bluuebunny/crossref_metadata_2025 huggingface dataset:
The world's smallest whale population?
Authors: Wade Paul R. , Kennedy Amy , LeDuc Rick , Barlow Jay , Carretta Jim , Shelden Kim , Perryman Wayne , Pitman Robert , Robertson Kelly , Rone Brenda , Salinas Juan Carlos , Zerbini Alexandre , Brownell Robert L. , Clapham Phillip J.
Published: July 2010

The North Pacific right whale (Eubalaena japonica) was heavily exploited by both nineteenth century whaling and recent (1960s) illegal Soviet catches. Today, the species remains extremely rare especially in the eastern North Pacific. Here, we use photographic and genotype data to calculate the first mark–recapture estimates of abundance for right whales in the Bering Sea and Aleutian Islands. The estimates were very similar: photographic = 31 (95% CL 23–54), genotyping = 28 (95% CL 24–42). We also estimated the population contains eight females (95% CL 7–18) and 20 males (95% CL 17–37). Although these estimates may relate to a Bering Sea subpopulation, other data suggest that the total eastern North Pacific population is unlikely to be much larger. Its precarious status today—the world's smallest whale population for which an abundance estimate exists—is a direct consequence of uncontrolled and illegal whaling, and highlights the past failure of international management to prevent such abuses.
Diversity, competition, extinction: the ecophysics of language change
Authors: Solé Ricard V. , Corominas-Murtra Bernat , Fortuny Jordi
Published: July 2010

As indicated early by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of information exchanges and communicative constraints in groups of agents under selective scenarios. These models have been very helpful in providing a rationale on how complex forms of communication emerge under evolutionary pressures. However, other patterns of large-scale organization can be described using mathematical methods ignoring communicative traits. These approaches consider shorter time scales and have been developed by exploiting both theoretical ecology and statistical physics methods. The models are reviewed here and include extinction, invasion, origination, spatial organization, coexistence and diversity as key concepts and are very simple in their defining rules. Such simplicity is used in order to catch the most fundamental laws of organization and those universal ingredients responsible for qualitative traits. The similarities between observed and predicted patterns indicate that an ecological theory of language is emerging, supporting (on a quantitative basis) its ecological nature, although key differences are also present. Here, we critically review some recent advances and outline their implications and limitations as well as highlight problems for future research.
Bioactive ceramic-reinforced composites for bone augmentation
Authors: Tanner K. E.
Published: July 2010

Biomaterials have been used to repair the human body for millennia, but it is only since the 1970s that man-made composites have been used. Hydroxyapatite (HA)-reinforced polyethylene (PE) is the first of the ‘second-generation’ biomaterials that have been developed to be bioactive rather than bioinert. The mechanical properties have been characterized using quasi-static, fatigue, creep and fracture toughness testing, and these studies have allowed optimization of the production method. Thein vitroandin vivobiological properties have been investigated with a range of filler content and have shown that the presence of sufficient bioactive filler leads to a bioactive composite. Finally, the material has been applied clinically, initially in the orbital floor and later in the middle ear. From this initial combination of HA in PE other bioactive ceramic polymer composites have been developed.
The many lives of Charles Darwin: early biographies and the definitive evolutionist
Authors: Lightman Bernard
Published: July 2010

This article focuses on the early book-length biographies of Darwin published from his death in 1882 up to 1900. By making 1900 the cutoff point I can examine the biographies produced when the iconic figure was not yet set in stone, and before the rediscovery of Mendel's work in the early twentieth century and the anniversary celebrations of 1909 changed the way in which Darwin was regarded. Darwin's biographers dealt with three major themes. First, several biographers emphasized his scientific abilities, in particular his powers of observation and his prowess in conducting experiments. Second, many biographers discussed his character, a key issue in determining whether or not he could be trusted as a scientific guide. Finally, his scientific theories and religious beliefs, and how they related to the evolutionary controversy, formed a topic taken up by most biographers. By focusing on these three themes, the biographies published before 1900 were important in shaping the image of Darwin that was forming in American and British culture.
Charge-density waves arising from two electron bands
Authors: Buker Donald W.
Published: July 2010

A theory for a quasi-one-dimensional incommensurate charge-density wave state arising from electron–phonon (el–phon) interaction connecting electron states in two different bands is presented. An expression for the fundamental component of the energy gap as a function of the effective el–phon coupling, valid for all coupling strengths, has been found. For a single band, the expression simplifies to a reciprocal hyperbolic-sine dependence on the reciprocal effective coupling. The effective coupling, although simply related to the
n
assumed phonon-band frequencies, is not generally expressible as a sum of independent functions of these frequencies. The theory is applied to tetrathiofulvalinium–tetracyanoquinodimethane and to potassium blue bronze.
Four-branch vibrational spectrum of double-walled carbon nanotube model
Authors: Shubov Marianna A. , Rojas-Arenaza Miriam
Published: July 2010

Asymptotic distribution of the discrete spectrum eigenvalues for a recently developed model of a double-walled carbon nanotube is presented in this paper. The corresponding initial boundary-value problem is reduced to an evolution equation, whose dynamics generator is a non-self-adjoint matrix differential operator with a purely discrete spectrum. It is shown in the paper that the entire spectrum asymptotically splits into four spectral branches. Asymptotic representation is derived for the eigenvalues along each spectral branch as the number of an eigenvalue tends to infinity. To prove the results, a two-step procedure involving the construction of the left- and right-reflection matrices has been used.
An acoustic analogy formulation for moving sources in uniformly moving media
Authors: Najafi-Yazdi Alireza , Brès Guillaume A. , Mongeau Luc
Published: July 2010

Acoustic analogy methods are used as post-processing tools to predict aerodynamically generated sound from numerical solutions of unsteady flow. The Ffowcs Williams–Hawkings (FW–H) equation and related formulations, such as Farassat’s Formulations 1 and 1A, are among the commonly used analogies because of their relative low computation cost and their robustness. These formulations assume the propagation of sound waves in a medium at rest. The present paper describes a surface integral formulation based on the convective wave equation, which takes into account the presence of a mean flow. The formulation was derived to be easy to implement as a numerical post-processing tool for computational fluid dynamics codes. The new formulation constitutes one possible extension of Farassat’s Formulation 1 and 1A based on the convective form of the FW–H equation.
Micro-architectured materials: past, present and future
Authors: Fleck N. A. , Deshpande V. S. , Ashby M. F.
Published: July 2010

Micro-architectured materials offer the opportunity of obtaining unique combinations of material properties. First, a historical perspective is given to the expansion of material property space by the introduction of new alloys and new microstructures. Principles of design of micro-architecture are then given and the role of nodal connectivity is emphasized for monoscale and multi-scale microstructures. The stiffness, strength and damage tolerance of lattice materials are reviewed and compared with those of fully dense solids. It is demonstrated that micro-architectured materials are able to occupy regions of material property space (such as high stiffness, strength and fracture toughness at low density) that were hitherto empty. Some challenges for the development of future materials are highlighted.
Dynamic modelling of a single-walled carbon nanotube for nanoparticle delivery
Authors: Lee Haw-Long , Chang Win-Jin
Published: July 2010

In this paper, the dynamic behaviour of a single-walled carbon nanotube (SWCNT) for nanoparticle delivery is studied using non-local elasticity theory. The response of the delivery system depends on the time history and velocity of the moving nanoparticle. In addition, the interaction between the SWCNT and the moving nanoparticle, and the foundation of the SWCNT can also influence the dynamic behaviour of the system. The effects of foundation stiffness, confined stiffness, velocity ratio, non-local parameter and travel time on the behaviour are analysed using the Runge–Kutta method. The numerical solution is in agreement with the analytical result for the special case. The numerical analysis shows that increasing the non-local parameter, confined stiffness and foundation stiffness decreases the dynamic displacement of SWCNT. However, increasing the velocity ratio increases the maximum displacement.
Scaling of sensorimotor control in terrestrial mammals
Authors: More Heather L. , Hutchinson John R. , Collins David F. , Weber Douglas J. , Aung Steven K. H. , Donelan J. Maxwell
Published: July 2010

Sensorimotor control is greatly affected by two factors—the time it takes for an animal to sense and respond to stimuli (responsiveness), and the ability of an animal to distinguish between sensory stimuli and generate graded muscle forces (resolution). Here, we demonstrate that anatomical limitations force a necessary trade-off between responsiveness and resolution with increases in animal size. To determine whether responsiveness is prioritized over resolution, or resolution over responsiveness, we studied how size influences the physiological mechanisms underlying sensorimotor control. Using both new electrophysiological experiments and existing data, we determined the maximum axonal conduction velocity (CV) in animals ranging in size from shrews to elephants. Over the 100-fold increase in leg length, CV was nearly constant, increasing proportionally with mass to the 0.04 power. As a consequence, larger animals are burdened with relatively long physiological delays, which may have broad implications for their behaviour, ecology and evolution, including constraining agility and requiring prediction to help control movements.
Character displacement in the fighting colours of
Hetaerina
damselflies
Authors: Anderson Christopher N. , Grether Gregory F.
Published: July 2010

Aggression between species is a seldom-considered but potentially widespread mechanism of character displacement in secondary sexual characters. Based on previous research showing that similarity in wing coloration directly influences interspecific territorial aggression in
Hetaerina
damselflies, we predicted that wing coloration would show a pattern of character displacement (divergence in sympatry). A geographical survey of four
Hetaerina
damselfly species in Mexico and Texas showed evidence for character displacement in both species pairs that regularly occurs sympatrically.
Hetaerina titia
, a species that typically has large black wing spots and small red wing spots, shifted to having even larger black spots and smaller red wing spots at sites where a congener with large red wing spots is numerically dominant (
Hetaerina americana
or
Hetaerina occisa
).
Hetaerina americana
showed the reverse pattern, shifting towards larger red wing spots where
H. titia
is numerically dominant. This pattern is consistent with the process of agonistic character displacement, but the ontogenetic basis of the shift remains to be demonstrated.
RETRACTED: Parasite prevalence and the worldwide distribution of cognitive ability
Authors: Eppig Christopher , Fincher Corey L. , Thornhill Randy
Published: July 2010

In this study, we hypothesize that the worldwide distribution of cognitive ability is determined in part by variation in the intensity of infectious diseases. From an energetics standpoint, a developing human will have difficulty building a brain and fighting off infectious diseases at the same time, as both are very metabolically costly tasks. Using three measures of average national intelligence quotient (IQ), we found that the zero-order correlation between average IQ and parasite stress ranges fromr= −0.76 tor= −0.82 (p< 0.0001). These correlations are robust worldwide, as well as within five of six world regions. Infectious disease remains the most powerful predictor of average national IQ when temperature, distance from Africa, gross domestic productper capitaand several measures of education are controlled for. These findings suggest that the Flynn effect may be caused in part by the decrease in the intensity of infectious diseases as nations develop.
Identification of an ant queen pheromone regulating worker sterility
Authors: Holman Luke , Jørgensen Charlotte G. , Nielsen John , d'Ettorre Patrizia
Published: July 2010

The selective forces that shape and maintain eusocial societies are an enduring puzzle in evolutionary biology. Ordinarily sterile workers can usually reproduce given the right conditions, so the factors regulating reproductive division of labour may provide insight into why eusociality has persisted over evolutionary time. Queen-produced pheromones that affect worker reproduction have been implicated in diverse taxa, including ants, termites, wasps and possibly mole rats, but to date have only been definitively identified in the honeybee. Using the black garden antLasius niger, we isolate the first sterility-regulating ant queen pheromone. The pheromone is a cuticular hydrocarbon that comprises the majority of the chemical profile of queens and their eggs, and also affects worker behaviour, by reducing aggression towards objects bearing the pheromone. We further show that the pheromone elicits a strong response in worker antennae and that its production by queens is selectively reduced following an immune challenge. These results suggest that the pheromone has a central role in colony organization and support the hypothesis that worker sterility represents altruistic self-restraint in response to an honest quality signal.
The evolution of menopause in cetaceans and humans: the role of demography
Authors: Johnstone Rufus A. , Cant Michael A.
Published: July 2010

Human females stop reproducing long before they die. Among other mammals, only pilot and killer whales exhibit a comparable period of post-reproductive life. The grandmother hypothesis suggests that kin selection can favour post-reproductive survival when older females help their relatives to reproduce. But although there is an evidence that grandmothers can provide such assistance, it is puzzling why menopause should have evolved only among the great apes and toothed whales. We have previously suggested (Cant & Johnstone 2008Proc. Natl Acad. Sci. USA105, 5332–5336 (doi:10.1073/pnas.0711911105)) that relatedness asymmetries owing to female-biased dispersal in ancestral humans would have favoured younger females in reproductive competition with older females, predisposing our species to the evolution of menopause. But this argument appears inapplicable to menopausal cetaceans, which exhibit philopatry of both sexes combined with extra-group mating. Here, we derive general formulae for ‘kinship dynamics’, the age-related changes in local relatedness that occur in long-lived social organisms as a consequence of dispersal and mortality. We show that the very different social structures of great apes and menopausal whales both give rise to an increase in local relatedness with female age, favouring late-life helping. Our analysis can therefore help to explain why, of all long-lived, social mammals, it is specifically among the great apes and toothed whales that menopause and post-reproductive helping have evolved.
Sensitive males: inbreeding depression in an endangered bird
Authors: Brekke Patricia , Bennett Peter M. , Wang Jinliang , Pettorelli Nathalie , Ewen John G.
Published: July 2010

Attempts to conserve threatened species by establishing new populations via reintroduction are controversial. Theory predicts that genetic bottlenecks result in increased mating between relatives and inbreeding depression. However, few studies of wild sourced reintroductions have carefully examined these genetic consequences. Our study assesses inbreeding and inbreeding depression in a free-living reintroduced population of an endangered New Zealand bird, the hihi (Notiomystis cincta). Using molecular sexing and marker-based inbreeding coefficients estimated from 19 autosomal microsatellite loci, we show that (i) inbreeding depresses offspring survival, (ii) male embryos are more inbred on average than female embryos, (iii) the effect of inbreeding depression is male-biased and (iv) this population has a substantial genetic load. Male susceptibility to inbreeding during embryo and nestling development may be due to size dimorphism, resulting in faster growth rates and more stressful development for male embryos and nestlings compared with females. This work highlights the effects of inbreeding at early life-history stages and the repercussions for the long-term population viability of threatened species.
Conserved role of SIRT1 orthologs in fasting-dependent inhibition of the lipid/cholesterol regulator SREBP
Authors: Walker Amy K. , Yang Fajun , Jiang Karen , Ji Jun-Yuan , Watts Jennifer L. , Purushotham Aparna , Boss Olivier , Hirsch Michael L. , Ribich Scott , Smith Jesse J. , Israelian Kristine , Westphal Christoph H. , Rodgers Joseph T. , Shioda Toshi , Elson Sarah L. , Mulligan Peter , Najafi-Shoushtari Hani , Black Josh C. , Thakur Jitendra K. , Kadyk Lisa C. , Whetstine Johnathan R. , Mostoslavsky Raul , Puigserver Pere , Li Xiaoling , Dyson Nicholas J. , Hart Anne C. , Näär Anders M.
Published: July 2010

The sterol regulatory element-binding protein (SREBP) transcription factor family is a critical regulator of lipid and sterol homeostasis in eukaryotes. In mammals, SREBPs are highly active in the fed state to promote the expression of lipogenic and cholesterogenic genes and facilitate fat storage. During fasting, SREBP-dependent lipid/cholesterol synthesis is rapidly diminished in the mouse liver; however, the mechanism has remained incompletely understood. Moreover, the evolutionary conservation of fasting regulation of SREBP-dependent programs of gene expression and control of lipid homeostasis has been unclear. We demonstrate here a conserved role for orthologs of the NAD+-dependent deacetylase SIRT1 in metazoans in down-regulation of SREBP orthologs during fasting, resulting in inhibition of lipid synthesis and fat storage. Our data reveal that SIRT1 can directly deacetylate SREBP, and modulation of SIRT1 activity results in changes in SREBP ubiquitination, protein stability, and target gene expression. In addition, chemical activators of SIRT1 inhibit SREBP target gene expression in vitro and in vivo, correlating with decreased hepatic lipid and cholesterol levels and attenuated liver steatosis in diet-induced and genetically obese mice. We conclude that SIRT1 orthologs play a critical role in controlling SREBP-dependent gene regulation governing lipid/cholesterol homeostasis in metazoans in response to fasting cues. These findings may have important biomedical implications for the treatment of metabolic disorders associated with aberrant lipid/cholesterol homeostasis, including metabolic syndrome and atherosclerosis.
Protein phosphatase 1-dependent transcriptional programs for long-term memory and plasticity
Authors: Gräff Johannes , Koshibu Kyoko , Jouvenceau Anne , Dutar Patrick , Mansuy Isabelle M.
Published: July 2010

Gene transcription is essential for the establishment and the maintenance of long-term memory (LTM) and for long-lasting forms of synaptic plasticity. The molecular mechanisms that control gene transcription in neuronal cells are complex and recruit multiple signaling pathways in the cytoplasm and the nucleus. Protein kinases (PKs) and phosphatases (PPs) are important players in these mechanisms. Protein serine/threonine phosphatase 1 (PP1), in particular, was recently shown to be important for transcription-dependent memory by regulating chromatin remodeling. However, the impact of PP1 on gene transcription in adult neurons remains not fully delineated. Here, we demonstrate that the nuclear pool of PP1 is associated with transcriptional events involving molecular components of signaling cascades acting as positive and negative regulators of memory and brain plasticity. The data show that inhibiting this pool selectively in forebrain neurons improves memory performance, enhances long-term potentiation (LTP), and modulates gene transcription. These findings highlight an important role for PP1 in the regulation of gene transcription in LTM and synaptic plasticity in the adult brain.
Guidelines for the Use of RNA Purification Kits
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W.
Published: July 2010

INTRODUCTION

With the proliferation of researchers investigating various aspects of RNA biology has come a corresponding proliferation of commercially available kits for RNA purification. Some of these kits have specialized uses and applications, and it is not always possible to simply mix and match the different protocols. Although the instructions are often written with a minimum of specifics concerning the chemical basis for the separation characteristics that the kits use, the competent researcher will want to understand these important features. Unfortunately, commercial sources work hard to hide the specifics of their methods. Fortunately, patent documents are publicly available, and the government mandates material safety data disclosures of the composition of at least those components that represent a threat to environmental health and safety. Thus, it is possible to infer many aspects of such “proprietary” materials, which in most cases are only slightly and unimportantly modified from published techniques. We do not describe in detail the specific steps involved in the use of particular kits; they are detailed in the literature that comes with each kit and their components (e.g., proprietary buffers). Instead, we detail some advantages and disadvantages of using RNA purification kits.
Transmission Electron Microscopy (TEM) of Plant Tissues
Authors: Hülskamp Martin , Schwab Birgit , Grini Paul , Schwarz Heinz
Published: July 2010

INTRODUCTION

Transmission electron microscopy (TEM) requires extensive preparation of plant tissues to achieve optimal results. Samples must be fixed to preserve ultrastructure, dehydrated to withstand the high vacuum of an electron microscope, and embedded in a suitable resin to permit very thin sections to be produced. This protocol provides details for fixation, dehydration with ethanol, and embedding in Spurr’s, an epoxide resin with low viscosity that is well-suited for plant tissues.
Immunofluorescent Staining of Drosophila Larval Brain Tissue
Authors: Daul Aric L. , Komori Hideyuki , Lee Cheng-Yu
Published: July 2010

INTRODUCTION

The Drosophila larval brain is a well-established model for investigating the role of stem cells in development. Neuroblasts (neural stem cells) must be competent to generate many thousands of differentiated neurons through asymmetric divisions during normal development. Studies in fly neuroblasts have been instrumental in identifying how the establishment and maintenance of cell polarity influence cell fate, and they have produced a wide array of molecular cell-polarity markers. Moreover, neuroblasts and their progeny can be positively identified using a variety of cell-fate markers. This article describes procedures for the collection and processing of Drosophila larval brains for examination by immunolocalization of cell-fate and cell-polarity markers. The protocol can be used for dissecting, fixing, and staining brains from larvae at any developmental stage. The number of brains processed using this method is limited only by how many brains can be dissected in 20 min, which is the maximum amount of time dissected tissues should remain in buffer before fixation. This protocol can be used for simultaneous costaining of multiple proteins.
Multicolor Fluorescence RNA In Situ Hybridization of Drosophila Brain Tissue
Authors: Daul Aric L. , Komori Hideyuki , Lee Cheng-Yu
Published: July 2010

INTRODUCTION

RNA in situ hybridization is a useful method for determining the transcriptional expression pattern of a gene when antibodies are not available. Using this technique, it is possible to assay the expression of multiple RNA species using distinct labels on RNA probes, or simultaneously examine RNA and protein localization within larval tissues. This protocol describes RNA in situ hybridization of Drosophila brain tissue. It utilizes a fluorophore-conjugated tyramide that is easily made in the laboratory for a fraction of the cost of the commercially produced product.
Targeting the Zebrafish Optic Tectum Using In Vivo Electroporation
Authors: Hoegler Kenric J. , Horne John H.
Published: July 2010

INTRODUCTION

In vivo electroporation is a method for delivery of plasmids and other oligonucleotide reagents that offers precise temporal control. In zebrafish, in vivo electroporation is particularly well-suited to delivering green fluorescent protein (GFP) expression vectors to the developing central nervous system. This protocol describes a modification of in vivo electroporation that can be used to specifically target the developing optic tectum of zebrafish embryos beginning at 24 h post-fertilization (hpf). The electroporation electrodes required for this approach can be constructed easily from relatively inexpensive materials. Microinjection of plasmid DNA to the midbrain ventricle followed by precise positioning of the electroporation electrodes allows for the targeting of developing neurons in only one hemisphere of the optic tectum. Using this protocol, the optic tectum can be effectively targeted in a high percentage (79%) of expressing embryos. This method can also be used to simultaneously deliver expression vectors and loss-of-function reagents, which can provide precise temporal control of the knockdown of gene function.
Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements
Authors: Lacayo Catherine I. , Malkin Alexander J. , Holman Hoi-Ying N. , Chen Liang , Ding Shi-You , Hwang Mona S. , Thelen Michael P.
Published: July 2010

The chemical and structural organization of the plant cell wall was examined in Zinnia elegans tracheary elements (TEs), which specialize by developing prominent secondary wall thickenings underlying the primary wall during xylogenesis in vitro. Three imaging platforms were used in conjunction with chemical extraction of wall components to investigate the composition and structure of single Zinnia TEs. Using fluorescence microscopy with a green fluorescent protein-tagged Clostridium thermocellum family 3 carbohydrate-binding module specific for crystalline cellulose, we found that cellulose accessibility and binding in TEs increased significantly following an acidified chlorite treatment. Examination of chemical composition by synchrotron radiation-based Fourier-transform infrared spectromicroscopy indicated a loss of lignin and a modest loss of other polysaccharides in treated TEs. Atomic force microscopy was used to extensively characterize the topography of cell wall surfaces in TEs, revealing an outer granular matrix covering the underlying meshwork of cellulose fibrils. The internal organization of TEs was determined using secondary wall fragments generated by sonication. Atomic force microscopy revealed that the resulting rings, spirals, and reticulate structures were composed of fibrils arranged in parallel. Based on these combined results, we generated an architectural model of Zinnia TEs composed of three layers: an outermost granular layer, a middle primary wall composed of a meshwork of cellulose fibrils, and inner secondary wall thickenings containing parallel cellulose fibrils. In addition to insights in plant biology, studies using Zinnia TEs could prove especially productive in assessing cell wall responses to enzymatic and microbial degradation, thus aiding current efforts in lignocellulosic biofuel production.
When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys
Authors: GARRARD GEORGIA E. , BEKESSY SARAH A. , McCARTHY MICHAEL A. , WINTLE BRENDAN A.
Published: July 2010

There is now a substantial body of literature documenting the detectability of plants and animals under standard survey conditions. Despite the evidence that many flora and fauna species have detection probabilities of less than one, it is still the default assumption of most environmental impact assessment processes that if a species is present, it will be detected. Here we briefly review a number of existing studies that have estimated the survey effort necessary to detect animal species, based on what is known about their detection rates in standard surveys. We then propose a novel method, based on failure‐time analysis, for quantifying the detectability of and determining appropriate survey effort for plant species during flora surveys. We provide computer code for implementing the method in the Bayesian freeware WinBUGS. Methods for estimating detectability can be used to inform minimum survey requirements and have important applications in environmental impact assessment and monitoring.
Susceptibility to gut leakiness: a possible mechanism for endotoxaemia in non‐alcoholic steatohepatitis
Authors: Farhadi Ashkan , Gundlapalli Sushama , Shaikh Maliha , Frantzides Constantine , Harrell Laura , Kwasny Mary M. , Keshavarzian Ali
Published: July 2010

Introduction: One of the proposed second hit mechanisms in the pathophysiology of non‐alcoholic steatohepatitis (NASH) is hepatic oxidative stress triggered by elevated levels of endotoxin. We investigated one possible mechanism for the endotoxaemia – disruption of intestinal barrier integrity.

Methods: We enrolled 16 subjects with fatty liver (10 NASH; 6 steatosis) and 12 healthy subjects. Steatosis and NASH were diagnosed by liver biopsy using the Brunt criteria. Gastrointestinal permeability was measured using urinary excretion of 5‐h lactulose/mannitol (L/M) ratio and 24‐h sucralose. Permeability testing was repeated after aspirin challenge.

Results: Groups had similar baseline urinary 0–5 h L/M ratio (small bowel permeability) and 0–24 h sucralose (whole‐gut permeability). Aspirin increased 0–5 h urinary L/M in most subjects. In contrast, aspirin significantly increased whole‐gut permeability only in NASH subjects. In fact, the major increase in the urinary sucralose occurred in the 6–24 h samples, which points towards the colon as the major site responsible for aspirin‐induced leakiness in NASH patients. Serum endotoxin levels were significantly higher in NASH subjects.

Discussion: Our findings suggest that aspirin acts on the colon to unmask a susceptibility to gut leakiness in patients with NASH. This effect may be the underlying mechanism for increased serum endotoxin, which is the second hit (after altered lipid metabolism) that is required to initiate a necroinflammatory cascade in hepatocytes which are already primed with obesity‐induced abnormal lipid homoeostasis.
Unanalyzed evidence in law‐enforcement agencies
Authors: Strom Kevin J. , Hickman Matthew J.
Published: July 2010

Research Summary

This study investigated forensic evidence processing in a nationally representative sample of state and local law‐enforcement agencies (n = 3,153). For a 5‐year period, agencies reported that 14% of all unsolved homicides (an estimated 3,975 cases) and 18% of all unsolved rapes (an estimated 27,595 cases) contained forensic evidence that had not been submitted to a forensic crime laboratory for analysis. Approximately 40% of these unanalyzed homicide and rape cases were reported to have contained DNA evidence. The lack of a suspect in the case was the most frequently cited reason for not submitting forensic evidence for analysis.

Policy Implications

Despite an increased diffusion of knowledge regarding the value of forensic evidence in the prosecution and defense of criminal cases, the investigative capabilities of forensic science are not being realized by law enforcement. Additional training for law enforcement on the use of forensic science to develop investigative leads is critical, as is the creation of departmental policies that prioritize and streamline the analysis of forensic evidence for homicide and rape cases—even in “no‐suspect” cases. Ensuring adequate resources and information sharing for forensic processing especially of violent crimes, is also critical.
Sodium–bicarbonate cotransporter NBCn1 in the kidney medullary thick ascending limb cell line is upregulated under acidic conditions and enhances ammonium transport
Authors: Lee Soojung , Lee Hye Jeong , Yang Han Soo , Thornell Ian M. , Bevensee Mark O. , Choi Inyeong
Published: July 2010

In this study, we examined the effect of bicarbonate transporters on ammonium/ammonia uptake in the medullary thick ascending limb cell line ST‐1. Cells were treated with 1 mm ouabain and 0.2 mm bumetanide to minimize carrier‐mediated NH4+ transport, and the intracellular accumulation of 14C‐methylammonium/methylammonia (14C‐MA) was determined. In CO2/HCO3−‐free solution, cells at normal pH briefly accumulated 14C‐MA over 7 min and reached a plateau. In CO2/HCO3− solution, however, cells markedly accumulated 14C‐MA over the experimental period of 30 min. This CO2/HCO3−‐dependent accumulation was reduced by the bicarbonate transporter blocker, 4,4′‐diisothiocyanatostilbene‐2,2′‐disulfonate (DIDS; 0.5 mm). Replacing Cl− with gluconate reduced the accumulation, but the reduction was more substantial in the presence of DIDS. Incubation of cells at pH 6.8 (adjusted with NaHCO3 in 5% CO2) for 24 h lowered the mean steady‐state intracellular pH to 6.96, significantly lower than 7.28 for control cells. The presence of DIDS reduced 14C‐MA accumulation in control conditions but had no effect after acidic incubation. Immunoblotting showed that NBCn1 was upregulated after acidic incubation and in NH4Cl‐containing media. The Cl−–HCO3− exchanger AE2 was present, but its expression remained unaffected by acidic incubation. Expressed in Xenopus oocytes, NBCn1 increased carrier‐mediated 14C‐MA transport, which was abolished by replacing Na+. Two‐electrode voltage clamp of oocytes exhibited negligible current after NH4Cl application. These results suggest that DIDS‐sensitive HCO3− extrusion normally governs NH4+/NH3 uptake in the medullary thick ascending limb cells. We propose that, in acidic conditions, DIDS‐sensitive HCO3− extrusion is inactivated, while NBCn1 is upregulated to stimulate NH4+ transport.
Role of GABAergic neurones in the nucleus tractus solitarii in modulation of cardiovascular activity
Authors: Zubcevic Jasenka , Potts Jeffrey T.
Published: July 2010

GABAergic neurones are interspersed throughout the nucleus tractus solitarii (NTS), and their tonic activity is crucial to the maintenance of cardiorespiratory homeostasis. However, the mechanisms that regulate the magnitiude of GABAergic inhibition in the NTS remain unknown. We hypothesized that the level of GABAergic inhibition is proportionally regulated by the level of excitatory synaptic input to the NTS from baroreceptors. Using thein situworking heart–brainstem preparation in normotensive and spontaneously hypertensive rats, we blocked GABAAreceptor‐mediated neurotransmission in the NTS with gabazine (a specific GABAAreceptor antagonist) at two levels of perfusion pressure (low PP, 60–70 mmHg; and high PP, 105–125 mmHg) while monitoring the immediate changes in cardiorespiratory variables. In normotensive rats, gabazine produced an immediate bradycardia consistent with disinhibition of NTS circuit neurones that regulate heart rate (HR) which was proportional to the level of arterial pressure (ΔHR at low PP, −57 ± 9 beats min−1; at high PP, −177 ± 9 beats min−1;P< 0.001), suggesting that GABAergic circuitry in the NTS modulating heart rate was arterial pressure dependent. In contrast, there was no significant difference in the magnitude of gabazine‐induced bradycardia in spontaneously hypertensive rats at low or high PP (ΔHR at low PP, −45 ± 10 beats min−1; at high PP, −58 ± 7 beats min−1). With regard to thoracic sympathetic nerve activity (tSNA), at high PP there was a significant reduction in tSNA during the inspiratory (I) phase of the respiratory cycle, but only in the normotensive rat (Δ∫tSNA =−18.7 ± 10%). At low PP, gabazine caused an elevation of the postinspiration phase of tSNA in both normotensive (Δ∫tSNA = 23.7 ± 2.9%) and hypertensive rats (Δ∫tSNA = 44.2 ± 14%). At low PP, gabazine produced no change in tSNA during the mid‐expiration phase in either rat strain, but at high PP we observed a significant reduction in the mid‐expiration phase tSNA, but only in the spontaneously hypertensive rat (Δ∫tSNA =−25.2 ± 8%). Gabazine at both low and high PP produced a reduction in the late expiration phase of tSNA in the hypertensive rat (low PP, Δ∫tSNA =−29.4 ± 4.4%; high PP, ΔtSNA =−22.8 ± 3%), whereas in the normotensive rat this was only significant at high PP (Δ∫tSNA =−42.5 ± 6.1%). Therefore, in the spontaneously hypertensive rat, contrary to the GABAAreceptor‐mediated control of HR, it appears that GABAAreceptor‐mediated control of tSNA in the NTS is arterial pressure dependent. This study provides new insight into the origin of GABAergic inhibition in NTS circuitry affecting heart rate and sympathetic activity.
Formation of epitaxial graphene on SiC(0001) using vacuum or argon environments
Authors: Luxmi  , Srivastava N. , Feenstra R. M. , Fisher P. J.
Published: July 2010

The formation of graphene on the (0001) surface of SiC (the Si-face) is studied by atomic force microscopy, low-energy electron microscopy, and scanning tunneling microscopy/spectroscopy. The graphene forms due to preferential sublimation of Si from the surface at high temperature, and the formation has been studied in both high-vacuum and 1 atm argon environments. In vacuum, a few monolayers of graphene forms at temperatures around 1400 °C, whereas in argon a temperature of about 1600 °C is required in order to obtain a single graphene monolayer. In both cases considerable step motion on the surface is observed, with the resulting formation of step bunches separated laterally by ≳10 μm. Between the step bunches, a layer-by-layer growth of the graphene is found. The presence of a disordered, secondary graphitic phase on the surface of the graphene is also identified.
Synthesis and calorimetric studies of oxide multilayer systems: Solid oxide fuel cell cathode and electrolyte materials
Authors: Kemik Nihan , Ushakov Sergey V. , Schichtel Nicole , Korte Carsten , Takamura Yayoi , Navrotsky Alexandra
Published: July 2010

The authors used differential scanning calorimetry and high temperature oxide melt calorimetry to investigate the interface energies in various multilayer systems. For yttria stabilized zirconia (YSZ)/Al2O3 multilayers, the presence of interfaces is shown to affect the temperature and the enthalpy of crystallization; and therefore these interfaces play an important role in phase stability. From the thermal analysis results, it can be concluded that in YSZ/Al2O3 multilayers, the Al2O3 crystallization temperature increases and the enthalpy becomes less exothermic compared to the values for single alumina films. It is also shown that crystalline perovskite films of La(Sr)MnO3 can be deposited on NaCl substrates and can be collected from the substrate after the deposition which makes them suitable for high temperature calorimetry.
Carbon nanotube field emitter irradiated by proton beam
Authors: Lee Seung-Min , Kim Wal-Jun , Kim Yong-Hyup , Yang Taekeun , Han Juneyong
Published: July 2010

The present study adopts proton irradiation to solve the problems, such as performance degradation due to outgassing and weak adhesion, of a carbon nanotube (CNT) field emitter fabricated by the indirect coating method. The protons collide against the CNT layer and the copper film, and results in thinning out of the CNTs and particle migration of the copper constituents. This process reduces the turn-on field and increases the lifetime of CNT emitters, respectively. Numerical simulations have been performed to understand the results from experiments by using a software, SRIM 2008.
Fabrication of surface plasmon waveguides and devices in Cytop with integrated microfluidic channels
Authors: Chiu Charles , Lisicka-Skrzek Ewa , Tait R. Niall , Berini Pierre
Published: July 2010

Long range surface plasmon-polariton waveguides and devices suitable for biosensing were fabricated and characterized physically and optically. The structures consist of thin (∼35 nm) patterned Au stripes embedded in thick Cytop claddings (∼8 μm each). Portions of Au stripes were exposed by patterning and etching though the top Cytop cladding using an O2 plasma etch. The etched Cytop cavities act as microfluidic channels to contain and direct the sensing fluid. Intermediate process steps were verified through physical characterization as were fully fabricated structures. Optical testing was performed on Cytop-embedded structures and on channel-filled (with sensing fluid) structures. The structures were excited through end-fire coupling to optical fibers.
Experimental Results for H
2
Formation from H
−
and H and Implications for First Star Formation
Authors: Kreckel H. , Bruhns H. , Čížek M. , Glover S. C. O. , Miller K. A. , Urbain X. , Savin D. W.
Published: July 2010

Early Rising Hydrogen

Formation of molecular hydrogen through electron-expelling collisions of H atoms and H
−
anions is regarded as a key step in the cooling process that led to assembly of the first stars in the early universe.

Kreckel
et al.

(p.
69
; see the Perspective by

Bromm

) performed highly precise laboratory measurements of the rate of this reaction at a range of different energies. The study required construction of a dedicated apparatus to carefully tune the relative velocity of merged atom and ion beams. The data validated prior theoretically calculated reaction cross sections, which were then extended for use in cosmological models.
An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor
Bcl11b
Authors: Li Long , Leid Mark , Rothenberg Ellen V.
Published: July 2010

One Two T

T cells develop in the thymus, where they proceed through several developmental stages, losing alternative lineage potential as they progress. The molecular regulation of this developmental process, however, is not fully understood (see the Perspective by

Di Santo

).

P. Li
et al.

(p.
85
, published online 10 June),

L. Li
et al.

(p.
89
), and

Ikawa
et al.

(p.
93
) now identify expression of the zinc finger transcription factor
Bcl11b
as the earliest checkpoint in T cell development in mice. Genetic deletion of
Bcl11b
in developing T cells inhibited commitment to the T cell lineage. Under conditions that should have stimulated T lineage differentiation,
Bcl11b
-deficient T cell progenitors failed to up-regulate genes associated with lineage-committed T cells and maintained stem cell– and progenitor cell–associated gene expression. In both developing and committed T cells, loss of
Bcl11b
resulted in the generation of cells that resembled natural killer (NK) cells in both phenotype and function. These NK-like cells could be expanded easily in vitro and possessed antitumor cytotoxicity, but they did not exhibit cytotoxicity against normal cells and were not tumorigenic. Because T cells are much easier to obtain from human patients than NK cells, deletion of
Bcl11b
in T cells may thus provide a source of easy-to-grow NK cells for cell-based antitumor therapies.
Does the Hydrated Electron Occupy a Cavity?
Authors: Larsen Ross E. , Glover William J. , Schwartz Benjamin J.
Published: July 2010

Filling a Cavity

Unlike liquid ammonia, water cannot sustain a steady concentration of isolated electrons. Nonetheless, high-energy irradiation can introduce a small number of free charges that engage in potent reductive chemistry and have clear spectroscopic signatures. The manner in which water solubilizes these hydrated electrons has remained uncertain, but the general consensus has been that repulsive interactions drive the nearest water molecules away, leaving the electron in a nearly spherical empty cavity.

Larsen
et al.

(p.
65
; see the Perspective by
Jordan and Johnson
) upend this consensus with simulations based on a more thorough potential function for modeling the competing attractions and repulsions between the electron and surrounding water. The calculations suggest that the hydrated electron actually draws water in, occupying a region denser than the pure bulk liquid. The model reproduces experimental spectral and dynamic observations as effectively as, and in some cases better than, the cavity framework.
Graphite in an Apollo 17 Impact Melt Breccia
Authors: Steele A. , McCubbin F. M. , Fries M. , Glamoclija M. , Kater L. , Nekvasil H.
Published: July 2010

Ancient carbonaceous material possibly delivered during meteorite bombardment has been found in lunar rock.
Conflicting Papers on Hold as XMRV Frenzy Reaches New Heights
Authors: Enserink Martin
Published: July 2010

Scientists at the U.S. National Institutes of Health and the Food and Drug Administration have been reported to have confirmed the link, first published in
Science
last year, between a human retrovirus and the elusive condition called chronic fatigue syndrome.
The Seductive Allure of Behavioral Epigenetics
Authors: Miller Greg
Published: July 2010

Could chemical changes to DNA underlie some of society's more vexing problems? Or is this hot new field getting ahead of itself?
Evaluation of One- and Two-Color Gene Expression Arrays for Microbial Comparative Genome Hybridization Analyses in Routine Applications
Authors: Schwarz Roland , Joseph Biju , Gerlach Gabriele , Schramm-Glück Anja , Engelhard Kathrin , Frosch Matthias , Müller Tobias , Schoen Christoph
Published: July 2010

DNA microarray technology has already revolutionized basic research in infectious diseases, and whole-genome sequencing efforts have allowed for the fabrication of tailor-made spotted microarrays for an increasing number of bacterial pathogens. However, the application of microarrays in diagnostic microbiology is currently hampered by the high costs associated with microarray experiments and the specialized equipment needed. Here, we show that a thorough bioinformatic postprocessing of the microarray design to reduce the amount of unspecific noise also allows the reliable use of spotted gene expression microarrays for gene content analyses. We further demonstrate that the use of only single-color labeling to halve the costs for dye-labeled nucleotides results in only a moderate decrease in overall specificity and sensitivity. Therefore, gene expression microarrays using only single-color labeling can also reliably be used for gene content analyses, thus reducing the costs for potential routine applications such as genome-based pathogen detection or strain typing.