bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of
In Vitro
Fitness Recovery of HIV-1
Authors: Lorenzo-Redondo Ramón , Bordería Antonio V. , Lopez-Galindez Cecilio 
Published: November 2010

ABSTRACT

The study on the evolutionary consequences of an RNA viral population's fluctuations can be approached by
in vitro
experiments. This work describes the fitness recovery of HIV-1 after 20 large-population passages in 10 debilitated clones. The serial passages promoted an increase in viral fitness. In addition, we detected a significant number of mutations fixed in the complete genome consensus sequence of the final viral populations. Among the mutations, events of convergent evolution with important phenotypic characteristics occurred in several independent clones. One common change, V35I, in the nuclear localization signal of the p17 protein appeared in four viruses of three different lineages. Other common alterations mapped in position E196K of the reverse transcriptase or in position S316K of the V3 loop of the gp120 residue that is associated with the X4/R5 phenotype. Together with this mutational analysis, we studied the quasispecies heterogeneity of the initial and final viruses, revealing that fitness increase correlated with an augmentation in the genetic heterogeneity of viral quasispecies. However, while heterogeneity was mostly composed of synonymous (
dS
) mutations in the first 10 passages performed, at passage 21 it switched to nonsynonymous (
dN
) substitutions, with significant differences in
dN
−
dS
values between passages 11 and 21. In summary, the HIV-1
in vitro
fitness recovery depicts a multiphase process occurring first by generation of mutations followed by fixation of the beneficial ones, depicting a classical Darwinian process.
Nucleoprotein-RNA Orientation in the Measles Virus Nucleocapsid by Three-Dimensional Electron Microscopy
Authors: Desfosses Ambroise , Goret Gaël , Farias Estrozi Leandro , Ruigrok Rob W. H. , Gutsche Irina 
Published: November 2010

ABSTRACTRecombinant measles virus nucleoprotein-RNA (N-RNA) helices were analyzed by negative-stain electron microscopy. Three-dimensional reconstructions of trypsin-digested and intact nucleocapsids coupled to the docking of the atomic structure of the respiratory syncytial virus (RSV) N-RNA subunit into the electron microscopy density map support a model that places the RNA at the exterior of the helix and the disordered C-terminal domain toward the helix interior, and they suggest the position of the six nucleotides with respect to the measles N protomer.
Seeing the Portal in Herpes Simplex Virus Type 1 B Capsids
Authors: Rochat R. H. , Liu X. , Murata K. , Nagayama K. , Rixon F. J. , Chiu W. 
Published: November 2010

ABSTRACT
Resolving the nonicosahedral components in large icosahedral viruses remains a technical challenge in structural virology. We have used the emerging technique of Zernike phase-contrast electron cryomicroscopy to enhance the image contrast of ice-embedded herpes simplex virus type 1 capsids. Image reconstruction enabled us to retrieve the structure of the unique portal vertex in the context of the icosahedral capsid and, for the first time, show the subunit organization of a portal in a virus infecting eukaryotes. Our map unequivocally resolves the 12-subunit portal situated beneath one of the pentameric vertices, thus removing uncertainty over the location and stoichiometry of the herpesvirus portal.
Nonneutralizing HIV-1 gp41 Envelope Cluster II Human Monoclonal Antibodies Show Polyreactivity for Binding to Phospholipids and Protein Autoantigens
Authors: Dennison S. Moses , Anasti Kara , Scearce Richard M. , Sutherland Laura , Parks Robert , Xia Shi-Mao , Liao Hua-Xin , Gorny Miroslaw K. , Zolla-Pazner Susan , Haynes Barton F. , Alam S. Munir 
Published: November 2010

ABSTRACTHIV-1 gp41 envelope antibodies, which are frequently induced in HIV-1-infected individuals, are predominantly nonneutralizing. The rare and difficult-to-induce neutralizing antibodies (2F5 and 4E10) that target gp41 membrane-proximal epitopes (MPER) are polyspecific and require lipid binding for HIV-1 neutralization. These results raise the questions of how prevalent polyreactivity is among gp41 antibodies and how the binding properties of gp41-nonneutralizing antibodies differ from those of antibodies that are broadly neutralizing. In this study, we have characterized a panel of human gp41 antibodies with binding specificities within the immunodominant cluster I (gp41 amino acids [aa] 579 to 613) or cluster II (gp41 aa 644 to 667) for reactivity to autoantigens, to the gp140 protein, and with MPER peptide-lipid conjugates. We report that while none of the gp41 cluster I antibodies studied were polyspecific, all three gp41 cluster II antibodies bound either to lipids or autoantigens, thus showing the propensity of cluster II antibodies to manifest polyreactivity. All cluster II gp41 monoclonal antibodies (MAbs), including those that were lipid reactive, failed to bind to gp41 MPER peptide-lipid complexes. Cluster II antibodies bound strongly with nanomolar binding affinity (dissociation constant [Kd]) to oligomeric gp140 proteins, and thus, they recognize conformational epitopes on gp41 that are distinct from those of neutralizing gp41 antibodies. These results demonstrate that lipid-reactive gp41 cluster II antibodies are nonneutralizing due to their inability to bind to the relevant neutralizing epitopes on gp41.
Kaposi's Sarcoma-Associated Herpesvirus ORF57 Interacts with Cellular RNA Export Cofactors RBM15 and OTT3 To Promote Expression of Viral ORF59
Authors: Majerciak Vladimir , Uranishi Hiroaki , Kruhlak Michael , Pilkington Guy R. , Massimelli Maria Julia , Bear Jenifer , Pavlakis George N. , Felber Barbara K. , Zheng Zhi-Ming 
Published: November 2010

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes ORF57, which promotes the accumulation of specific KSHV mRNA targets, including ORF59 mRNA. We report that the cellular export NXF1 cofactors RBM15 and OTT3 participate in ORF57-enhanced expression of KSHV ORF59. We also found that ectopic expression of RBM15 or OTT3 augments ORF59 production in the absence of ORF57. While RBM15 promotes the accumulation of ORF59 RNA predominantly in the nucleus compared to the levels in the cytoplasm, we found that ORF57 shifted the nucleocytoplasmic balance by increasing ORF59 RNA accumulation in the cytoplasm more than in the nucleus. By promoting the accumulation of cytoplasmic ORF59 RNA, ORF57 offsets the nuclear RNA accumulation mediated by RBM15 by preventing nuclear ORF59 RNA from hyperpolyadenylation. ORF57 interacts directly with the RBM15 C-terminal portion containing the SPOC domain to reduce RBM15 binding to ORF59 RNA. Although ORF57 homologs Epstein-Barr virus (EBV) EB2, herpes simplex virus (HSV) ICP27, varicella-zoster virus (VZV) IE4/ORF4, and cytomegalovirus (CMV) UL69 also interact with RBM15 and OTT3, EBV EB2, which also promotes ORF59 expression, does not function like KSHV ORF57 to efficiently prevent RBM15-mediated nuclear accumulation of ORF59 RNA and RBM15's association with polyadenylated RNAs. Collectively, our data provide novel insight elucidating a molecular mechanism by which ORF57 promotes the expression of viral intronless genes.
Cell Type-Specific Proteasomal Processing of HIV-1 Gag-p24 Results in an Altered Epitope Repertoire
Authors: Steers Nicholas J. , Currier Jeffrey R. , Kijak Gustavo H. , di Targiani Robert C. , Saxena Ashima , Marovich Mary A. , Kim Jerome H. , Michael Nelson L. , Alving Carl R. , Rao Mangala 
Published: November 2010

ABSTRACT

Proteasomes are critical for the processing of antigens for presentation through the major histocompatibility complex (MHC) class I pathway. HIV-1 Gag protein is a component of several experimental HIV-1 vaccines. Therefore, understanding the processing of HIV-1 Gag protein and the resulting epitope repertoire is essential. Purified proteasomes from mature dendritic cells (DC) and activated CD4
+
T cells from the same volunteer were used to cleave full-length Gag-p24 protein, and the resulting peptide fragments were identified by mass spectrometry. Distinct proteasomal degradation patterns and peptide fragments were unique to either mature DC or activated CD4
+
T cells. Almost half of the peptides generated were cell type specific. Two additional differences were observed in the peptides identified from the two cell types. These were in the HLA-B35-Px epitope and the HLA-B27-KK10 epitope. These epitopes have been linked to HIV-1 disease progression. Our results suggest that the source of generation of precursor MHC class I epitopes may be a critical factor for the induction of relevant epitope-specific cytotoxic T cells.
A Proapoptotic Peptide Derived from Reovirus Outer Capsid Protein μ1 Has Membrane-Destabilizing Activity
Authors: Kim Jae-Won , Lyi Sangbom M. , Parrish Colin R. , Parker John S. L. 
Published: November 2010

ABSTRACT
The reovirus outer capsid protein μ1 is responsible for cell membrane penetration during virus entry and contains determinants necessary for virus-induced apoptosis. Residues 582 to 611 of μ1 are necessary and sufficient for reovirus-induced apoptosis, and residues 594 and 595 independently regulate the efficiency of viral entry and reovirus-induced cell apoptosis, respectively. Two of three α-helices within this region, helix 1 (residues 582 to 611) and helix 3 (residues 644 to 675), play a role in reovirus-induced apoptosis. Here, we chemically synthesized peptides representing helix 1 (H1), H1:K594D, H1:I595K, and helix 3 (H3) and examined their biological properties. We found that H1, but not H3, was able to cause concentration- and size-dependent leakage of molecules from small unilamellar liposomes. We further found that direct application of H1, but not H1:K594D, H1:I595K, or H3, to cells resulted in cytotoxicity. Application of the H1 peptide to L929 cells caused rapid elevations in intracellular calcium concentration that were independent of phospholipase C activation. Cytotoxicity of H1 was not restricted to eukaryotic cells, as the H1 peptide also had bactericidal activity. Based on these findings, we propose that the proapoptotic function of the H1 region of μ1 is dependent on its capacity to destabilize cellular membranes and cause release of molecules from intracellular organelles that ultimately induces cell necrosis or apoptosis, depending on the dose.
High efficacy of bolus methylprednisolone in severe leptospirosis: a descriptive study in Sri Lanka
Authors: Kularatne Senanayake A M , Budagoda B D Sudhara S , de Alwis V Kapila D , Wickramasinghe W M R Sujantha , Bandara J M Ruwanthi P , Pathirage L P Manoji M K , Gamlath G Rohitha R D K , Wijethunga Thusitha J , Jayalath W A Thilak A , Jayasinghe Chandrika , Pinto Vasanthi , Somaratne Praneetha , Kumarasiri P V Ranjith 
Published: November 2010

ABSTRACT

Background
In 2008, an outbreak of leptospirosis caused high mortality in Sri Lanka. The General Hospital, Peradeniya recorded nine deaths in May, which prompted the medical staff to change the treatment protocol. Addition of intravenous methylprednisolone (MP) to the treatment regimen of severely ill patients was implemented on the basis of immune mediated pathogenesis of the disease to reduce mortality.

Methods
The day MP commenced (25 May 2008), the study period was divided into a ‘pre-MP period’ and an ‘MP period’. A clinical score ranging from 0–6 was applied to assess the severity of the infection. A score ≥2 was considered severe. Thus, 62 patients received bolus MP 500 mg intravenously for 3 days, followed by oral 8 mg for 5 days (MP given). Ten patients to whom MP was withheld were included in the MP period severe group (n=72). The same score was applied to pre-MP periods and 60 cases were identified as the historical control group (pre-MP period severe).

Results
There were 78 and 149 cases of leptospirosis in the pre-MP period and MP period, respectively. Of these cases, 17 and 16 patients died, with case death rates of 21.8% and 10.7%, respectively; the difference was significant (p=0.025). The survival rate at score 4 in the MP period severe group was 100% (16 of 16), compared to 38% (5 of 13) in pre-MP period severe group; this difference was highly significant (p&lt;0.001). Six patients who died despite MP therapy had a clinical score of 5 or 6; four were alcohol consumers, and two had heart disease and hypertension.

Conclusion
MP may reduce mortality in patients with severe leptospirosis, except in cases with established multiple organ dysfunction and comorbidities. Therefore, early administration of MP seems advisable.
Distinct Interactions Between c-Src and c-Met in Mediating Resistance to c-Src Inhibition in Head and Neck Cancer
Authors: Sen Banibrata , Peng Shaohua , Saigal Babita , Williams Michelle D. , Johnson Faye M. 
Published: November 2010

Abstract
Purpose: c-Src inhibition in cancer cells leads to an abrogation of invasion but a variable effect on apoptosis. The pathways downstream of c-Src promoting survival are not well characterized. Because cancer therapy that both decreases invasion and induces significant apoptosis would be ideal, we sought to characterize the mechanisms of resistance to c-Src inhibition.
Experimental Design: c-Src was inhibited in a panel of oral cancer cell lines and subsequent survival and signaling measured. The interactions between c-Src and c-Met were evaluated using immunoprecitation and an in vitro kinase assay. Cytotoxicity was measured and the Chou–Talalay combination index calculated. An orthotopic model of oral cancer was used to assess the effects of c-Met and c-Src inhibitors.
Results: Inhibition of c-Src resulted in c-Met inhibition in sensitive cells lines, but not in resistant cell lines. Isolated c-Met was a c-Src substrate in both sensitive and resistant cells, but there was no interaction of c-Src and c-Met in intact resistant cells. To examine the biological consequences of this mechanism, we demonstrated synergistic cytotoxicity, enhanced apoptosis, and decreased tumor size with the combination of c-Src and c-Met inhibitors.
Conclusions: Sustained c-Met activation can mediate resistance to c-Src inhibition. These data suggest that the differences between c-Met and c-Src signaling in sensitive and resistant cells are due to distinct factors promoting or inhibiting interactions, respectively, rather than to intrinsic structural changes in c-Src or c-Met. The synergistic cytotoxic effects of c-Src and c-Met inhibition may be important for the treatment of head and neck cancers. Clin Cancer Res; 17(3); 514–24. ©2010 AACR.
Formin Homology Domain–Containing Protein 1 Regulates Smooth Muscle Cell Phenotype
Authors: Staus Dean P. , Blaker Alicia L. , Medlin Matt D. , Taylor Joan M. , Mack Christopher P. 
Published: November 2010

Objective—
Our goal was to test whether formin homology protein 1 (FHOD1) plays a significant role in the regulation of smooth muscle cell (SMC) differentiation and, if so, whether Rho kinase (ROCK)–dependent phosphorylation in the diaphanous autoinhibitory domain is an important signaling mechanism that controls FHOD1 activity in SMC.

Methods and Results—
FHOD1 is highly expressed in aortic SMCs and in tissues with a significant SMC component. Exogenous expression of constitutively active FHOD1, but not wild-type, strongly activated SMC-specific gene expression in 10T1/2 cells. Treatment of SMC with the RhoA activator sphingosine-1-phosphate increased FHOD1 phosphorylation at Thr1141, and this effect was completely prevented by inhibition of ROCK with Y-27632. Phosphomimetic mutations to ROCK target residues enhanced FHOD1 activity, suggesting that phosphorylation interferes with FHOD1 autoinhibition. Importantly, knockdown of FHOD1 in SMC strongly inhibited sphingosine-1-phosphate–dependent increases in SMC differentiation marker gene expression and actin polymerization, suggesting that FHOD1 plays a major role in RhoA-dependent signaling in SMC.

Conclusion—
Our results indicate that FHOD1 is a critical regulator of SMC phenotype and is regulated by ROCK-dependent phosphorylation. Thus, additional studies on the role of FHOD1 during development and the progression of cardiovascular disease will be important.
Hemodynamic–Morphologic Discriminants for Intracranial Aneurysm Rupture
Authors: Xiang Jianping , Natarajan Sabareesh K. , Tremmel Markus , Ma Ding , Mocco J , Hopkins L. Nelson , Siddiqui Adnan H. , Levy Elad I. , Meng Hui 
Published: November 2010

Background and Purpose—
The purpose of this study was to identify significant morphological and hemodynamic parameters that discriminate intracranial aneurysm rupture status using 3-dimensional angiography and computational fluid dynamics.

Methods—
One hundred nineteen intracranial aneurysms (38 ruptured, 81 unruptured) were analyzed from 3-dimensional angiographic images and computational fluid dynamics. Six morphological and 7 hemodynamic parameters were evaluated for significance with respect to rupture. Receiver operating characteristic analysis identified area under the curve (AUC) and optimal thresholds separating ruptured from unruptured aneurysms for each parameter. Significant parameters were examined by multivariate logistic regression analysis in 3 predictive models—morphology only, hemodynamics only, and combined—to identify independent discriminants, and the AUC receiver operating characteristic of the predicted probability of rupture status was compared among these models.

Results—

Morphological parameters (size ratio, undulation index, ellipticity index, and nonsphericity index) and hemodynamic parameters (average wall shear stress [WSS], maximum intra-aneurysmal WSS, low WSS area, average oscillatory shear index, number of vortices, and relative resident time) achieved statistical significance (
P
<0.01). Multivariate logistic regression analysis demonstrated size ratio to be the only independently significant factor in the morphology model (AUC, 0.83; 95% CI, 0.75 to 0.91), whereas WSS and oscillatory shear index were the only independently significant variables in the hemodynamics model (AUC, 0.85; 95% CI, 0.78 to 0.93). The combined model retained all 3 variables, size ratio, WSS, and oscillatory shear index (AUC, 0.89; 95% CI, 0.82 to 0.96).

Conclusion—
All 3 models—morphological (based on size ratio), hemodynamic (based on WSS and oscillatory shear index), and combined—discriminate intracranial aneurysm rupture status with high AUC values. Hemodynamics is as important as morphology in discriminating aneurysm rupture status.
The Leading Article in No. 179 of the Kölnische Zeitung
Authors: Boer Roland 
Published: November 2010

AbstractThis article offers a critical exegesis of an early and neglected text by Marx called “The Leading Article in No. 179 of the Kölnische Zeitung” (from 1842). It is of interest since it offers one of Marx’s most sustained engagements with theology, especially in the context of the dominant theological mode of public debate in Germany at the time, a context which is outlined briefly. Here we find Marx responding to that debate and seeking to extract himself from its terms. Some of his formulations are problematic, such as the assumption that theology is purely other-worldly (leading him to argue for the separation of theology and philosophy in this light and for the separation of church and state). But others are full of promise, such as, (1) one of the first uses of his famous materialist inversion, here on the question of history and religion; (2) an introduction to the immensely fruitful idea of fetishism that would reverberate and mutate throughout his work until the well-known formulations in Capital; and (3) an argument to which this essay by Marx provides an initial glimmer, namely, that the secular state is the dialectical outcome of the Christian state and thereby no solution to the contradictions of the latter. Needless to say, the latter is extremely pertinent in today’s geopolitical climate.
Suicide Bombers or Martyrdom Operatives? Their Status among Muslim Thinkers, Jurists and Activists
Authors: Dadoo Y. 
Published: November 2010

AbstractThis article aims to expound the divergent shades of opinion on the phenomenon of suicide by employing the cardinal principles undergirding the philosophy of Islamic law. An overview of the attitudes to suicide amongst different societies and faith communities is given before focusing on this topic from a Muslim perspective which accommodates the setting provided by the higher intents of Islamic law, thus enabling us to assess those deeds substantially. It is noted that perspectives vary considerably and depend on the legal and ethical priorities of different individuals. In the process, the rich legacy of nuances adopted by scholars on either side leaves an impression of flexibility in their thinking. Consensus on this debate appears distant.
Comparison of two modes of delivery of first aid training including basic life support
Authors: Lippmann John , Livingston Patricia , Craike Melinda J 
Published: November 2010

Aims: Flexible-learning first aid courses are increasingly common due to reduced classroom contact time. This study compared retention of first aid knowledge and basic life support (BLS) skills three months after a two-day, classroom-based first aid course (STD) to one utilizing on-line theory learning at home followed by one day of classroom training (FLEX). Methods: In this prospective randomized controlled trial, 256 participants with internet access and no first aid related training for at least five years were randomly allocated to a STD or FLEX course. Assessment was conducted immediately after training and again three months later. Each participant was allocated a theory and a BLS score, which were summed and averaged to create an equally-weighted ‘combined score’ of first aid knowledge and skills. Results: There was no significant difference in theory scores between the STD and FLEX groups immediately after training and after three months. STD participants had significantly higher BLS scores immediately after training ( p = 0.001) and three months later ( p = 0.046). Males had significantly higher BLS scores after training ( p < 0.001), but not three months later ( p = 0.02). Participants older than 46 years had significantly lower BLS scores than younger participants ( p < 0.001). There was no significant difference in combined scores between the STD and FLEX groups or between genders, education or age groups either immediately after training or three months later. Conclusion: After replacing one day of classroom-based training with on-line theory training, there was no significant difference in the first aid competencies of the study population, as measured by an equally-weighted combined score of basic life support and first aid theory.
Distressed fathers and their children: A review of the literature
Authors: LeFrançois Brenda A. 
Published: November 2010

Background: Many men diagnosed with mental health problems are also fathers. This literature review addresses issues relating to both the fathering role taken on by men who have mental health problems as well as the impact of their mental health on their children. Material: An integrative review of the literature was conducted from studies originating in four countries, resulting in an analysis of 31 journal articles. Discussion and conclusions: Most of the quantitative literature focuses on the many risks and negative outcomes for children. However, qualitative studies suggest positive outcomes such as strong parent–child relationships, which demand further attention both in research and in practice.