaolin , Chen Minfen , Lei Xueping , Deng Lijuan , Yao Nan , Peng Qunlong , Chen Zhesheng , Ye Wencai , Zhang Dongmei
Published: November 2015

While searching for natural anti-hepatocellular carcinoma (HCC) components in Ailanthus altissima, we discovered that ailanthone had potent antineoplastic activity against HCC. However, the molecular mechanisms underlying the antitumor effect of ailanthone on HCC have not been examined. In this study, the antitumor activity and the underlying mechanisms of ailanthone were evaluated in vitro and in vivo. Mechanistic studies showed that ailanthone induced G0/G1-phase cell cycle arrest, as indicated by decreased expression of cyclins and CDKs and increased expression of p21 and p27. Our results demonstrated that ailanthone triggered DNA damage characterized by activation of the ATM/ATR pathway. Moreover, ailanthone-induced cell death was associated with apoptosis, as evidenced by an increased ratio of cells in the subG1 phase and by PARP cleavage and caspase activation. Ailanthone-induced apoptosis was mitochondrion-mediated and involved the PI3K/AKT signaling pathway in Huh7 cells. In vivo studies demonstrated that ailanthone inhibited the growth and angiogenesis of tumor xenografts without significant secondary adverse effects, indicating its safety for treating HCC. In conclusion, our study is the first to report the efficacy of ailanthone against Huh7 cells and to elucidate its underlying molecular mechanisms. These findings suggest that ailanthone is a potential agent for the treatment of liver cancer.
High-sensitivity elemental ionization for quantitative detection of halogenated compounds
Authors: Wang Haopeng , Minardi Carina S. , Badiei Hamid , Kahen Kaveh , Jorabchi Kaveh
Published: November 2015

In-plasma oxidative reactions followed by chemical ionization in negative mode offer high-sensitivity elemental quantification of organohalogens separated by GC.
Visual detection of serum asialohaptoglobin by plasmonic sandwich ELLSA – a new platform for cirrhosis diagnosis
Authors: Bose Partha Pratim , Mandal Gautam , Kumar Dharmendra , Duseja Ajay , Chatterjee Bishnu Pada
Published: November 2015

A cheap, fast, point-of-care and high throughput visual assay platform for estimation of asialo-Haptoglobin to monitor liver cirrhosis.
A systematic comparison of different techniques to determine the zeta potential of silica nanoparticles in biological medium
Authors: Sikora Aneta , Bartczak Dorota , Geißler Daniel , Kestens Vikram , Roebben Gert , Ramaye Yannic , Varga Zoltan , Palmai Marcell , Shard Alexander G. , Goenaga-Infante Heidi , Minelli Caterina
Published: November 2015

Comparison of ensemble (ELS) and particle-by-particle (TRPS and z-PTA) based techniques to measure the zeta potential of silica NPs dispersed in a complex serum matrix.
Superior catalytic activity derived from a two-dimensional Ti3C2 precursor towards the hydrogen storage reaction of magnesium hydride
Authors: Liu Yongfeng , Du Hufei , Zhang Xin , Yang Yaxiong , Gao Mingxia , Pan Hongge
Published: November 2015

A 2D Ti3C2 synthesized by the exfoliation of Ti3AlC2 powders exhibits superior catalytic properties for the hydrogen storage reaction of MgH2.