bluuebunny/crossref_metadata_2025_split huggingface dataset:
International Organizations as Policy Advisors
Authors: Fang Songying , Stone Randall W. 
Published: October 2012

AbstractHow can international organizations persuade governments to adopt policy recommendations that are based on private information when their interests conflict? We develop a game-theoretic model of persuasion that applies regardless of regime type and does not rely on the existence of domestic constituency constraints. In the model, an international organization (IO) and a domestic expert have private information about a crisis, but their preferences diverge from those of the government, which must choose whether to delegate decision making to the expert. Persuasion can take place if the international institution is able to send a credible signal. We find that this can take place only if the preferences of the IO and the domestic expert diverge and the institution holds the more moderate policy position. This result contrasts with conventional wisdom, which holds that the necessary condition for IOs to exert influence is support from a domestic constituency with aligned preferences. Our model suggests that, far from being an obstacle to international cooperation, polarized domestic politics may be a necessary condition for IOs to exert effective influence.
The life cycle and geographical distribution of the monorchiidProctotrema bartolii(Digenea) in the clamDarina solenoidesfrom the Patagonian coast, Argentina
Authors: Gilardoni C. , Carballo M.C. , Cremonte F. 
Published: October 2012

AbstractThe life cycle ofProctotrema bartoliiCarballo, Laurenti & Cremonte 2011 (Digenea: Monorchiidae) at Fracasso Beach (the type locality) (42°25′S, 64°07′W), Península Valdés, Argentina, was investigated. This digenean uses the clamDarina solenoides(Mactridae) as both the first and second intermediate hosts in the natural environment. The metacercariae were located mainly at the tip of the incurrent siphon, with an infection prevalence of 100%. Experimental infections in other macroinvertebrates, such as the clamTellina petitianaand the polychaeteGlycera americana, were successful, but these and other invertebrates are not naturally infected. SilversidesOdontesthes smittiandOdontesthesnigricans(Pisces: Atherinopsidae) and the mulletEleginops maclovinus(Eleginopidae) act as the definitive hosts of both experimentally and naturally obtained adults. Fish acquire infection by eating either the siphon or the entire clam.Proctotrema bartoliiseems to be endemic to the Magellan Region and is distributed where its intermediate clam host is present, from the San José Gulf in Península Valdés to the southern tip of South America.
Parasitoses of the human central nervous system
Authors: Finsterer J. , Auer H. 
Published: October 2012

AbstractCerebral involvement in parasitoses is an important clinical manifestation of most of the human parasitoses. Parasites that have been described to affect the central nervous system (CNS), either as the dominant or as a collateral feature, include cestodes (Taenia solium (neurocysticerciasis), Echinococcus granulosus (cerebral cystic echinococcosis), E. multilocularis (cerebral alveolar echinococcosis), Spirometra mansoni (neurosparganosis)), nematodes (Toxocara canis and T. cati (neurotoxocariasis), Trichinella spiralis (neurotrichinelliasis), Angiostrongylus cantonensis and A. costaricensis (neuroangiostrongyliasis), Gnathostoma spinigerum (gnathostomiasis)), trematodes (Schistosoma mansoni (cerebral bilharziosis), Paragonimus westermani (neuroparagonimiasis)), or protozoa (Toxoplasma gondii (neurotoxoplasmosis), Acanthamoeba spp. or Balamuthia mandrillaris (granulomatous amoebic encephalitis), Naegleria (primary amoebic meningo-encephalitis), Entamoeba histolytica (brain abscess), Plasmodium falciparum (cerebral malaria), Trypanosoma brucei gambiense/rhodesiense (sleeping sickness) or Trypanosoma cruzi (cerebral Chagas disease)). Adults or larvae of helminths or protozoa enter the CNS and cause meningitis, encephalitis, ventriculitis, myelitis, ischaemic stroke, bleeding, venous thrombosis or cerebral abscess, clinically manifesting as headache, epilepsy, weakness, cognitive decline, impaired consciousness, confusion, coma or focal neurological deficits. Diagnosis of cerebral parasitoses is dependent on the causative agent. Available diagnostic tools include clinical presentation, blood tests (eosinophilia, plasmodia in blood smear, antibodies against the parasite), cerebrospinal fluid (CSF) investigations, imaging findings and occasionally cerebral biopsy. Treatment relies on drugs and sometimes surgery. Outcome of cerebral parasitoses is highly variable, depending on the effect of drugs, whether they are self-limiting (e.g. Angiostrongylus costaricensis) or whether they remain undetected or asymptomatic, like 25% of neurocysticerciasis cases.
Messenger RNAs in metaphase II oocytes correlate with successful embryo development to the blastocyst stage
Authors: Biase Fernando Henrique , Everts Robin Edward , Oliveira Rosane , Santos-Biase Weruska Karyna Freitas , Fonseca Merighe Giovana Krempel , Smith Lawrence Charles , Martelli Lúcia , Lewin Harris , Meirelles Flávio Vieira 
Published: October 2012

SummaryThe mRNAs accumulated in oocytes provide support for embryo development until embryo genomic activation. We hypothesized that the maternal mRNA stock present in bovine oocytes is associated with embryo development until the blastocyst stage. To test our hypothesis, we analyzed the transcriptome of the oocyte and correlated the results with the embryo development. Our goal was to identify genes expressed in the oocyte that correlate with its ability to develop to the blastocyst stage. A fraction of oocyte cytoplasm was biopsied using micro-aspiration and stored for further expression analysis. Oocytes were activated chemically, cultured individually and classified according to their capacity to developin vitroto the blastocyst stage. Microarray analysis was performed on mRNA extracted from the oocyte cytoplasm fractions and correlated with its ability to develop to the blastocyst stage (good quality oocyte) or arrest at the 8–16-cell stage (bad quality oocyte). The expression of 4320 annotated genes was detected in the fractions of cytoplasm that had been collected from oocytes maturedin vitro.Gene ontology classification revealed that enriched gene expression of genes was associated with certain biological processes: ‘RNA processing’, ‘translation’ and ‘mRNA metabolic process’. Genes that are important to the molecular functions of ‘RNA binding’ and ‘translation factor activity, RNA binding’ were also enriched in oocytes. We identified 29 genes with differential expression between the two groups of oocytes compared (good versus bad quality). The content of mRNAs expressed in metaphase II oocytes influences the activation of the embryonic genome and enables further develop to the blastocyst stage.
Care for the cancer caregiver: A systematic review
Authors: Applebaum Allison J. , Breitbart William 
Published: October 2012

AbstractObjective:Informal caregivers (ICs) are relatives, friends, and partners who have a significant relationship with and provide assistance (i.e., physical, emotional) to a patient with a life- threatening, incurable illness. The multidimensional burden that results from providing care to a patient with cancer is well documented, and as a result, a growing number of psychosocial interventions have been developed specifically to address this burden. The purpose of the present study was to characterize the state of the science of psychosocial interventions for informal cancer caregivers.Method:A comprehensive systematic review of interventions for cancer caregivers was conducted via an electronic literature search of publications between 1980 and January 13, 2011. A final sample of 49 interventions was reviewed in detail.Results:The interventions, which varied in terms of modality and patient population, fell into the following eight categories: psychoeducation, problem-solving/skills building interventions, supportive therapy, family/couples therapy, cognitive-behavioral therapy, interpersonal therapy, complementary and alternative medicine interventions, and existential therapy. Benefits and disadvantages of each of the categories are discussed, with special attention given to studies that produced null findings.Significance of results:Beyond specific techniques, structured, goal-oriented, and time-limited interventions that are integrative appear to be the most feasible and offer the greatest benefits for ICs of cancer patients. Future studies are needed to examine the specific benefits and challenges of delivering interventions in alternative modalities (Internet, Skype) so that the needs of a greater number of ICs may be addressed.
A different sense of humanity: occupation in Francis Lieber's Code
Authors: Giladi Rotem 
Published: October 2012

AbstractAccounts narrating the history of the modern law of occupation display ambivalence to the 1863 Lieber Code. At times, they mark the humanity of its provisions on occupied territories; at others, they find its concept of humanity in occupation limited compared to subsequent developments. A broader reading of the Code against Lieber's published works, teaching, and correspondence reveals a unique – and disconcerting –sense of humanity pervading through its provisions. Lieber's different sense of humanity, not directed at individuals, throws light on the history of the law governing occupied territories today and paves the way for critical reflections on its conceptual bases.
Robust Digital Holography For Ultracold Atom Trapping
Authors: Gaunt Alexander L. , Hadzibabic Zoran 
Published: October 2012

AbstractWe have formulated and experimentally demonstrated an improved algorithm for design of arbitrary two-dimensional holographic traps for ultracold atoms. Our method builds on the best previously available algorithm, MRAF and improves on it in two ways. First, it allows for creation of holographic atom traps with a well defined background potential. Second, we experimentally show that for creating trapping potentials free of fringing artifacts it is important to go beyond the Fourier approximation in modelling light propagation. To this end, we incorporate full Helmholtz propagation into our calculations.
Cathode diameter and operating parameter effects on hafnium cathode evaporation for oxygen plasma cutting arc
Authors: Long Nguyen Phi , Katada Yusuke , Tanaka Yasunori , Uesugi Yoshihiko , Yamaguchi Yoshihiro 
Published: October 2012

Abstract
Evaporation of hafnium cathode in a plasma cutting arc torch was investigated numerically and experimentally to assess the effects of cathode diameter and operating parameters such as gas pressure, gas flow rate and arc current. A numerical model was developed for arc plasma with consideration of hafnium cathode evaporation. Using this model, the surface cathode temperature and the amount of cathode mass loss caused by evaporation were predicted for different operating parameters. Simulated results show that the cathode surface temperature decreases at the hafnium cathode centre with increasing gas flow rate and cathode diameter. However, an increase in gas pressure elevates the surface cathode temperature in the radial range of 0.35 mm. The total amount of mass loss of hafnium cathode evaporation was predicted to be enhanced with increasing gas flow rate, gas pressure and cathode diameter as well. Comparison of the calculated results with experimentally obtained results shows good agreement in terms of the average surface cathode temperature, with variation in gas pressure and cathode diameter.
Application of asymmetric statistical potentials to antibody–protein docking
Authors: Brenke Ryan , Hall David R. , Chuang Gwo-Yu , Comeau Stephen R. , Bohnuud Tanggis , Beglov Dmitri , Schueler-Furman Ora , Vajda Sandor , Kozakov Dima 
Published: October 2012

Abstract
Motivation: An effective docking algorithm for antibody–protein antigen complex prediction is an important first step toward design of biologics and vaccines. We have recently developed a new class of knowledge-based interaction potentials called Decoys as the Reference State (DARS) and incorporated DARS into the docking program PIPER based on the fast Fourier transform correlation approach. Although PIPER was the best performer in the latest rounds of the CAPRI protein docking experiment, it is much less accurate for docking antibody–protein antigen pairs than other types of complexes, in spite of incorporating sequence-based information on the location of the paratope. Analysis of antibody–protein antigen complexes has revealed an inherent asymmetry within these interfaces. Specifically, phenylalanine, tryptophan and tyrosine residues highly populate the paratope of the antibody but not the epitope of the antigen.
Results: Since this asymmetry cannot be adequately modeled using a symmetric pairwise potential, we have removed the usual assumption of symmetry. Interaction statistics were extracted from antibody–protein complexes under the assumption that a particular atom on the antibody is different from the same atom on the antigen protein. The use of the new potential significantly improves the performance of docking for antibody–protein antigen complexes, even without any sequence information on the location of the paratope. We note that the asymmetric potential captures the effects of the multi-body interactions inherent to the complex environment in the antibody–protein antigen interface.
Availability: The method is implemented in the ClusPro protein docking server, available at http://cluspro.bu.edu.
Contact: midas@bu.edu or vajda@bu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
An unbiased evaluation of gene prioritization tools
Authors: Börnigen Daniela , Tranchevent Léon-Charles , Bonachela-Capdevila Francisco , Devriendt Koenraad , De Moor Bart , De Causmaecker Patrick , Moreau Yves 
Published: October 2012

AbstractMotivation: Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates—so as to maximize the yield and biological relevance of further downstream validation experiments and functional studies. During the past few years, several gene prioritization tools have been defined, and some of them have been implemented and made available through freely available web tools. In this study, we aim at comparing the predictive performance of eight publicly available prioritization tools on novel data. We have performed an analysis in which 42 recently reported disease-gene associations from literature are used to benchmark these tools before the underlying databases are updated.Results: Cross-validation on retrospective data provides performance estimate likely to be overoptimistic because some of the data sources are contaminated with knowledge from disease-gene association. Our approach mimics a novel discovery more closely and thus provides more realistic performance estimates. There are, however, marked differences, and tools that rely on more advanced data integration schemes appear more powerful.Contact: yves.moreau@esat.kuleuven.beSupplementary information: Supplementary data are available at Bioinformatics online.
Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks
Authors: Flassig R. J. , Sundmacher K. 
Published: October 2012

AbstractMotivation: Biochemical reaction networks in the form of coupled ordinary differential equations (ODEs) provide a powerful modeling tool for understanding the dynamics of biochemical processes. During the early phase of modeling, scientists have to deal with a large pool of competing nonlinear models. At this point, discrimination experiments can be designed and conducted to obtain optimal data for selecting the most plausible model. Since biological ODE models have widely distributed parameters due to, e.g. biologic variability or experimental variations, model responses become distributed. Therefore, a robust optimal experimental design (OED) for model discrimination can be used to discriminate models based on their response probability distribution functions (PDFs).Results: In this work, we present an optimal control-based methodology for designing optimal stimulus experiments aimed at robust model discrimination. For estimating the time-varying model response PDF, which results from the nonlinear propagation of the parameter PDF under the ODE dynamics, we suggest using the sigma-point approach. Using the model overlap (expected likelihood) as a robust discrimination criterion to measure dissimilarities between expected model response PDFs, we benchmark the proposed nonlinear design approach against linearization with respect to prediction accuracy and design quality for two nonlinear biological reaction networks. As shown, the sigma-point outperforms the linearization approach in the case of widely distributed parameter sets and/or existing multiple steady states. Since the sigma-point approach scales linearly with the number of model parameter, it can be applied to large systems for robust experimental planning.Availability: An implementation of the method in MATLAB/AMPL is available at http://www.uni-magdeburg.de/ivt/svt/person/rf/roed.html.Contact: flassig@mpi-magdeburg.mpg.deSupplementary information: Supplementary data are are available at Bioinformatics online.
Global network alignment using multiscale spectral signatures
Authors: Patro Rob , Kingsford Carl 
Published: October 2012

Abstract
Motivation: Protein interaction networks provide an important system-level view of biological processes. One of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. By providing a mapping between the networks of different species, alignments can be used to inform hypotheses about the functions of unannotated proteins, the existence of unobserved interactions, the evolutionary divergence between the two species and the evolution of complexes and pathways.
Results: We introduce GHOST, a global pairwise network aligner that uses a novel spectral signature to measure topological similarity between subnetworks. It combines a seed-and-extend global alignment phase with a local search procedure and exceeds state-of-the-art performance on several network alignment tasks. We show that the spectral signature used by GHOST is highly discriminative, whereas the alignments it produces are also robust to experimental noise. When compared with other recent approaches, we find that GHOST is able to recover larger and more biologically significant, shared subnetworks between species.
Availability: An efficient and parallelized implementation of GHOST, released under the Apache 2.0 license, is available at http://cbcb.umd.edu/kingsford_group/ghost
Contact: rob@cs.umd.edu
Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index
Authors: Paredes Sur Herrera , Melgar Michael F. , Sethupathy Praveen 
Published: October 2012

Abstract
Motivation: It has been known for more than 2 decades that after RNA polymerase II (RNAPII) initiates transcription, it can enter into a paused or stalled state immediately downstream of the transcription start site before productive elongation. Recent advances in high-throughput genomic technologies facilitated the discovery that RNAPII pausing at promoters is a widespread physiologically regulated phenomenon. The molecular underpinnings of pausing are incompletely understood. The CCCTC-factor (CTCF) is a ubiquitous nuclear factor that has diverse regulatory functions, including a recently discovered role in promoting RNAPII pausing at splice sites.
Results: In this study, we analyzed CTCF binding sites and nascent transcriptomic data from three different cell types, and found that promoter-proximal CTCF binding is significantly associated with RNAPII pausing.
Contact: praveen_sethupathy@med.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Case of pleural metastasis of prostate cancer
Authors: Yasuda Koichiro , Maeda Ai , Yukawa Takuro , Saisho Shinsuke , Okita Riki , Hirami Yuji , Shimizu Katsuhiko , Nakata Masao 
Published: October 2012

AbstractThe most frequent sites of prostate cancer metastases are the bone and lung. Pleural metastasis of prostate cancer is clinically rare. We report a case with solitary pleural thickening arising from the metastasis of prostate cancer. A 71‐year‐old man was referred to our hospital for further examination of pleural thickening detected during a chest computed tomography (CT) examination. A video‐assisted pleural biopsy was performed. The pathological findings showed that the tumor cells had spread from the parietal pleura to adipose tissue around the costal muscles. The tumor cells were positive for prostate‐specific antigen (PSA) and negative for calretinin, cytokeratin (Ck5/6) and D2‐40. These findings suggested that the pleural lesion was a metastasis of the prostate cancer.
Adipose stromal cell and sarpogrelate orchestrate the recovery of inflammation‐induced angiogenesis in aged hindlimb ischemic mice
Authors: Fan Weiwei , Li Chengxiang , Qin Xing , Wang Shenxu , Da Hu , Cheng Kang , Zhou Ri , Tong Chao , Li Xiujuan , Bu Qingting , Li Congye , Han Yaling , Ren Jun , Cao Feng 
Published: October 2012

SummaryAging population displays a much higher risk of peripheral arterial disease (PAD) possibly due to the higher susceptibility, poor prognosis, and fewer therapeutic options. This study was designed to examine the impact of combined multipotent adipose‐derived stromal cells (mADSCs) and sarpogrelate treatment on aging hindlimb ischemia and the mechanism of action involved. mADSCs (1.0 × 107) constitutively expressing enhanced green fluorescent protein (eGFP) or firefly luciferase (Fluc) reporter were engrafted into the hindlimb of aged Vegfr2‐luc transgenic or FVB/N mice subjected to unilateral femoral artery occlusion, followed by a further administration of sarpogrelate. Multimodality molecular imaging was employed to noninvasively evaluate mADSCs' survival and therapeutic efficacy against aging hindlimb ischemia. Aged Tg(Vegfr2‐luc) mice exhibited decreased inflammatory response, and downregulation of vascular endothelial growth factor (VEGF)/vascular endothelial growth factor receptor‐2 (VEGFR2) compared with young ones following hindlimb ischemia induction, resulting in angiogenesis insufficiency and decompensation for ischemia recovery. Engrafted mADSCs augmented inflammation‐induced angiogenesis to yield pro‐angiogenic/anti‐apoptotic effects partly via the VEGF/VEGFR2/mTOR/STAT3 pathway. Nonetheless, mADSCs displayed limited survival and efficacy following transplantation. Sarpogrelate treatment with mADSCs further upregulated mammalian target of rapamycin (mTOR)/STAT3 signal and modulated pro‐/anti‐inflammatory markers including IL‐1β/TNF‐α/IFN‐γ and IL‐6/IL‐10, which ultimately facilitated mADSCs' survival and therapeutic benefit in vivo. Sarpogrelate prevented mADSCs from hypoxia/reoxygenation‐induced cell death via a mTOR/STAT3‐dependent pathway in vitro. This study demonstrated a role of in vivo kinetics of VEGFR2 as a biomarker to evaluate cell‐derived therapeutic angiogenesis in aging. mADSCs and sarpogrelate synergistically restored impaired angiogenesis and inflammation modulatory capacity in aged hindlimb ischemic mice, indicating its therapeutic promise for PAD in the elderly.