bluuebunny/crossref_metadata_2025 huggingface dataset:
An unusual abdominal mass in a renal transplant recipient
Authors: Leach T.D. , Sadek S.A. , Mason J.C.
Published: November 2010

Abstract: Renal transplant recipients are at increased risk of malignancy and infection. We present the case of a 72‐year‐old‐man with recurrent bladder carcinoma, abdominal aortic aneurysm repair, and end‐stage renal failure due to renovascular disease. He received a cadaveric renal allograft into his left iliac fossa, was given cyclosporin A, azathioprine, and prednisolone triple therapy immunosuppression, and had no rejection episodes. He presented four years post‐transplantation with a two‐year history of intermittent sweats and fevers. Previous episodes had been investigated with no firm diagnosis made. This time he had right iliac fossa pain of three weeks' duration. Examination revealed a tender mass. Investigations showed unchanged graft function, but elevated inflammatory indices. Ultrasonography and computed tomography detailed an infiltrating mass associated with the sigmoid colon, which colonoscopy failed to visualise. At laparotomy a 6‐cm tumor was removed, with adherent sigmoid colon and bladder dome. Macroscopically the mass was an abscess, and microscopy found acute and chronic inflammatory giant cells and fibrillary masses suggestive of actinomycosis, with no malignancy. The patient recovered uneventfully on antibiotics. At six months' follow‐up, examination, inflammatory markers, and radiographic imaging showed no evidence of recurrence. Twelve months later the patient died of rupture of his proximal abdominal aorta. There was no evidence of recurrence at postmortem examination. We conclude with a brief review of actinomycosis in transplant recipients.
Cryptococcal meningitis: an analysis among 5521 consecutive organ transplant recipients
Authors: Wu G. , Vilchez R.A. , Eidelman B. , Fung J. , Kormos R. , Kusne S.
Published: November 2010

Abstract:Cryptococcal meningitis has been reported to be an important cause of morbidity and mortality in renal transplant recipients. However, additional studies of recipients of other organ transplants suggested that these patients might be at low risk for cryptococcal meningitis. We examined the incidence and clinical features of cryptococcal meningitis among different groups of organ transplant patients at the University of Pittsburgh Medical Center. From January 1989 through July 1999, 28 patients were diagnosed with cryptococcal meningitis among 5521 transplant recipients. These included liver (11/2539), heart (8/372), kidney (7/2122), lung (1/432), and small bowel (1/56) recipients. The incidence of cryptococcal meningitis was higher in heart and small bowel recipients compared to other transplant populations (P = 0.005). The cryptococcal meningitis‐related mortality in transplant recipients was 50% and was associated with altered mental status (P = 0.001), absence of headache (P = 0.02), and liver failure (P = 0.002). Multivariable analysis indicated that liver failure was the only independent risk factor for poor prognosis (P = 0.043). All cases of liver failure occurred among liver transplant recipients. Cryptococcal meningitis is associated with significant mortality among organ transplant recipients. The presence of allograft failure in liver transplant recipients with cryptococcal meningitis may be an indicator of poor prognosis in this patient population.
Clinical characteristics of 13 solid organ transplant recipients with ganciclovir‐resistant cytomegalovirus infection
Authors: Isada C.M. , Yen‐Lieberman B. , Lurain N.S. , Schilz R. , Kohn D. , Longworth D.L. , Taege A.J. , Mossad S.B. , Maurer J. , Flechner S.M. , Mawhorter S.D. , Braun W. , Gordon S.M. , Schmitt S.K. , Goldman M. , Long J. , Haug M. , Avery R.K.
Published: November 2010

Abstract: Background. Ganciclovir‐resistant (GCV‐R) cytomegalovirus (CMV) is now being reported with increasing frequency in solid organ transplant recipients. Objective. To describe the clinical characteristics and outcomes of all solid organ transplant patients with GCV‐R CMV seen between 1990 and 2000 at a single center. Methods. Patients with clinically suspected GCV resistance had viral isolates subjected to phenotypic analysis by plaque reduction assay, and also genotypic analysis. Medical records of the 13 patients with GCV‐R CMV were reviewed for demographic, microbiologic, clinical, and pathologic data. Results. Thirteen patients were identified, including 5 kidney, 1 heart, and 7 lung transplant recipients. All but one patient (92%) were CMV donor seropositive, recipient negative (D+/R–), and 11/13 (85%) had tissue‐invasive CMV. CMV viremia was recurrent in 9/13 (69%); in 2 others, the first CMV episode was fatal. Overall, 9/13 (69%) of patients have died, all of CMV or its complications. Of the 10 who received foscarnet, only one survived. All patients had received GCV‐based prophylactic regimens; 8/13 patients (62%) had received CMV hyperimmune globulin (CMVIG) as part of prophylaxis, 6/13 (46%) had received oral ganciclovir, and 5/13 (38%) had received intermittent (3×/week) IV ganciclovir for prophylaxis. Conclusions. GCV‐R CMV is associated with CMV D+/R– status, tissue‐invasive disease, and high mortality even with foscarnet therapy. Exposure to less than fully therapeutic levels of GCV, in the form of oral or intermittent IV GCV, is common. The use of CMVIG in prophylaxis does not appear to prevent resistance. Further work remains to be done to elucidate the risk factors and optimal mode of prophylaxis and treatment for GCV‐R CMV.
Early results of targeted prophylaxis for coccidioidomycosis in patients undergoing orthotopic liver transplantation within an endemic area
Authors: Blair J.E. , Douglas D.D. , Mulligan D.C.
Published: November 2010

Abstract: Coccidioidomycosis (CM) is an endemic fungal infection of the desert southwestern United States. In immunocompromised hosts, such as transplant recipients, this infection is often a severe, disseminated disease with high mortality. A history of coccidioidal infection or positive serologic results increases the risk of CM after transplantation. At our institution, all liver transplant candidates with either positive history or serologic results for coccidioidal infection receive fluconazole in order to prevent recurrent infection after transplantation. Patients with neither a history of coccidioidal infection nor positive serologic results do not receive prophylaxis but are followed serologically every 3 months. From June 1999 to October 2001, 81 liver transplantations were performed at our institution in 76 patients with end‐stage liver disease. Four of these 76 patients received prophylactic fluconazole in order to prevent CM. None of these 4 patients had reactivation of CM. A new coccidioidal infection developed after orthotopic liver transplantation in 1 of 72 patients (1.4%). Close surveillance and targeted prophylaxis are safe and effective alternatives to universal prophylaxis for CM in patients undergoing liver transplantation in an endemic area.
T‐lymphocyte development and models of thymopoietic reconstitution
Authors: Robertson P. , Poznansky M.C.
Published: November 2010

Abstract: T‐cell development occurs in the thymus and involves a complex stepwise differentiation process from hematopoietic progenitor cell through to the emergence of positively selected, non‐self reactive naïve T cells, which emigrate from the organ into the blood stream. This process takes place in the three‐dimensional context of a delicate latticework of thymic stromal cells, including epithelial‐derived cells and dendritic cells that assist in the development of the mature T cell. The details of the steps in T‐cell development are now more comprehensively understood and furthermore in vitro systems are in development to reiterate this process in vitro. The clinical impact of this work is clearly the understanding of immune reconstitution in immune compromised patients (e.g., those with HIV/AIDS or post transplantation) and the development of novel techniques for regenerating the spectrum of T‐cell function in these individuals.
Polyomavirus in kidney and kidney‐‐pancreas transplant recipients
Authors: Trofe J. , Gaber L.W. , Stratta R.J. , Shokouh‐Amiri M.H. , Vera S.R. , Alloway R.R. , Lo A. , Gaber A.O. , Egidi M.F.
Published: November 2010

Abstract: Purpose. To report the incidence and clinical characteristics of polyomavirus (PV) nephritis in kidney (KTX) and kidney–pancreas transplant (KPTX) recipients.

Methods. Single center retrospective analysis of all cases of PV nephritis in KTX and KPTX patients transplanted between 1994 and 1999.

Results. Thirteen (5 KTX and 8 KPTX) patients (2.1%) had PV nephritis diagnosed on multiple biopsies (n = 22) among 504 KTX and 106 KPTX recipients. The incidence of PV nephritis was higher in cadaver donor transplants (2.6% cadaver vs. 0.7% living donors), after KPTX (1% KTX vs. 7.5% KPTX), in males (3.3% male vs. 0.7% female), and in diabetic patients (4.4% diabetic vs. 0.8% nondiabetic). The mean time to diagnosis of PV nephritis was 18 (range 6–48) months after KTX and 17 (range 9–31) months after KPTX. Three KTX patients and 5 KPTX patients had calcineurin inhibitor toxicity on biopsy prior to developing PV nephritis. Reduction in immunosuppression occurred in 100% of KTX and 63% of KPTX patients. Three patients (23%) developed rejection within 3 months of diagnosis of PV, 1 after a reduction in immunosuppression. Despite multiple antiviral treatment regimens, renal allograft failure requiring dialysis occurred in 60% of KTX and 50% of KPTX patients. All KPTX patients remain insulin independent and 2 were successfully retransplanted with living donor kidneys. 2 patients (15%) died but there was no mortality directly related to the virus.

Conclusions. Polyomavirus nephritis may be increasing in incidence and appears to be unresponsive to either conventional antiviral agents or a reduction in immunosuppression. Most of our cases occurred in male diabetic patients undergoing cadaveric donor transplantation and were preceded by biopsy‐proven nephrotoxicity. Further studies are needed to better define the pathogenesis of PV and effective antiviral treatment.
The Role of Tim9p in the Assembly of the TIM22 Import Complexes
Authors: Leuenberger Danielle , Curran Sean P. , Wong David , Koehler Carla M.
Published: November 2010

Tim9p is located in the soluble 70‐kDa Tim9p–Tim10p complex and the 300‐kDa membrane complex in the mitochondrial TIM22 protein import system, which mediates the import of inner membrane proteins. From a collection of temperature‐sensitive mutants, we have analyzed two in detail. tim9–3 contained two mutations and tim9–19 contained one mutation, all located near the ‘twin CX3C’ motif that is conserved in the small Tim proteins. As a result, the import components in the tim9–3 mutant mitochondria were severely reduced and assembled into complexes of aberrant sizes. Protein import was severely reduced and Tim9p and Tim10p binding to in vitro imported ADP/ATP carrier was impaired. In the tim9–19 mutant mitochondria, the 300‐kDa membrane complex was assembled, although the soluble 70‐kDa Tim9p–Tim10p complex was not detectable. Protein import was decreased only two‐fold. When coexpressed in Escherichia coli, tim9–19 and TIM10 proteins failed to assemble into a 70‐kDa complex. Our findings suggest that residues near the ‘twin CX3C’ motif are important for the assembly of Tim9p in both the Tim9p–Tim10p complex and the 300‐kDa membrane complex.
Nuclear Functions for Plasma Membrane‐Associated Proteins?
Authors: Benmerah Alexandre , Scott Mark , Poupon Viviane , Marullo Stefano
Published: November 2010

There are a growing number of observations that proteins, which were initially thought to perform a specific function in a given subcellular compartment, may also play additional roles in different locations within the cell. Proteins found in adhesion and endocytic structures of the plasma membrane and which also traffic to the nucleus perhaps represent the more spectacular examples of this phenomenon. The mechanisms involved in the transport of these molecules through the nuclear pores and their potential nuclear functions are discussed.
Frame Switch Splicing and Regulated Intramembrane Proteolysis: Key Words to Understand the Unfolded Protein Response
Authors: Mori Kazutoshi
Published: November 2010

Proteins must be correctly folded and assembled to fulfill their functions as assigned by genetic code. All living cells have developed systems to counteract protein unfolding or misfolding. A typical example of such a homeostatic response is triggered when unfolded proteins are accumulated in the endoplasmic reticulum. Eukaryotic cells cope with endoplasmic reticulum stress by attenuating translation, generally to decrease the burden on the folding machinery, as well as by inducing transcription of endoplasmic reticulum‐localized molecular chaperones and folding enzymes to augment folding capacity. These translational and transcriptional controls are collectively termed the unfolded protein response. The unfolded protein response is unique in that the molecular mechanisms it uses to transmit signals from the endoplasmic reticulum lumen to the nucleus are completely different from those used for signaling from the plasma membrane. Frame switch splicing (a term newly proposed here) and regulated intramembrane proteolysis (proposed by Brown et al., Cell 2000; 100: 391–398) employed by the unfolded protein response represent novel ways to activate a signaling molecule post‐transcriptionally and post‐translationally, respectively. They are critically involved in various cellular regulation pathways ranging from bacterial extracytoplasmic stress response to differentiation of mature B cells into antibody‐secreting plasma cells. Further, mammalian cells take advantage of differential properties between the two mechanisms to determine the fate of proteins unfolded or misfolded in the endoplasmic reticulum. This review focuses on the transcriptional control that occurs during the unfolded protein response in various species.
Nuclear Import of Viral DNA Genomes
Authors: Greber Urs F. , Fassati Ariberto
Published: November 2010

The genomes of many viruses traffic into the nucleus, where they are either integrated into host chromosomes or maintained as episomal DNA and then transcriptionally activated or silenced. Here, we discuss the existing evidence on how the lentiviruses, adenoviruses, herpesviruses, hepadnaviruses and autonomous parvoviruses enter the nucleus. Depending on the size of the capsid enclosing the genome, three principles of viral nucleic acids import are discussed. The first principle is that the capsid disassembles in the cytosol or in a docked state at the nuclear pore complex and a subviral genomic complex is trafficked through the pore. Second, the genome is injected from a capsid that is docked to the pore complex, and third, import factors are recruited to cytosolic capsids to increase capsid affinity to the pore complex, mediate translocation and allow disassembly in the nucleoplasm.
The HECT Ubiquitin Ligase Rsp5p Is Required for Proper Nuclear Export of mRNA in Saccharomyces cerevisiae
Authors: Rodriguez M. S. , Gwizdek C. , Haguenauer‐Tsapis R. , Dargemont C.
Published: November 2010

The nuclear transport of both proteins and RNAs has attracted considerable interest in recent years. However, regulation pathways of the nuclear transport machineries are still not well characterized. Previous studies indicated that ubiquitination is involved in poly(A)+ RNA nuclear export. For this reason, we systematically investigated ubiquitin‐protein ligasess from the homologous to E6‐AP carboxy terminus (HECT) family for potential individual roles in nuclear transport in Saccharomyces cerevisiae. Here we report that Rsp5, an essential yeast ubiquitin ligase involved in many cellular functions, when deleted or mutated in ligase activity, blocks the nuclear export of mRNAs. Affected messenger RNAs include both total poly(A)+ mRNA and heat‐shock mRNAs. Mutation of Rsp5 does not affect nuclear protein import or export. Deletion of RSP5 blocks mRNA export, even under conditions where its essential role in unsaturated fatty acids biosynthesis is bypassed. Using domain mapping, we find that the ligase activity is required for proper mRNA export, indicating that ubiquitination by Rsp5 acts directly or indirectly to affect RNA export. The finding that Rsp5p ligase mutations cause a more pronounced defect at high temperatures suggests that ubiquitination of transport factors by Rsp5p may also be essential during stress conditions.
Photochemistry of aromatic compounds
Authors: Mizuno Kazuhiko
Published: November 2010

This chapter deals with the photoisomerization, photoaddition and cycloaddition, photosubstitution, intramolecular photocyclization, intra- and inter-molecular photodimerization, photorearrangement reactions of aromatic compounds and related photoreactions.
Research Ethics II: Mentoring, Collaboration, Peer Review, and Data Management and Ownership
Authors: Horner Jennifer , Minifie Fred D.
Published: November 2010

Purpose

In this series of articles—Research Ethics I,Research Ethics II,andResearch EthicsIII—the authors provide a comprehensive review of the 9 core domains for the responsible conduct of research (RCR) as articulated by the Office of Research Integrity. InResearch Ethics II,the authors review the RCR domains of mentoring, collaboration, peer review, and data management and ownership.

Method

They relied on authoritative documents, both historical and contemporary, insightful commentary, and empirical research in order to identify current issues and controversies of potential interest to both faculty and students.

Conclusions

The authors close by urging readers to stay abreast of the manifold ethics issues facing today’s community of scientists, policymakers, and research institutions, and to adhere to best practices as they evolve.
An in situ cell to study phase transitions in individual aerosol particles on a substrate using scanning transmission x-ray microspectroscopy
Authors: Huthwelker T. , Zelenay V. , Birrer M. , Krepelova A. , Raabe J. , Tzvetkov G. , Vernooij M. G. C. , Ammann M.
Published: November 2010

A new in situ cell to study phase transitions and chemical processes on individual aerosol particles in the x-ray transmission microscope at the PolLux beamline of the Swiss light source has been built. The cell is machined from stainless steel and aluminum components and is designed to be used in the standard mount of the microscope without need of complicated rearrangements of the microscope. The cell consists of two parts, a back part which contains connections for the gas supply, heating, cooling devices, and temperature measurement. The second part is a removable clip, which hosts the sample. This clip can be easily exchanged and brought into a sampling unit for aerosol particles. Currently, the cell can be operated at temperatures ranging from −40 to +50 °C. The function of the cell is demonstrated using two systems of submicron size: inorganic sodium bromide aerosols and soot originating from a diesel passenger car. For the sodium bromide we demonstrate how phase transitions can be studied in these systems and that O1s spectra from aqueous sodium bromide solution can be taken from submicron sized particles. For the case of soot, we demonstrate that the uptake of water onto individual soot particles can be studied.
Crossed Andreev reflection on a topological insulator
Authors: Niu Zhi Ping
Published: November 2010

The nonlocal transport properties of a ferromagnet/superconductor/ferromagnet junction formed on the surface of a three-dimensional topological insulator are investigated. It is found the electron elastic cotunneling and crossed Andreev reflection depend sensitively on the directions of the magnetizations of the two ferromagnets. The basic mechanism behind this effect is that due to the translation invariant along the y-axis, during the tunneling the wave-vector ky of the incident electron must be conserved. The effects of the superconductor length and the bias voltage on the electron elastic cotunneling and crossed Andreev reflection are discussed. If the exchange field is larger than the chemical potential in the ferromagnet leads, a perfect electron elastic cotunneling or crossed Andreev reflection can be obtained in the low-energy regime by varying the magnetization direction in one of the ferromagnet leads.
Scale invariance of normalized cross-helicity throughout the inertial range of solar wind turbulence
Authors: Podesta J. J. , Borovsky J. E.
Published: November 2010

Solar wind measurements over the period from 1995 through 2006 are used to study fluctuations in the plasma bulk velocity and magnetic field over the range of magnetohydrodynamic (MHD) scales commonly referred to as the inertial range. Power spectra of the solar wind velocity, magnetic field, proton density, total energy (kinetic plus magnetic), and cross-helicity are analyzed for 176 time intervals in which the interplanetary magnetic field is restricted to a single magnetic sector. The data yield measurements of the normalized cross-helicity σc, the ratio of the cross-helicity spectrum to the energy spectrum, that span the entire inertial range at 1 AU and extend previous measurements by more than one decade in wavenumber. The results show that σc is approximately constant throughout the inertial range, independent of wavenumber, consistent with existing theoretical ideas. At the highest frequencies measured, |σc| is observed to decrease toward zero, however, this decrease is caused by measurement noise and is not a real physical effect. Other new results obtained in this study are (1) the average spectral index for the total energy—kinetic plus magnetic—is found to be closer to 3/2 than 5/3 with an average value 1.540±0.033 for highly Alfvénic wind, in agreement with simulations of incompressible MHD turbulence with a strong ambient magnetic field; (2) the spectral index for the total energy is a function of |σc| that varies from roughly 5/3 when σc≈0 to approximately 3/2 when |σc|≈1; (3) the spectral index for the total energy exhibits a solar cycle dependence during solar cycle 23 with above average values (steeper spectra) in the early rising phase of the cycle and below average values (shallower spectra) during the declining phase of the cycle—the controlling parameter for this solar cycle dependence appears to be |σc|.
Evolution of the magnetic anisotropy with particle size in antiferromagnetic Cr2O3 nanoparticles
Authors: Tobia D. , De Biasi E. , Granada M. , Troiani H. E. , Zampieri G. , Winkler E. , Zysler R. D.
Published: November 2010

We report the magnetic properties of antiferromagnetic Cr2O3 from bulk material down to 6 nm nanoparticles. We have found a decrease in the lattice parameters and the cell volume when the size diminishes. On the contrary, the magnetic anisotropy constant, Keff, shows a nonmonotonic behavior. The Keff decreases from its bulk value, shows a minimum near ϕ∼30 nm and displays an important increase for smaller sizes. We analyzed the size dependence of Keff in terms of the magnetocrystalline and surface contributions, and we fitted the Keff size evolution on the basis of a phenomenological model taking into account the magnetically ordered core and the surface contribution.
Photoluminescence spectroscopy of Cr3+ in CaY2Mg2Ge3O12
Authors: Örücü H. , Collins J. , Di Bartolo B.
Published: November 2010

We have conducted a thorough investigation of the luminescence spectrum of Cr3+ in CaY2Mg2Ge3O12. The spectrum presents a line whose width is 60 cm−1 at 25 K and 82 cm−1 at 200 K, and a number of peaks of vibronic origin superimposed on a large band that extends from 700 to 800 nm. Going up in temperature the superimposed peaks broaden and disappear while the band persists. The response of the system to pulsed excitation presents at low temperature a great variety of patterns at different wavelengths. These patterns tend to collapse into one as the temperature is raised. This investigation confirms that the continuous interest in Cr-doped garnets is rewarding in terms of interesting experimental results.
Electronic structure of InAs quantum dots with GaAsSb strain reducing layer: Localization of holes and its effect on the optical properties
Authors: Klenovský P. , Křápek V. , Munzar D. , Humlíček J.
Published: November 2010

The electronic structure of InAs quantum dots covered with the GaAs1−ySby strain reducing layer has been studied using the k⃗⋅p⃗ theory. We explain previous experimental observations of the red shift of the photoluminescence emission with increasing y and its blue shift with increasing excitation power. For y>0.19, type-II dots are formed with holes localized in the GaAsSb close to the dot base; two segments at the opposite sides of the dot, forming molecular-like states, result from the piezoelectric field. We also propose an experiment that could be used to identify the hole localization using a vertical electric field.
Nanodiamond-gated diamond field-effect transistor for chemical sensing using hydrogen-induced transfer doping for channel formation
Authors: Ahmad Rezal K. , Parada Ana Carolina , Tumilty Niall , Jackman Richard B.
Published: November 2010

A method for attaching nanodiamonds (NDs) to H-terminated diamond devices displaying surface conductivity, configured as an ion-sensitive field-effect transistor and resistor sensor, is demonstrated. From Hall effect measurements, there was minimal sign of degradation of the p-type surface conductivity after ND coating (∼1013 carriers/cm2, ∼27 cm2/V s). In response to pH changes, the device showed an improved response to the as-hydrogenated sensor, from 19 mV/pH to a maximum of 37 mV/pH. Configured in resistor mode, exposure to 2,4-dinitrotoluene vapor gave rise to sensitive detection, while the uncoated H-terminated device exhibited reaction instability. The mechanisms behind these observations are discussed.
Reversible room-temperature magnetocaloric effect in Mn5PB2
Authors: Xie Z. G. , Geng D. Y. , Zhang Z. D.
Published: November 2010

Magnetic properties and magnetocaloric effect of the Mn5PB2 compound have been investigated. The maximum values of magnetic entropy change −ΔSM at 302 K are 4.93 and 2.64 J kg−1 K−1 for magnetic field changes of 5 and 2 T, respectively, which are closely related with a second-order magnetic transition from the ferromagnetic to the paramagnetic state. The reversible magnetocaloric effect with relatively large magnetic entropy change makes the Mn5PB2 compound (free of rare earths) and Mn5PB2-based materials attractive candidates for room-temperature magnetic refrigeration.
The International Organization for Migration and the International Government of Borders
Authors: Andrijasevic Rutvica , Walters William
Published: November 2010

Early debates often read globalisation as a powerful tendency destined to make state borders less pertinent. Recent research has challenged this view by suggesting that globalisation and (re)bordering frequently advance hand-in-hand, culminating in a condition that might be described as ‘gated globalism’. But somewhat neglected in this recent wave of research is the role that particular international agencies are playing in shaping the norms and forms that pertain to emergent regimes of border control—what we call the international government of borders. Focusing on the International Organization for Migration (IOM) and its involvement in the promotion of what it calls better ‘border management’, this paper aims to partially redress this oversight. The IOM is interesting because it illustrates how the control of borders has become constituted as an object of technical expertise and intervention within programmes and schemes of international authority. Two themes are pursued. First, recent work on neoliberal governmentality is useful for illuminating the forms of power and subtle mechanisms of influence that characterise the IOM's attempt to managerialise border policies in countries as different as Armenia, Ethiopia, and Serbia. Second, the international government of borders comprises diverse and heterogeneous practices, ranging from the hosting of training seminars for local security and migration officials to the promotion of schemes to purchase and install cutting-edge surveillance equipment. In such different ways one can observe in very material terms how the project of making borders into a problem of ‘management’ conflicts with a perception of borders as a site of social struggle and politics.
Human Blacklisting: The Global Apartheid of the EU's External Border Regime
Authors: van Houtum Henk
Published: November 2010

Over the last few years, the global face of the EU has been changing. The EU is spinning a global border web with regard to the battle against irregular migration. At the borders of the EU, a powerful and security-obsessed distinction between travellers is increasingly being constructed between the travellers who ‘belong to’ the EU and those who do not, based on the fate of birth. To this end, the EU has composed a so-called ‘white and black’ Schengen list, recently relabelled a ‘positive and negative’ list, which is used as a criterion for visa applications. What is striking is that on the negative list a significantly high number of Muslim and developing states are listed. Hence, there is an implicit, strong inclination to use this list not only as a tool to guarantee security in physical terms or in terms of ‘Western’ identity protection but also as a means of keeping the world's poorest out. Such global apartheid geopolitics—loaded with rhetoric on selective access, burden, and masses—provokes the dehumanisation and illegalisation of the travel of those who were born in what the EU has defined as the ‘wrong country’, the wastable and deportable lives from countries on the negative list. Such unauthorised travelling is increasingly dangerous as the high death toll suggests. It has led to a new and yet all too familiar geopolitical landscape in Europe, a scene many of us hope to never see again in postwar Europe, a landscape of barbed wire surveillance and camps. And hence, the EU—which started out as a means to produce a zone of peace and comfort ruled by law and order—has now in its self-proclaimed war on illegal migrants created a border industry that coconstructs more, not less, ‘illegality’, xenophobia, and fear: the EU as a global border machine.
The ‘Border Within’: Inhabiting the Border in Trieste
Authors: Bialasiewicz Luiza , Minca Claudio
Published: November 2010

In this paper we look to the Italian border city of Trieste—at various points in its past, a cosmopolitan port, Austria's urbs europeissima, but also a battleground for competing understandings of territoriality, identity, and belonging and a paragon of the violent application of an ethnoterritorial logic to a plurinational, plurilingual urban context; a paragon of the violence of modern borders. At the same time—and precisely by virtue of its border condition—Trieste has often found itself within the cracks of European modernity, rendering it a unique site for the rearticulation and reappropriation of that which Walter Mignolo terms “global designs”. In our analysis, we ask what lessons the experience of a city like Trieste in ‘inhabiting the border’ can hold for Mignolo's notion of “border thinking” and for the elaboration of alternative geopolitical imaginaries.
Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations
Authors: Flechsig Holger , Mikhailov Alexander S.
Published: November 2010

Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated.
iMAT: an integrative metabolic analysis tool
Authors: Zur Hadas , Ruppin Eytan , Shlomi Tomer
Published: November 2010

Summary: iMAT is an Integrative Metabolic Analysis Tool, enabling the integration of transcriptomic and proteomic data with genome-scale metabolic network models to predict enzymes' metabolic flux, based on the method previously described by Shlomi et al. The prediction of metabolic fluxes based on high-throughput molecular data sources could help to advance our understanding of cellular metabolism, since current experimental approaches are limited to measuring fluxes through merely a few dozen enzymes.

Availability and Implementation:  http://imat.cs.tau.ac.il/

Contact:  zurhadas@post.tau.ac.il; ruppin@post.tau.ac.il; tomersh@cs.technion.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments
Authors: van Heeringen Simon J. , Veenstra Gert Jan C.
Published: November 2010

Summary: Accurate prediction of transcription factor binding motifs that are enriched in a collection of sequences remains a computational challenge. Here we report on GimmeMotifs, a pipeline that incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing (ChIP-seq) data. Similar redundant motifs are compared using the weighted information content (WIC) similarity score and clustered using an iterative procedure. A comprehensive output report is generated with several different evaluation metrics to compare and evaluate the results. Benchmarks show that the method performs well on human and mouse ChIP-seq datasets. GimmeMotifs consists of a suite of command-line scripts that can be easily implemented in a ChIP-seq analysis pipeline.

Availability: GimmeMotifs is implemented in Python and runs on Linux. The source code is freely available for download at http://www.ncmls.eu/bioinfo/gimmemotifs/.

Contact:  s.vanheeringen@ncmls.ru.nl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Aquaculture site selection for Japanese kelp (Laminaria japonica) in southern Hokkaido, Japan, using satellite remote sensing and GIS-based models
Authors: Radiarta I Nyoman , Saitoh Sei-Ichi , Yasui Hajime
Published: November 2010

Radiarta, I N., Saitoh, S-I., and Yasui, H. 2011. Aquaculture site selection for Japanese kelp (Laminaria japonica) in southern Hokkaido, Japan, using satellite remote sensing and GIS-based models. – ICES Journal of Marine Science, 68: 773–780. Japanese kelp (Laminaria japonica) is an important species cultured and harvested in Japan. The most suitable areas for hanging culture in southern Hokkaido were determined using geographic information system (GIS) models and a multicriteria evaluation approach. Analyses of physical parameters (sea surface temperature and suspended solid from SeaWiFS and MODIS) and available bathymetric data indicated that some 74% (1139 km2) of the total potential area with bottom depths <60 m had the two highest suitability scores. A local sensitivity analysis indicated that suspended solids were more important than temperature in affecting model output. This study demonstrates that GIS databases of different formats and sources can be used effectively to construct spatial models for kelp aquaculture.
Transcriptome response to different carbon sources in Acetobacter aceti
Authors: Sakurai Kenta , Arai Hiroyuki , Ishii Masaharu , Igarashi Yasuo
Published: November 2010

The draft genome sequence of Acetobacter aceti NBRC 14818 was determined by whole-genome shotgun sequencing and the transcriptome profile in cells exponentially grown on ethanol, acetate or glucose was analysed by using a DNA microarray. The genes for all enzymes that constitute the complete tricarboxylic acid (TCA) cycle and glyoxylate pathway were identified in the genome. The TCA cycle genes showed higher expression levels in A. aceti cells grown on acetate or glucose and the glyoxylate pathway genes were significantly induced by ethanol or acetate. Many SOS-response genes were upregulated in cells grown on ethanol, indicating that ethanol provoked damage of DNA and proteins. The superoxide dismutase and catalase genes showed high expression levels in culture on glucose, indicating that oxidation of glucose induced oxidative stress. A. aceti NBRC 14818 was found to have a highly branched respiratory chain. The genes for two type I and one type II NADH dehydrogenase were identified. The genes for one of the type I enzymes were highly expressed when cells were grown on acetate or glucose, but were significantly downregulated in culture on ethanol, probably because ubiquinones were directly reduced by pyrroloquinoline quinone-dependent alcohol dehydrogenase. Four sets of the genes for quinol oxidases, one bo
3-type (BO3), one bd-type and two cyanide-insensitive-types (CIOs), were identified in the genome. The genes for BO3, which might have proton-pumping activity, were highly expressed under the conditions tested, but were downregulated in the glucose culture. In contrast, the genes for one of the CIOs were significantly upregulated in cells grown on glucose. The two CIOs, which are expected to have lower energy-coupling efficiency, seemed to have a higher contribution in glucose-grown cells. These results indicate that energy conservation efficiency is fine-tuned by changing the respiratory components according to the growth conditions in A. aceti cells.
Genome-wide characterization of centromeric satellites from multiple mammalian genomes
Authors: Alkan Can , Cardone Maria Francesca , Catacchio Claudia Rita , Antonacci Francesca , O'Brien Stephen J. , Ryder Oliver A. , Purgato Stefania , Zoli Monica , Della Valle Giuliano , Eichler Evan E. , Ventura Mario
Published: November 2010

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.
Functional Assignments for the Carboxyl-Terminal Domains of the Ferrochelatase from Synechocystis PCC 6803: The CAB Domain Plays a Regulatory Role, and Region II Is Essential for Catalysis
Authors: Sobotka Roman , Tichy Martin , Wilde Annegret , Hunter C. Neil
Published: November 2010

Ferrochelatase (FeCH) catalyzes the insertion of Fe2+ into protoporphyrin, forming protoheme. In photosynthetic organisms, FeCH and magnesium chelatase lie at a biosynthetic branch point where partitioning down the heme and chlorophyll (Chl) pathways occurs. Unlike their mammalian, yeast, and other bacterial counterparts, cyanobacterial and algal FeCHs as well as FeCH2 isoform from plants possess a carboxyl-terminal Chl a/b-binding (CAB) domain with a conserved Chl-binding motif. The CAB domain is connected to the FeCH catalytic core by a proline-rich linker sequence (region II). In order to dissect the regulatory, catalytic, and structural roles of the region II and CAB domains, we analyzed a FeCH ƊH347 mutant that retains region II but lacks the CAB domain and compared it with the ƊH324-FeCH mutant that lacks both these domains. We found that the CAB domain is not required for catalytic activity but is essential for dimerization of FeCH; its absence causes aberrant accumulation of Chl-protein complexes under high light accompanied by high levels of the Chl precursor chlorophyllide. Thus, the CAB domain appears to serve mainly a regulatory function, possibly in balancing Chl biosynthesis with the synthesis of cognate apoproteins. Region II is essential for the catalytic function of the plastid-type FeCH enzyme, although the low residual activity of the ƊH324-FeCH is more than sufficient to furnish the cellular demand for heme. We propose that the apparent surplus of FeCH activity in the wild type is critical for cell viability under high light due to a regulatory role of FeCH in the distribution of Chl into apoproteins.
The effects of a large reduction in alcohol prices on hospitalizations related to alcohol: a population‐based natural experiment
Authors: Herttua Kimmo , Mäkelä Pia , Martikainen Pekka
Published: November 2010

Aims  Finland experienced a large reduction in alcohol prices in 2004 due to in the lowering of alcohol taxes by about one‐third and the abolition of duty‐free allowances for travellers from the European Union. We examined the effects of these changes on alcohol‐related hospitalizations.

Design and participants  Time—series intervention analyses of monthly aggregations of hospitalization for acute and chronic causes among men and women aged 15–39, 40–49, 50–69 and more than 69 years.

Setting  Finland, 1996–2006.

Findings  After the price reduction the chronic hospitalization rate for men increased among those below age 70 years. It was largest among those aged 50–69 years: 22%, which implies an increase of 18.0 monthly hospitalizations per 100 000 person‐years, and there was an 11% and 16% (11.5 and 4.8 monthly hospitalizations) increase among those aged 40–49 and 15–39, respectively. Among the women the rate increased by 23% (4.0 monthly hospitalizations) in the 50–69‐year‐olds, and decreased in the under‐40s. The increase in all the population groups was due mainly to an increase in mental and behavioural disorders due to alcohol. Acute hospitalizations increased by 17% and 20% (6.2 and 7.0 per month) among men aged 40–49 and 50–69 years, respectively, and by 38% among women aged 50–69 years (2.3 per month).

Conclusions  The results, obtained in a natural experimental setting when trends and seasonal variation had been taken into account, suggest that the reduction in alcohol prices led to increases in alcohol‐related hospitalization in certain population groups, mainly among 50–69‐year‐olds, in Finland.
Daily administration of the TP receptor antagonist terutroban improved endothelial function in high‐cardiovascular‐risk patients with atherosclerosis
Authors: Lesault Pierre‐François , Boyer Laurent , Pelle Gabriel , Covali‐Noroc Ala , Rideau Dominique , Akakpo Servais , Teiger Emmanuel , Dubois‐Randé Jean‐Luc , Adnot Serge
Published: November 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Terutroban is a selective TP receptor antagonist, i.e. a specific antagonist of the thromboxane A2 and prostaglandin endoperoxide receptors, shown to improve endothelial function after a single administration in patients with coronary artery disease.

WHAT THIS STUDY ADDS

• This randomized, double‐blind, placebo‐controlled trial demonstrates that repeated‐dose terutroban for 15 days improves endothelial function and inhibits thromboxane A2‐induced platelet aggregation in high‐cardiovascular‐risk patients taking 300 mg of aspirin per day. Terutroban may prove useful for preventing cardiovascular events in such patients.

AIMS The specific TP receptor antagonist terutroban improves endothelial function after a single dose in patients with coronary artery disease. Our aim was to evaluate the effects and dose dependency of repeated‐dose terutroban on endothelial function and platelet aggregation in high‐cardiovascular‐risk patients with carotid atherosclerosis.

METHODS We randomly allocated 48 patients taking 300 mg aspirin per day to placebo or to one of three terutroban dosages (2.5, 5 or 10 mg) for 15 days in a double‐blind study. Flow‐mediated vasodilatation was evaluated before and 2 h after the first oral dose on day 0 and 2 h after the last oral dose on day 14.

RESULTS On day 0 and day 14, all three terutroban dosages improved flow‐mediated vasodilatation and abolished platelet aggregation induced by the TP receptor agonist U46619, without changing the aggregation response to ADP or collagen.

CONCLUSION Terutroban, by chronically improving endothelium‐dependent vasodilatation and inhibiting platelet aggregation, may prove useful for preventing cardiovascular events in high‐risk patients.
A systematic review of therapeutic interventions for poststroke depression and the role of nurses
Authors: De Man‐van Ginkel Janneke M , Gooskens Floor , Schuurmans Marieke J , Lindeman Eline , Hafsteinsdottir Thóra B ,   on Behalf of the Rehabilitation Guideline Stroke Working Group
Published: November 2010

Aims and objectives.  This systematic review explores the nursing role in the management of poststroke depression and identifies effective non‐pharmacological interventions that nurses can use in the daily care of patients with stroke.

Background.  Depression is a common complication poststroke and affects one‐third of patients with stroke. It has a negative impact on functional recovery and social activities and is associated with increased morbidity and mortality. Detection and diagnosis of poststroke depression is inconsistent, and many depressed patients are under‐treated. Although nurses recognise that observation and assessment are parts of their role in rehabilitation care, little is known about their role in assessing depression or the interventions they can use.

Design.  A systematic review was conducted using the Cochrane method.

Methods.  Literature for the period 1993–2008 was searched in the electronic databases of CINAHL, Medline (PubMed), Nursing Journals (PubMed) and PsycINFO using the following keywords: cerebrovascular accident, stroke, depression, poststroke depression, treatment, therapy, treatment outcome, management.

Results.  Fifteen articles and one systematic review were identified. There was strong evidence that information provision reduces the severity of depression. Other interventions with positive effects on the occurrence or severity of poststroke depression were as follows: life review therapy, motivational interviewing, a specific nursing support programme and physical exercise.

Conclusion.  Depression after stroke is an important problem with adverse effects on the patient’s ability to participate in rehabilitation and on rehabilitation outcome. The interventions described can be implemented in nursing care of patients with poststroke depression. The variety of such interventions and the diversity of their nature and design are consistent with the practice of rehabilitation nursing.

Relevance to clinical practice.  The findings of this review enable nurses to intervene effectively to reduce the occurrence and severity of depression in patients with stroke.