bluuebunny/crossref_metadata_2025 huggingface dataset:
Centrality in primate–parasite networks reveals the potential for the transmission of emerging infectious diseases to humans
Authors: Gómez José María , Nunn Charles L. , Verdú Miguel
Published: April 2013

Most emerging infectious diseases (EIDs) in humans have arisen from animals. Identifying high-risk hosts is therefore vital for the control and surveillance of these diseases. Viewing hosts as connected through the parasites they share, we use network tools to investigate predictors of parasitism and sources of future EIDs. We generated host–parasite networks that link hosts when they share a parasite, using nonhuman primates as a model system because—owing to their phylogenetic proximity and ecological overlap with humans—they are an important source of EIDs to humans. We then tested whether centrality in the network of host species—a measurement of the importance of a given node (i.e., host species) in the network—is associated with that host serving as a potential EID source. We found that centrality covaries with key predictors of parasitism, such as population density and geographic range size. Importantly, we also found that primate species having higher values of centrality in the primate–parasite network harbored more parasites identified as EIDs in humans and had parasite communities more similar to those found in humans. These relationships were robust to the use of different centrality metrics and to multiple ways of controlling for variation in how well each species has been studied (i.e., sampling effort). Centrality may therefore estimate the role of a host as a source of EIDs to humans in other multispecific host–parasite networks.
Analogues of simple and complex cells in rhesus monkey auditory cortex
Authors: Tian Biao , Kuśmierek Paweł , Rauschecker Josef P.
Published: April 2013

Receptive fields (RFs) of neurons in primary visual cortex have traditionally been subdivided into two major classes: “simple” and “complex” cells. Simple cells were originally defined by the existence of segregated subregions within their RF that respond to either the on- or offset of a light bar and by spatial summation within each of these regions, whereas complex cells had ON and OFF regions that were coextensive in space [Hubel DH, et al. (1962)
J Physiol
160:106–154]. Although other definitions based on the linearity of response modulation have been proposed later [Movshon JA, et al. (1978)
J Physiol
283:53–77; Skottun BC, et al. (1991)
Vision Res
31(7-8):1079–1086], the segregation of ON and OFF subregions has remained an important criterion for the distinction between simple and complex cells. Here we report that response profiles of neurons in primary auditory cortex of monkeys show a similar distinction: one group of cells has segregated ON and OFF subregions in frequency space; and another group shows ON and OFF responses within largely overlapping response profiles. This observation is intriguing for two reasons: (
i
) spectrotemporal dissociation in the auditory domain provides a basic neural mechanism for the segregation of sounds, a fundamental prerequisite for auditory figure-ground discrimination; and (
ii
) the existence of similar types of RF organization in visual and auditory cortex would support the existence of a common canonical processing algorithm within cortical columns.
Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription
Authors: Pennington Katie L. , Marr Sharon K. , Chirn Gung-Wei , Marr Michael T.
Published: April 2013

Transcription factor (TF)IID is a central player in activated transcription initiation. Recent evidence suggests that the role and composition of TFIID are more diverse than previously understood. To investigate the effects of changing the composition of TFIID in a simple system, we depleted TATA box-binding protein–associated factor (TAF)1 from
Drosophila
cells and determined the consequences on metal-induced transcription at an inducible gene, metallothionein B. We observe a marked increase in the levels of both the mature message and pre-mRNA in TAF1-depleted cells. Under conditions of continued metal exposure, we show that TAF1 depletion increases the magnitude of the initial transcription burst but has no effect on the timing of that burst. We also show that TAF1 depletion causes delay in the shutoff of transcription upon removal of the stimulus. Thus, TAFs are involved in both establishing an upper limit of transcription during induction and efficiently turning the gene off once the inducer is removed. Using genome-wide nascent sequencing, we identify hundreds of genes that are controlled in a similar manner, indicating that the findings at this inducible gene are likely generalizable to a large set of promoters. There is a long-standing appreciation for the importance of the spatial and temporal control of transcription. Here we uncover an important third dimension of control: the magnitude of the response. Our results show that the magnitude of the transcriptional response to the same signaling event, even at the same promoter, can vary greatly depending on the composition of the TFIID complex in the cell.
Precise timing of ATPase activation drives targeting of tail-anchored proteins
Authors: Rome Michael E. , Rao Meera , Clemons William M. , Shan Shu-ou
Published: April 2013

The localization of tail-anchored (TA) proteins, whose transmembrane domain resides at the extreme C terminus, presents major challenges to cellular protein targeting machineries. In eukaryotic cells, the highly conserved ATPase, guided entry of tail-anchored protein 3 (Get3), coordinates the delivery of TA proteins to the endoplasmic reticulum. How Get3 uses its ATPase cycle to drive this fundamental process remains unclear. Here, we establish a quantitative framework for the Get3 ATPase cycle and show that ATP specifically induces multiple conformational changes in Get3 that culminate in its ATPase activation through tetramerization. Further, upstream and downstream components actively regulate the Get3 ATPase cycle to ensure the precise timing of ATP hydrolysis in the pathway: the Get4/5 TA loading complex locks Get3 in the ATP-bound state and primes it for TA protein capture, whereas the TA substrate induces tetramerization of Get3 and activates its ATPase reaction 100-fold. Our results establish a precise model for how Get3 harnesses the energy from ATP to drive the membrane localization of TA proteins and illustrate how dimerization-activated nucleotide hydrolases regulate diverse cellular processes.
Histone chaperone FACT action during transcription through chromatin by RNA polymerase II
Authors: Hsieh Fu-Kai , Kulaeva Olga I. , Patel Smita S. , Dyer Pamela N. , Luger Karolin , Reinberg Danny , Studitsky Vasily M.
Published: April 2013

FACT (facilitates chromatin transcription) is a histone chaperone that promotes chromatin recovery during transcription, with additional roles in cell differentiation. Although several models of the action of FACT during transcription have been proposed, they remain to be experimentally evaluated. Here we show that human FACT (hFACT) facilitates transcription through chromatin and promotes nucleosome recovery in vitro. FACT action depends on the presence of histone H2A/H2B dimers in the nucleosome. Kinetic analysis suggests that hFACT decreases the lifetime of nonproductive RNA polymerase II (Pol II)–nucleosome complexes and facilitates the formation of productive complexes containing nucleosomal DNA partially uncoiled from the octamer. Taken together, our data suggest that hFACT interacts with DNA-binding surfaces of H2A/H2B dimers, facilitating uncoiling of DNA from the histone octamer. Thus, hFACT–H2A/H2B interactions play a key role in overcoming the nucleosomal barrier by Pol II and promoting nucleosome survival during transcription.
PCNA is efficiently loaded on the DNA recombination intermediate to modulate polymerase δ, η, and ζ activities
Authors: Li Jian , Holzschu Donald L. , Sugiyama Tomohiko
Published: April 2013

Proliferating cell nuclear antigen (PCNA) is required for DNA homologous recombination (HR), but its exact role is unclear. Here, we investigated the loading of PCNA onto a synthetic D-loop (DL) intermediate of HR and the functional interactions of PCNA with Rad51 recombinase and DNA polymerase (Pol) δ, Pol η, and Pol ζ. PCNA was loaded onto the synthetic DL as efficiently as it was loaded onto a primed DNA substrate. Efficient PCNA loading requires Replication Protein A, which is associated with the displaced ssDNA loop and provides a binding site for the clamp-loader Replication Factor C. Loaded PCNA greatly stimulates DNA synthesis by Pol δ within the DL but does not affect primer recognition by Pol δ. This suggests that the essential role of PCNA in HR is not recruitment of Pol δ to the DL but stimulation of Pol δ to displace a DNA strand during DL extension. Both Pol η and Pol ζ extended the DL more efficiently than Pol δ in the absence of PCNA, but little or no stimulation was observed in the presence of PCNA. Finally, Rad51 inhibited both the loading of PCNA onto the DL and the extension of the DL by Pol δ and Pol η. However, preloaded PCNA on the DL counteracts the Rad51-mediated inhibition of the DL extension. This suggests that the inhibition of postinvasion DNA synthesis by Rad51 occurs mostly at the step of PCNA loading.
Conserved glycolipid termini in capsular polysaccharides synthesized by ATP-binding cassette transporter-dependent pathways in Gram-negative pathogens
Authors: Willis Lisa M. , Stupak Jacek , Richards Michele R. , Lowary Todd L. , Li Jianjun , Whitfield Chris
Published: April 2013

Bacterial capsules are surface layers made of long-chain polysaccharides. They are anchored to the outer membrane of many Gram-negative bacteria, including pathogens such as
Escherichia coli
,
Neisseria meningitidis
,
Haemophilus influenzae
, and
Pasteurella multocida
. Capsules protect pathogens from host defenses including complement-mediated killing and phagocytosis and therefore represent a major virulence factor. Capsular polysaccharides are synthesized by enzymes located in the inner (cytoplasmic) membrane and are then translocated to the cell surface. Whereas the enzymes that synthesize the polysaccharides have been studied in detail, the structure and biosynthesis of the anchoring elements have not been definitively resolved. Here we determine the structure of the glycolipid attached to the reducing terminus of the polysialic acid capsular polysaccharides from
E. coli
K1 and
N. meningitidis
group B and the heparosan-like capsular polysaccharide from
E. coli
K5. All possess the same unique glycolipid terminus consisting of a lyso-phosphatidylglycerol moiety with a β-linked poly-(3-deoxy-
d
-
manno
-oct-2-ulosonic acid) (poly-Kdo) linker attached to the reducing terminus of the capsular polysaccharide.
Nuclear receptor corepressor (NCOR1) regulates in vivo actions of a mutated thyroid hormone receptor α
Authors: Fozzatti Laura , Kim Dong Wook , Park Jeong Won , Willingham Mark C. , Hollenberg Anthony N. , Cheng Sheue-Yann
Published: April 2013

Genetic evidence from patients with mutations of the thyroid hormone receptor α gene (
THRA
) indicates that the dominant negative activity of mutants underlies the pathological manifestations. However, the molecular mechanisms by which TRα1 mutants exert dominant negative activity in vivo are not clear. We tested the hypothesis that the severe hypothyroidism in patients with
THRA
mutations is due to an inability of TRα1 mutants to properly release the nuclear corepressors (NCORs), thereby inhibiting thyroid hormone-mediated transcription activity. We crossed
Thra1

PV

mice, expressing a dominant negative TRα1 mutant (TRα1PV), with mice expressing a mutant
Ncor1
allele (
Ncor1

ΔID

mice) that cannot recruit the TR or PV mutant. TRα1PV shares the same C-terminal mutated sequences as those of patients with frameshift mutations of the
THRA
gene. Remarkably, NCOR1ΔID ameliorated abnormalities in the thyroid-pituitary axis of
Thra1

PV/+

mice. The severe retarded growth, infertility, and delayed bone development were partially reverted in
Thra1

PV/+

mice expressing NCOR1ΔID. The impaired adipogenesis was partially corrected by de-repression of peroxisome-proliferator activated receptor γ and CCAAT/enhancer-binding protein α gene, due to the inability of TRα1PV to recruit NCOR1ΔID to form a repressor complex. Thus, the aberrant recruitment of NCOR1 by TRα1 mutants could lead to clinical hypothyroidism in humans. Therefore, therapies aimed at the TRα1–NCOR1 interaction or its downstream actions could be tested as potential targets in treating TRα1 mutant-mediated hypothyroidism in patients.
Origin of intrinsic irregular firing in cortical interneurons
Authors: Stiefel Klaus M. , Englitz Bernhard , Sejnowski Terrence J.
Published: April 2013

Cortical spike trains are highly irregular both during ongoing, spontaneous activity and when driven at high firing rates. There is uncertainty about the source of this irregularity, ranging from intrinsic noise sources in neurons to collective effects in large-scale cortical networks. Cortical interneurons display highly irregular spike times (coefficient of variation of the interspike intervals >1) in response to dc-current injection in vitro. This is in marked contrast to cortical pyramidal cells, which spike highly irregularly in vivo, but regularly in vitro. We show with in vitro recordings and computational models that this is due to the fast activation kinetics of interneuronal K
+
currents. This explanation holds over a wide parameter range and with Gaussian white, power-law, and Ornstein–Uhlenbeck noise. The intrinsically irregular spiking of interneurons could contribute to the irregularity of the cortical network.
Strength of PD-1 signaling differentially affects T-cell effector functions
Authors: Wei Fang , Zhong Shi , Ma Zhengyu , Kong Hong , Medvec Andrew , Ahmed Rafi , Freeman Gordon J. , Krogsgaard Michelle , Riley James L.
Published: April 2013

High surface expression of programmed death 1 (PD-1) is associated with T-cell exhaustion; however, the relationship between PD-1 expression and T-cell dysfunction has not been delineated. We developed a model to study PD-1 signaling in primary human T cells to study how PD-1 expression affected T-cell function. By determining the number of T-cell receptor/peptide-MHC complexes needed to initiate a Ca
2+
flux, we found that PD-1 ligation dramatically shifts the dose–response curve, making T cells much less sensitive to T-cell receptor–generated signals. Importantly, other T-cell functions were differentially sensitive to PD-1 expression. We observed that high levels of PD-1 expression were required to inhibit macrophage inflammatory protein 1 beta production, lower levels were required to block cytotoxicity and IFN-γ production, and very low levels of PD-1 expression could inhibit TNF-α and IL-2 production as well as T-cell expansion. These findings provide insight into the role of PD-1 expression in enforcing T-cell exhaustion and the therapeutic potential of PD-1 blockade.
Accumulation of the FACT complex, as well as histone H3.3, serves as a target marker for somatic hypermutation
Authors: Aida Masatoshi , Hamad Nesreen , Stanlie Andre , Begum Nasim A. , Honjo Tasuku
Published: April 2013

Somatic hypermutation (SHM) requires not only the expression of activation-induced cytidine deaminase, but also transcription in the target regions. However, how transcription guides activation-induced cytidine deaminase in targeting SHM to the Ig genes is not fully understood. Here, we found that the “facilitates chromatin transcription” (FACT) complex promotes SHM by RNAi screening of transcription elongation factors. Furthermore, FACT and histone H3.3, a hallmark of transcription-coupled histone turnover, are enriched at the V(D)J region, 5′ flanking sequence of the Sμ switch region and the light chain Jκ 5 segment region in the Ig loci. The regions with the most abundant deposition of FACT and H3.3 were also the most efficient targets of SHM. These results demonstrate the importance of histone-exchanging dynamics at the chromatin of SHM targets, especially in Ig genes.
The Spanish Guitar in the Newspapers, Novels, Drama and Verse of Eighteenth-Century England
Authors: Page Christopher
Published: April 2013

For Paul Sparks

For the most part, the history of the Spanish guitar in eighteenth-century England seems to be no history at all. There appears to be little to place between Samuel Pepys and the beginning of the nineteenth century when the six-string guitar emerged as a favoured instrument of the parlour musician. Thus it is widely supposed that the gut-strung guitar was little used in England until Fernando Sor and other foreign players made it fashionable in the decades after Waterloo (1815). This article proposes to correct that deeply entrenched view with a chronological checklist of material, much of it presented in this connection for the first time, that illuminates the fortunes of the guitar in eighteenth-century England, principally London.
Pioneer Piano Makers in London, 1737–74: Newly Discovered Documentary Sources
Authors: Debenham Margaret , Cole Michael
Published: April 2013

The most historically significant and widely influential pianoforte designs, both for use in public concerts and for domestic music making, first appeared in the later 1760s, mostly as the work of immigrant German-born craftsmen working in London. But their work was preceded by a handful of pioneering instrument makers whose lives have been largely unreported until now. In this paper the authors report on the life and work of three such immigrant craftsmen who made pianofortes and related instruments in London in the period 1740–65. Two of them, Roger Plenius and Herman Viator, met with great personal misfortunes, while the other, Frederick Neubauer, crowned his career with a great triumph which has never been widely reported, though unhappily not one of his instruments is known to survive. The authors' findings are drawn from newly located contemporary newspaper notices and original manuscripts held at The National Archives, Kew and the Bancroft Library, London.
DNA synthesis by Pol η promotes fragile site stability by preventing under-replicated DNA in mitosis
Authors: Bergoglio Valérie , Boyer Anne-Sophie , Walsh Erin , Naim Valeria , Legube Gaëlle , Lee Marietta Y.W.T. , Rey Laurie , Rosselli Filippo , Cazaux Christophe , Eckert Kristin A. , Hoffmann Jean-Sébastien
Published: April 2013

Human DNA polymerase η (Pol η) is best known for its role in responding to UV irradiation–induced genome damage. We have recently observed that Pol η is also required for the stability of common fragile sites (CFSs), whose rearrangements are considered a driving force of oncogenesis. Here, we explored the molecular mechanisms underlying this newly identified role. We demonstrated that Pol η accumulated at CFSs upon partial replication stress and could efficiently replicate non-B DNA sequences within CFSs. Pol η deficiency led to persistence of checkpoint-blind under-replicated CFS regions in mitosis, detectable as FANCD2-associated chromosomal sites that were transmitted to daughter cells in 53BP1-shielded nuclear bodies. Expression of a catalytically inactive mutant of Pol η increased replication fork stalling and activated the replication checkpoint. These data are consistent with the requirement of Pol η–dependent DNA synthesis during S phase at replication forks stalled in CFS regions to suppress CFS instability by preventing checkpoint-blind under-replicated DNA in mitosis.
Sanpodo controls sensory organ precursor fate by directing Notch trafficking and binding γ-secretase
Authors: Upadhyay Alok , Kandachar Vasundhara , Zitserman Diana , Tong Xin , Roegiers Fabrice
Published: April 2013

In Drosophila peripheral neurogenesis, Notch controls cell fates in sensory organ precursor (SOP) cells. SOPs undergo asymmetric cell division by segregating Numb, which inhibits Notch signaling, into the pIIb daughter cell after cytokinesis. In contrast, in the pIIa daughter cell, Notch is activated and requires Sanpodo, but its mechanism of action has not been elucidated. As Sanpodo is present in both pIIa and pIIb cells, a second role for Sanpodo in regulating Notch signaling in the low-Notch pIIb cell has been proposed. Here we demonstrate that Sanpodo regulates Notch signaling levels in both pIIa and pIIb cells via distinct mechanisms. The interaction of Sanpodo with Presenilin, a component of the γ-secretase complex, was required for Notch activation and pIIa cell fate. In contrast, Sanpodo suppresses Notch signaling in the pIIb cell by driving Notch receptor internalization. Together, these results demonstrate that a single protein can regulate Notch signaling through distinct mechanisms to either promote or suppress signaling depending on the local cellular context.
A tumor suppressor role of the Bub3 spindle checkpoint protein after apoptosis inhibition
Authors: Morais da Silva Sara , Moutinho-Santos Tatiana , Sunkel Claudio E.
Published: April 2013

Most solid tumors contain aneuploid cells, indicating that the mitotic checkpoint is permissive to the proliferation of chromosomally aberrant cells. However, mutated or altered expression of mitotic checkpoint genes accounts for a minor proportion of human tumors. We describe a Drosophila melanogaster tumorigenesis model derived from knocking down spindle assembly checkpoint (SAC) genes and preventing apoptosis in wing imaginal discs. Bub3-deficient tumors that were also deficient in apoptosis displayed neoplastic growth, chromosomal aneuploidy, and high proliferative potential after transplantation into adult flies. Inducing aneuploidy by knocking down CENP-E and preventing apoptosis does not induce tumorigenesis, indicating that aneuploidy is not sufficient for hyperplasia. In this system, the aneuploidy caused by a deficient SAC is not driving tumorigenesis because preventing Bub3 from binding to the kinetochore does not cause hyperproliferation. Our data suggest that Bub3 has a nonkinetochore-dependent function that is consistent with its role as a tumor suppressor.
Automated annotation and quantification of glycans using liquid chromatography–mass spectrometry
Authors: Yu Chuan-Yih , Mayampurath Anoop , Hu Yunli , Zhou Shiyue , Mechref Yehia , Tang Haixu
Published: April 2013

Summary: As a common post-translational modification, protein glycosylation plays an important role in many biological processes, and it is known to be associated with human diseases. Mass spectrometry (MS)-based glycomic profiling techniques have been developed to measure the abundances of glycans in complex biological samples and applied to the discovery of putative glycan biomarkers. To automate the annotation of glycomic profiles in the liquid chromatography-MS (LC–MS) data, we present here a user-friendly software tool, MultiGlycan, implemented in C# on Windows systems. We tested MultiGlycan by using several glycomic profiling datasets acquired using LC–MS under different preparations and show that MultiGlycan executes fast and generates robust and reliable results.

Availability: MultiGlycan can be freely downloaded at http://darwin.informatics.indiana.edu/MultiGlycan/.

Contact:  chuyu@indiana.edu or hatang@indiana.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
How do patients with heart failure with preserved ejection fraction die?
Authors: Chan Michelle M.Y. , Lam Carolyn S.P.
Published: April 2013

Understanding how patients with heart failure with preserved ejection fraction (HFPEF) die provides insight into the natural history and pathophysiology of this complex syndrome, thereby allowing better prediction of response to therapy in designing clinical trials. This review summarizes the current state of knowledge surrounding mortality rates, modes of death, and prognostic factors in HFPEF. Despite the lack of uniform reporting, the following conclusions may be drawn from previous studies. The mortality burden of HFPEF is substantial, ranging from 10% to 30% annually, and higher in epidemiological studies than in clinical trials. Mortality rates compared with heart failure with reduced ejection fraction (HFREF) appear to be strongly influenced by the type of study, but are clearly elevated compared with age‐ and co‐morbidity‐matched controls without heart failure. The majority of deaths in HFPEF are cardiovascular deaths, comprising 51–60% of deaths in epidemiological studies and ∼70% in clinical trials. Among cardiovascular deaths, sudden death and heart failure death are the leading cardiac modes of death in HFPEF clinical trials. Compared with HFREF, the proportions of cardiovascular deaths, sudden death, and heart failure deaths are lower in HFPEF. Conversely, non‐cardiovascular deaths constitute a higher proportion of deaths in HFPEF than in HFREF, particularly in epidemiological studies, where this difference may be related to fewer coronary heart deaths in HFPEF. Key mortality risk factors, including age, gender, body mass index, burden of co‐morbidities, and coronary artery disease, offer some explanation for the differences in mortality rates observed across studies.
Value of N‐terminal pro brain natriuretic peptide levels in different types of Fontan circulation
Authors: Heck Pinar Bambul , Müller Jan , Weber Ruth , Hager Alfred
Published: April 2013

Aims

N‐terminal pro brain natriuretic peptide (NT‐proBNP) is an important biomarker in congestive heart failure. This has also been confirmed in congenital heart disease. However, its clinical value in patients with different types of Fontan circulation remains questionable.

Methods and results

We prospectively analysed 124 patients with various types of Fontan surgery between October 2006 and February 2011. We included 49 patients with older Fontan modification [atriopulmonary connection (APC) and atrioventricular connection (AVC)] and 75 patients with total cavopulmonary connection (TCPC). The NT‐proBNP levels of patients with APC/AVC were significantly higher than in patients with TCPC (P < 0.001), even after accounting for sex, age, ventricular function, atrioventricular regurgitation, ventricular morphology, and arrhythmia (P = 0.035). Levels of NT‐proBNP positively correlated with atrioventricular valve regurgitation (r = 0.29, P = 0.013) and ventricular dysfunction (r = 0.23, P = 0.052) only in patients with TCPC, but not in patients with APC or AVC (r = 0.01, P = 0.509 and r = 0.10, P = 0.493, respectively).

Conclusion

Levels of NT‐pro BNP are related to the type of Fontan circulation. The older types (APC/AVC) that involve more atrial tissue in the systemic venous pathway show higher NT‐proBNP levels independently of their cardiac status. Their NT‐proBNP levels should be interpreted with care.
Rousseau and the Reserve of Nature: A Rejoinder to Derrida
Authors: Di Palma Marco Michael
Published: April 2013

This article re-examines Derrida's presentation of Rousseau's philosophy of nature and culture in
De la grammatologie
to interrogate that work's conclusions about the inescapability of the logic of the
supplément
. Drawing on a close reading of the first book of
Émile
, it argues that Rousseau's ontological commitments neither originate from nor entail a metaphysics of pure presence. The challenge to Derrida derives from the category of habit understood as an ontological principle that structures the conceptualization of nature in
Émile
. Rousseau's formulation of nature as a
réserve
, a theory of innateness as sleeping potentiality, indicates not a ‘presence’ but a store of potencies bearing an indeterminate ontology. As well as a capacity and an agency, nature is also a state of being. Habit, meanwhile, reveals the two senses of nature — as teleology and being — and mediates between them. Nature, for its part, arises as the outcome, as well as the origin and determination, of habit. This signifies that nature and culture are not the terms of a dichotomy but arise simultaneously when habit draws from nature's reserve. The article concludes that Derrida simplifies and exploits Rousseau by reading him through the distorting lens of Lévi-Strauss's structuralist anthropology.
REGRESSION OF TAKAYASU RETINOPATHY AFTER REVASCULARIZATION OF OCCLUDED BRANCHES OF THE AORTIC ARCH BY PERCUTANEOUS ANGIOPLASTY
Authors: Peter Jayanthi , Joseph George , David Sarada , Danda Debashish
Published: April 2013

Purpose:

To present a patient with decreased vision because of Takayasu retinopathy who had improvement in vision and regression of retinopathy after percutaneous angioplasty of occluded aortic arch vessels.

Methods:

Interventional case report.

Results:

A 37-year-old woman with multiple cerebral infarcts and recurrent seizures was referred with painless progressive reduction in vision in the right eye of few months’ duration and left eye for 2 years. Vision was 20/120 in the right eye and perception of light in the left eye. There was mild disk pallor in the right eye, optic atrophy in the left eye, and microaneursyms in both eyes. Angiographic findings were consistent with type I Takayasu arteritis. Angioplasty and stenting was performed initially to the right subclavian and common carotid arteries and to the left subclavian, and left internal carotid arteries 6 weeks later. There was improvement in vision to 20/80 and regression of Takayasu retinopathy in the right eye at 3 months post procedure that improved further to 20/50, 6 months post procedure. Vision, as expected, remained poor in the left eye despite revascularization.

Conclusion:

Restoration of flow in the aortic arch vessels may result in reversal of ischemic retinal changes in patients with Takayasu retinopathy.
Antisense peptide nucleic acid-functionalized cationic nanocomplex for
in vivo
mRNA detection
Authors: Shen Yuefei , Shrestha Ritu , Ibricevic Aida , Gunsten Sean P. , Welch Michael J. , Wooley Karen L. , Brody Steven L. , Taylor John-Stephen A. , Liu Yongjian
Published: April 2013

Acute lung injury (ALI) is a complex syndrome with many aetiologies, resulting in the upregulation of inflammatory mediators in the host, followed by dyspnoea, hypoxemia and pulmonary oedema. A central mediator is inducible nitric oxide synthase (iNOS) that drives the production of NO and continued inflammation. Thus, it is useful to have diagnostic and therapeutic agents for targeting iNOS expression. One general approach is to target the precursor iNOS mRNA with antisense nucleic acids. Peptide nucleic acids (PNAs) have many advantages that make them an ideal platform for development of antisense theranostic agents. Their membrane impermeability, however, limits biological applications. Here, we report the preparation of an iNOS imaging probe through electrostatic complexation between a radiolabelled antisense PNA-YR
9
· oligodeoxynucleotide (ODN) hybrid and a cationic shell-cross-linked knedel-like nanoparticle (cSCK). The Y (tyrosine) residue was used for
123
I radiolabelling, whereas the R
9
(arginine
9
) peptide was included to facilitate cell exit of untargeted PNA. Complete binding of the antisense PNA-YR
9
· ODN hybrid to the cSCK was achieved at an 8 : 1 cSCK amine to ODN phosphate (N/P) ratio by a gel retardation assay. The antisense PNA-YR
9
· ODN · cSCK nanocomplexes efficiently entered RAW264.7 cells, whereas the PNA-YR
9
· ODN alone was not taken up. Low concentrations of
123
I-labelled antisense PNA-YR
9
· ODN complexed with cSCK showed significantly higher retention of radioactivity when iNOS was induced in lipopolysaccharide+interferon-γ-activated RAW264.7 cells when compared with a mismatched PNA. Moreover, statistically, greater retention of radioactivity from the antisense complex was also observed
in vivo
in an iNOS-induced mouse lung after intratracheal administration of the nanocomplexes. This study demonstrates the specificity and sensitivity by which the radiolabelled nanocomplexes can detect iNOS mRNA
in vitro
and
in vivo
and their potential for early diagnosis of ALI.
Cancer cell sensing and therapy using affinity tag-conjugated gold nanorods
Authors: Yasun Emir , Kang Huaizhi , Erdal Huseyin , Cansiz Sena , Ocsoy Ismail , Huang Yu-Fen , Tan Weihong
Published: April 2013

Through the developments in controlling the shape of gold nanoparticles, synthesis of gold nanorods (AuNRs) can be considered as a milestone discovery in the area of nanomaterial-based cancer treatments. Besides having tuneable absorption maxima at near infrared (NIR) range, AuNRs have superior absorption cross section at NIR frequencies compared with other gold nanoparticles. When this unique optical property is combined with the specificity against cancer cells used by affinity tag conjugations, AuNRs become one of the most important nanoparticles used in both cancer cell sensing and in therapy. In this review, the impact of size and shape control of nanoparticles, especially AuNRs, on cancer cell treatments and a range of aptamer-conjugated AuNR applications in this regard are reviewed.
Ecology, economy and management of an agroindustrial frontier landscape in the southeast Amazon
Authors: Brando Paulo M. , Coe Michael T. , DeFries Ruth , Azevedo Andrea A.
Published: April 2013

The papers in this special issue address a major challenge facing our society: feeding a population that is simultaneously growing and increasing its
per capita
food consumption, while preventing widespread ecological and social impoverishment in the tropics. By focusing mostly on the Amazon's most dynamic agricultural frontier, Mato Grosso, they collectively clarify some key elements of achieving more sustainable agriculture. First, stakeholders in commodity-driven agricultural Amazonian frontiers respond rapidly to multiple forces, including global markets, international pressures for sustainably produced commodities and national-, state- and municipality-level policies. These forces can encourage or discourage deforestation rate changes within a short time-period. Second, agricultural frontiers are linked systems, land-use change is linked with regional climate, forest fires, water quality and stream discharge, which in turn are linked with the well-being of human populations. Thus, land-use practices at the farm level have ecological and social repercussions far removed from it. Third, policies need to consider the full socio-economic system to identify the efficacy and consequences of possible land management strategies. Monitoring to devise suitable management approaches depends not only on tracking land-use change, but also on monitoring the regional ecological and social consequences. Mato Grosso's achievements in reducing deforestation are impressive, yet they are also fragile. The ecological and social consequences and the successes and failures of management in this region can serve as an example of possible trajectories for other commodity-driven tropical agricultural frontiers.
The natural and social history of the indigenous lands and protected areas corridor of the Xingu River basin
Authors: Schwartzman Stephan , Boas André Villas , Ono Katia Yukari , Fonseca Marisa Gesteira , Doblas Juan , Zimmerman Barbara , Junqueira Paulo , Jerozolimski Adriano , Salazar Marcelo , Junqueira Rodrigo Prates , Torres Maurício
Published: April 2013

The 280 000 km² Xingu indigenous lands and protected areas (ILPAs) corridor, inhabited by 24 indigenous peoples and about 215 riverine (ribeirinho) families, lies across active agriculture frontiers in some of the historically highest-deforestation regions of the Amazon. Much of the Xingu is anthropogenic landscape, densely inhabited and managed by indigenous populations over the past millennium. Indigenous and riverine peoples' historical management and use of these landscapes have enabled their long-term occupation and ultimately their protection. The corridor vividly demonstrates how ILPAs halt deforestation and why they may account for a large part of the 70 per cent reduction in Amazon deforestation below the 1996–2005 average since 2005. However, ongoing and planned dams, road paving, logging and mining, together with increasing demand for agricultural commodities, continued degradation of upper headwaters outside ILPA borders and climate change impacts may render these gains ephemeral. Local peoples will need new, bottom-up, forms of governance to gain recognition for the high social and biological diversity of these territories in development policy and planning, and finance commensurate with the value of their ecosystem services. Indigenous groups' reports of changing fire and rainfall regimes may themselves evidence climate change impacts, a new and serious threat.
Export-oriented deforestation in Mato Grosso: harbinger or exception for other tropical forests?
Authors: DeFries Ruth , Herold Martin , Verchot Louis , Macedo Marcia N. , Shimabukuro Yosio
Published: April 2013

The Brazilian state of Mato Grosso was a global deforestation hotspot in the early 2000s. Deforested land is used predominantly to produce meat for distal consumption either through cattle ranching or soya bean for livestock feed. Deforestation declined dramatically in the latter part of the decade through a combination of market forces, policies, enforcement and improved monitoring. This study assesses how representative the national-level drivers underlying Mato Grosso's export-oriented deforestation are in other tropical forest countries based on agricultural exports, commercial agriculture and urbanization. We also assess how pervasive the governance and technical monitoring capacity that enabled Mato Grosso's decline in deforestation is in other countries. We find that between 41 and 54 per cent of 2000–2005 deforestation in tropical forest countries (other than Brazil) occurred in countries with drivers similar to Brazil. Very few countries had national-level governance and capacity similar to Brazil. Results suggest that the ecological, hydrological and social consequences of land-use change for export-oriented agriculture as discussed in this Theme Issue were applicable in about one-third of all tropical forest countries in 2000–2005. However, the feasibility of replicating Mato Grosso's success with controlling deforestation is more limited. Production landscapes to support distal consumption similar to Mato Grosso are likely to become more prevalent and are unlikely to follow a land-use transition model with increasing forest cover.
Watershed responses to Amazon soya bean cropland expansion and intensification
Authors: Neill Christopher , Coe Michael T. , Riskin Shelby H. , Krusche Alex V. , Elsenbeer Helmut , Macedo Marcia N. , McHorney Richard , Lefebvre Paul , Davidson Eric A. , Scheffler Raphael , Figueira Adelaine Michela e Silva , Porder Stephen , Deegan Linda A.
Published: April 2013

The expansion and intensification of soya bean agriculture in southeastern Amazonia can alter watershed hydrology and biogeochemistry by changing the land cover, water balance and nutrient inputs. Several new insights on the responses of watershed hydrology and biogeochemistry to deforestation in Mato Grosso have emerged from recent intensive field campaigns in this region. Because of reduced evapotranspiration, total water export increases threefold to fourfold in soya bean watersheds compared with forest. However, the deep and highly permeable soils on the broad plateaus on which much of the soya bean cultivation has expanded buffer small soya bean watersheds against increased stormflows. Concentrations of nitrate and phosphate do not differ between forest or soya bean watersheds because fixation of phosphorus fertilizer by iron and aluminium oxides and anion exchange of nitrate in deep soils restrict nutrient movement. Despite resistance to biogeochemical change, streams in soya bean watersheds have higher temperatures caused by impoundments and reduction of bordering riparian forest. In larger rivers, increased water flow, current velocities and sediment flux following deforestation can reshape stream morphology, suggesting that cumulative impacts of deforestation in small watersheds will occur at larger scales.
Using Arabidopsis to Study Shoot Branching in Biomass Willow
Authors: Ward Sally P. , Salmon Jemma , Hanley Steven J. , Karp Angela , Leyser Ottoline
Published: April 2013

The success of the short-rotation coppice system in biomass willow (Salix spp.) relies on the activity of the shoot-producing meristems found on the coppice stool. However, the regulation of the activity of these meristems is poorly understood. In contrast, our knowledge of the mechanisms behind axillary meristem regulation in Arabidopsis (Arabidopsis thaliana) has grown rapidly in the past few years through the exploitation of integrated physiological, genetic, and molecular assays. Here, we demonstrate that these assays can be directly transferred to study the control of bud activation in biomass willow and to assess similarities with the known hormone regulatory system in Arabidopsis. Bud hormone response was found to be qualitatively remarkably similar in Salix spp. and Arabidopsis. These similarities led us to test whether Arabidopsis hormone mutants could be used to assess allelic variation in the cognate Salix spp. hormone genes. Allelic differences in Salix spp. strigolactone genes were observed using this approach. These results demonstrate that both knowledge and assays from Arabidopsis axillary meristem biology can be successfully applied to Salix spp. and can increase our understanding of a fundamental aspect of short-rotation coppice biomass production, allowing more targeted breeding.
Long distance autonomous trajectory tracking for an orchard vehicle
Authors: Bayar Gokhan
Published: April 2013

Purpose

The purpose of this paper is to present work which is a part of the Comprehensive Automation for Specialty Crops project (CASC). Desired trajectory tracking objective has been previously performed by using a non‐model based approach in this project. Long distance autonomous drive has been achieved; however the results haven't met the expectations of the project requirements. In order to provide these requirements, this study is conducted. In this study, long distance autonomous trajectory tracking for an orchard vehicle is studied. Besides longitudinal motion, lateral motion of the vehicle is also considered. The longitudinal and lateral errors are objected to keep into a region of less than 10 cm.

Design/methodology/approach

Car‐like robot kinematic modeling approach is used to create desired trajectory. In order to control longitudinal velocity and steering angle of the vehicle, a controller methodology is proposed. Stability of the controller proposed is shown by using Lyapunov stability approach.

Findings

The proposed model is adapted into a four‐wheeled autonomous orchard vehicle and tested in an experimental orchard for long distance autonomous drives. More than 15 km autonomous drive is successfully achieved and the details are presented in this paper.

Originality/value

In this study, long distance autonomous trajectory tracking for an orchard vehicle is focused. A model based control strategy, including the information about longitudinal and lateral motion of the vehicle, is constructed. A new approach to create steering angles for turning operations of the orchard vehicle is introduced. It is objected that the longitudinal and lateral errors should be less than 10 cm during the trajectory tracking task.
Users' attitudes toward service robots in South Korea
Authors: Park Eunil , del Pobil Angel P.
Published: April 2013

Purpose

The purpose of this paper is to understand users' acceptance of service robots by integrating perceived enjoyment of service robots and users' need to belong in a technology acceptance model (TAM) framework. Service robots are currently being used in homes and firms to provide various services.

Design/methodology/approach

The authors conducted a web‐based survey from 904 users in South Korea to test a research model and employed structural equation modelling as the analysis method.

Findings

This study found that perceived enjoyment and the need to belong played an important role in the perceived ease of use and usefulness of service robots. Furthermore, it was discovered that the research supported relationships proposed by the original TAM with regard to users' attitudes and intentions to use service robots. Therefore, this study provides a framework to understand users' acceptance of service robots.

Originality/value

This paper is of value to researchers designing and improving service robots for use in our society.
A time‐controllable Allan variance method for MEMS IMU
Authors: Zhao Hongyu , Wang Zhelong , Shang Hong , Hu Weijian , Qin Gao
Published: April 2013

Purpose

The purpose of this paper is to reduce the calculation burden and speed up the estimation process of Allan variance method while ensuring the exactness of the analysis results.

Design/methodology/approach

A series of six‐hour static tests have been implemented at room temperature, and the static measurements have been collected from MEMS IMU. In order to characterize the various types of random noise terms for the IMU, the basic definition and main procedure of the Allan variance method are investigated. Unlike the normal Allan variance method, which has the shortcomings of processing large data sets and requiring long computation time, a modified Allan variance method is proposed based on the features of data distribution in the log‐log plot of the Allan standard deviation versus the averaging time.

Findings

Experiment results demonstrate that the modified Allan variance method can effectively estimate the noise coefficients for MEMS IMU, with controllable computation time and acceptable estimation accuracy.

Originality/value

This paper proposes a time‐controllable Allan variance method which can quickly and accurately identify different noise terms imposed by the stochastic fluctuations.
Optimizing human‐robot teleoperation interfaces for mobile manipulators
Authors: Will Jeffrey D. , Moore Kevin L. , Lynn Ian K.
Published: April 2013

Purpose

Mobile manipulators offer great capability, but their teleoperation is often an overwhelming task for humans due to the many degrees‐of‐freedom of control available from both the mobile platform and the associated manipulator. The purpose of this paper is to address the question of how these controls should be mapped to the robotic mobile platform and its manipulator for “optimal teleoperation”, for the special case of an omnidirectional mobile platform and two joint (with wrist) planar manipulator.

Design/methodology/approach

In this paper, the authors summarize the results of a study to optimize the teleoperation interface for a two‐link planar manipulator with a wrist that was mounted on an omni‐directional mobile platform.

Findings

The research comprised a carefully‐controlled study using 33 human subjects in seven different treatments of possible control interfaces.

Research limitations/implications

Users performed movement and manipulation tasks, and their performance was measured on several scales.

Practical implications

Based on this study, the authors present guidelines for optimizing mobile manipulator control interfaces and motivate future research using the method of controlled multi‐user trials.

Social implications

This research has the potential to guide the improvement of interfaces for mobile robots in military, service, and security applications.

Originality/value

The value of this research extends to optimizing remote control schemes to relieve operator fatigue and optimize interface design.