bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleic Acid Amplification Tests for Diagnosis of
Neisseria gonorrhoeae
and
Chlamydia trachomatis
Rectal Infections
Authors: Bachmann Laura H. , Johnson Robert E. , Cheng Hong , Markowitz Lauri , Papp John R. , Palella Frank J. , Hook Edward W. 
Published: March 2010

ABSTRACT

It is uncertain which methods for the diagnosis of rectal gonococcal and chlamydial infection are optimal. This study evaluated the performance of culture and nucleic acid amplification tests (NAATs) for rectal chlamydial and gonococcal diagnosis. From July 2003 until February 2007, 441 rectal test sets were collected from individuals attending a sexually transmitted disease clinic and three HIV clinics who gave a history of anal intercourse or were women at high risk for
Neisseria gonorrhoeae
or
Chlamydia trachomatis
infections. Rectal swab specimens were tested using culture and commercial NAATs employing transcription-mediated amplification (TMA), strand displacement amplification (SDA), and PCR amplification. Test performance was evaluated using a rotating standard by which patients were classified as infected if either two or three comparator tests were positive. Test sensitivities for the detection of
N. gonorrhoeae
ranged from 66.7% to 71.9% for culture to 100% for TMA. Specificities were 99.7% to 100% for culture and greater than 95.5% for all three NAATs. Test sensitivities for
C. trachomatis
ranged from 36.1% to 45.7% for culture and among NAATS from 91.4% to 95.8% for PCR to 100% for TMA. Specificities of the NAATs ranged from 95.6% to 98.5% (two-of-three standard) and from 88.8% to 91.8% (three-of-three standard). Over 60% and 80% of gonococcal and chlamydial infections, respectively, among men who have sex with men and over 20% of chlamydial infections in women would have been missed if the rectal site had not been tested. Currently available NAATs are more sensitive for the detection of chlamydial and gonococcal infection at the rectal site than is culture.
Identification of
81
LGxGxxIxW
89
and
171
EDRW
174
Domains from Human Immunodeficiency Virus Type 1 Vif That Regulate APOBEC3G and APOBEC3F Neutralizing Activity
Authors: Dang Ying , Davis Roderick W. , York Ian A. , Zheng Yong-Hui 
Published: March 2010

ABSTRACT

The human cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) potently restrict human immunodeficiency virus type 1 (HIV-1) replication, but they are neutralized by the viral protein Vif. Vif bridges A3G and A3F with a Cullin 5 (Cul5)-based E3 ubiquitin ligase and mediates their proteasomal degradation. This mechanism has been extensively studied, and several Vif domains have been identified that are critical for A3G and A3F neutralization. Here, we identified two additional domains. Via sequence analysis of more than 2,000 different HIV-1 Vif proteins, we identified two highly conserved amino acid sequences,
81
LGxGxSIEW
89
and
171
EDRWN
175
. Within the
81
LGxGxSIEW
89
sequence, residues L81, G82, G84, and, to a lesser extent, I87 and W89 play very critical roles in A3G/A3F neutralization. In particular, residues L81 and G82 determine Vif binding to A3F, residue G84 determines Vif binding to both A3G and A3F, and residues
86
SIEW
89
affect Vif binding to A3F, A3G, and Cul5. Accordingly, this
81
LGxGxSIEW
89
sequence was designated the
81
LGxGxxIxW
89
domain. Within the
171
EDRWN
175
sequence, all residues except N175 are almost equally important for regulation of A3F neutralization, and consistently, they determine Vif binding only to A3F. Accordingly, this domain was designated
171
EDRW
174
. The LGxGxxIxW domain is also partially conserved in simian immunodeficiency virus Vif from rhesus macaques (SIVmac239) and has a similar activity. Thus,
81
LGxGxxIxW
89
and
171
EDRW
174
are two novel functional domains that are very critical for Vif function. They could become new targets for inhibition of Vif activity during HIV replication.
Inhibition of Xenotropic Murine Leukemia Virus-Related Virus by APOBEC3 Proteins and Antiviral Drugs
Authors: Paprotka Tobias , Venkatachari Narasimhan J. , Chaipan Chawaree , Burdick Ryan , Delviks-Frankenberry Krista A. , Hu Wei-Shau , Pathak Vinay K. 
Published: March 2010

ABSTRACT

Xenotropic murine leukemia virus-related virus (XMRV), a gammaretrovirus, has been isolated from human prostate cancer tissue and from activated CD4
+
T cells and B cells of patients with chronic fatigue syndrome, suggesting an association between XMRV infection and these two diseases. Since APOBEC3G (A3G) and APOBEC3F (A3F), which are potent inhibitors of murine leukemia virus and Vif-deficient human immunodeficiency virus type 1 (HIV-1), are expressed in human CD4
+
T cells and B cells, we sought to determine how XMRV evades suppression of replication by APOBEC3 proteins. We found that expression of A3G, A3F, or murine A3 in virus-producing cells resulted in their virion incorporation, inhibition of XMRV replication, and G-to-A hypermutation of the viral DNA with all three APOBEC3 proteins. Quantitation of A3G and A3F mRNAs indicated that, compared to the human T-cell lines CEM and H9, prostate cell lines LNCaP and DU145 exhibited 50% lower A3F mRNA levels, whereas A3G expression in 22Rv1, LNCaP, and DU145 cells was nearly undetectable. XMRV proviral genomes in LNCaP and DU145 cells were hypermutated at low frequency with mutation patterns consistent with A3F activity. XMRV proviral genomes were extensively hypermutated upon replication in A3G/A3F-positive T cells (CEM and H9), but not in A3G/A3F-negative cells (CEM-SS). We also observed that XMRV replication was susceptible to the nucleoside reverse transcriptase (RT) inhibitors zidovudine (AZT) and tenofovir and the integrase inhibitor raltegravir. In summary, the establishment of XMRV infection in patients may be dependent on infection of A3G/A3F-deficient cells, and cells expressing low levels of A3G/A3F, such as prostate cancer cells, may be ideal producers of infectious XMRV. Furthermore, the anti-HIV-1 drugs AZT, tenofovir, and raltegravir may be useful for treatment of XMRV infection.
High-Resolution Cryo-Electron Microscopy Structures of Murine Norovirus 1 and Rabbit Hemorrhagic Disease Virus Reveal Marked Flexibility in the Receptor Binding Domains
Authors: Katpally Umesh , Voss Neil R. , Cavazza Tommaso , Taube Stefan , Rubin John R. , Young Vivienne L. , Stuckey Jeanne , Ward Vernon K. , Virgin Herbert W. , Wobus Christiane E. , Smith Thomas J. 
Published: March 2010

ABSTRACT
Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to ∼8-Å resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions.
“Resistance” to PSC-RANTES Revisited: Two Mutations in Human Immunodeficiency Virus Type 1 HIV-1
SF162
or Simian-Human Immunodeficiency Virus SHIV
SF162-p3
Do Not Confer Resistance
Authors: Nedellec Rebecca , Coetzer Mia , Lederman Michael M. , Offord Robin E. , Hartley Oliver , Mosier Donald E. 
Published: March 2010

ABSTRACT

Resistance of human immunodeficiency virus type 1 (HIV-1) to small-molecule CCR5 inhibitors is well demonstrated, but resistance to macromolecular CCR5 inhibitors (e.g., PSC-RANTES) that act by both CCR5 internalization and receptor blockade had not been reported until recently (3). The report of a single simian-human immunodeficiency virus SHIV
SF162-p3
variant with one V3 and one gp41 sequence change in gp160 that conferred both altered replicative fitness and resistance to PSC-RANTES was therefore surprising. We introduced the same two mutations into both the parental HIV-1
SF162
and the macaque-adapted SHIV
SF162-p3
and found minor differences in entry fitness but no changes in sensitivity to inhibition by either PSC-RANTES or the small-molecule allosteric inhibitor TAK-779. We attribute the earlier finding to confounding fitness effects with inhibitor sensitivity.
Role of Annexin A2 in the Production of Infectious Hepatitis C Virus Particles
Authors: Backes Perdita , Quinkert Doris , Reiss Simon , Binder Marco , Zayas Margarita , Rescher Ursula , Gerke Volker , Bartenschlager Ralf , Lohmann Volker 
Published: March 2010

ABSTRACT
Hepatitis C virus (HCV) is an important human pathogen affecting 170 million chronically infected individuals. In search for cellular proteins involved in HCV replication, we have developed a purification strategy for viral replication complexes and identified annexin A2 (ANXA2) as an associated host factor. ANXA2 colocalized with viral nonstructural proteins in cells harboring genotype 1 or 2 replicons as well as in infected cells. In contrast, we found no obvious colocalization of ANXA2 with replication sites of other positive-strand RNA viruses. The silencing of ANXA2 expression showed no effect on viral RNA replication but resulted in a significant reduction of extra- and intracellular virus titers. Therefore, it seems likely that ANXA2 plays a role in HCV assembly rather than in genome replication or virion release. Colocalization studies with individually expressed HCV nonstructural proteins indicated that NS5A specifically recruits ANXA2, probably by an indirect mechanism. By the deletion of individual NS5A subdomains, we identified domain III (DIII) as being responsible for ANXA2 recruitment. These data identify ANXA2 as a novel host factor contributing, with NS5A, to the formation of infectious HCV particles.
DifferentIn VivoEffects of HIV-1 Immunodominant Epitope-Specific Cytotoxic T Lymphocytes on Selection of Escape Mutant Viruses
Authors: Koizumi Hirokazu , Hashimoto Masao , Fujiwara Mamoru , Murakoshi Hayato , Chikata Takayuki , Borghan Mohamed Ali , Hachiya Atsuko , Kawashima Yuka , Takata Hiroshi , Ueno Takamasa , Oka Shinichi , Takiguchi Masafumi 
Published: March 2010

ABSTRACTHIV-1 escape mutants are well known to be selected by immune pressure via HIV-1-specific cytotoxic T lymphocytes (CTLs) and neutralizing antibodies. The ability of the CTLs to suppress HIV-1 replication is assumed to be associated with the selection of escape mutants from the CTLs. Therefore, we first investigated the correlation between the ability of HLA-A*1101-restricted CTLs recognizing immunodominant epitopesin vitroand the selection of escape mutants. The result showed that there was no correlation between the ability of these CTLs to suppress HIV-1 replicationin vitroand the appearance of escape mutants. The CTLs that had a strong ability to suppress HIV-1 replicationin vitrobut failed to select escape mutants expressed a higher level of PD-1in vivo, whereas those that had a strong ability to suppress HIV-1 replicationin vitroand selected escape mutants expressed a low level of PD-1.Ex vivoanalysis of these CTLs revealed that the latter CTLs had a significantly stronger ability to recognize the epitope than the former ones. These results suggest that escape mutations are selected by HIV-1-specific CTLs that have a stronger ability to recognize HIV-1in vivobut notin vitro.
A pilot study evaluating an intervention designed to raise awareness of clinical trials among potential participants in the developing world
Authors: Dhai Ames , Etheredge Harriet , Cleaton-Jones Peter 
Published: March 2010

BackgroundThis pilot study evaluated the speaking book ‘What it means to be part of a clinical trial’. The book aims at empowering populations with information on their rights and responsibilities when enrolled in clinical research. Wide publication of the book—at significant cost—is anticipated. It is important that the book is evaluated within the communities for whom it is intended, and the necessary changes (if any) are made, before translation and large-scale publication takes place.ObjectiveThe objective of the study was to measure the efficacy and ease of use of the book.MethodsParticipants were recruited from a catering company. Participants were questioned on their knowledge of clinical trials and were then given the book. Instructions for use of the book were given to one group (‘experimental’ group). The other group (‘control’ group) was not given any instructions. A week later, the investigators returned, repeated the knowledge questions and asked ‘ease of use’ questions.ResultsA two-way repeated measure of covariants showed a statistically significant positive increase in knowledge of clinical trials among the intervention group (p=0.02). Results for the control group displayed trends that were not statistically significant. Percentage analysis of ‘ease of use’ questions proved that the book is easy to use, although some changes would be beneficial.ConclusionThis study revealed that the speaking book is easy to use. It significantly increased knowledge of clinical trials among the study sample if instructions on use of the book were provided.
Do strong value-based attitudes influence estimations of future events?: Table 1
Authors: Juth Niklas , Lynöe Niels 
Published: March 2010

The purpose of the present study was to examine whether or not strong values might influence physicians' estimations of future events. In an empirical study about physicians' attitudes towards physician assisted suicide (PAS) we asked about the physicians' main reasons for being pro, doubtful or contra PAS and also asked them to estimate what would happen with patients' trust if PAS were to be legally accepted in Swedish society. Finally we asked the physicians about their own trust in healthcare in the event of PAS being legally accepted.We found that in contrast to those who were pro PAS and doubtful, the group who were against PAS did not discriminate between their own opinion and their estimation of what they thought might happen with patients' trust in the future.Against the backdrop of the present study, we present a hypothesis maintaining that feeling strongly against controversial medical procedures is associated with being inclined to let one's own beliefs influence our capacity to interpret and estimate empirical results. We think this hypothesis merits closer examination.
A survey and analysis of electronic business document standards
Authors: Kabak Yildiray , Dogac Asuman 
Published: March 2010

No document standard is sufficient for all purposes because the requirements significantly differ among businesses, industries, and geopolitical regions. On the other hand, the ultimate aim of business document interoperability is to exchange business data among partners without any prior agreements related to the document syntax and semantics. Therefore, an important characteristic of a document standard is its ability to adapt to different contexts, its extensibility, and its customization. The UN/CEFACT Core Component Technical Specification (CCTS) is an important landmark in this direction.
In this article, we present a survey and an analysis of some of the prominent UN/CEFACT CCTS-based electronic document standards. We describe their document design principles and discuss how they handle customization and extensibility. We address their industry relevance and the recent efforts for their harmonization and convergence. We conclude by mentioning some emerging efforts for the semantic interoperability of different document standards.
Evaluation of Left Atrial Lesions After Initial and Repeat Atrial Fibrillation Ablation
Authors: Badger Troy J. , Daccarett Marcos , Akoum Nazem W. , Adjei-Poku Yaw A. , Burgon Nathan S. , Haslam Thomas S. , Kalvaitis Saul , Kuppahally Suman , Vergara Gaston , McMullen Lori , Anderson Paul A. , Kholmovski Eugene , MacLeod Rob S. , Marrouche Nassir F. 
Published: March 2010

Background—
We evaluated scar lesions after initial and repeat catheter ablation of atrial fibrillation (AF) and correlated these regions to low-voltage tissue on repeat electroanatomic mapping. We also identified gaps in lesion sets that could be targeted and closed during repeat procedures.

Methods and Results—

One hundred forty-four patients underwent AF ablation and received a delayed-enhancement MRI at 3 months after ablation. The number of pulmonary veins (PV) with circumferential lesions were assessed and correlated with procedural outcome. Eighteen patients with AF recurrence underwent repeat ablation. MRI scar regions were compared with electroanatomic maps during the repeat procedure. Regions of incomplete scar around the PVs were then identified and targeted during repeat ablation to ensure complete circumferential lesions. After the initial procedure, complete circumferential scarring of all 4 PV antrum (PVA) was achieved in only 7% of patients, with the majority of patients (69%) having <2 completely scarred PVA. After the first procedure, the number of PVs with complete circumferential scarring and total left atrial wall (LA) scar burden was associated with better clinical outcome. Patients with successful AF termination had higher average total left atrial wall scar of 16.4%±9.8 (
P
=0.004) and percent PVA scar of 66.2±25.4 (
P
=0.01) compared with patients with AF recurrence who had an average total LA wall scar 11.3%±8.1 and PVA percent scar 50.0±24.7. In patients who underwent repeat ablation, the PVA scar percentage was 56.1%±21.4 after the first procedure compared with 77.2%±19.5 after the second procedure. The average total LA scar after the first ablation was 11.0%±4.1, whereas the average total LA scar after second ablation was 21.2%±7.4. All patients had an increased number of completely scarred pulmonary vein antra after the second procedure. MRI scar after the first procedure and low-voltage regions on electroanatomic mapping obtained during repeat ablation demonstrated a positive quantitative correlation of
R
2
=0.57.

Conclusions—
Complete circumferential PV scarring difficult to achieve but is associated with better clinical outcome. Delayed-enhancement MRI can accurately define scar lesions after AF ablation and can be used to target breaks in lesion sets during repeat ablation.
The Hebrew Consecutive Wāw as a North West Semitic “Augment”: A Typological Comparison with Indo-European
Authors: Wikander Ola 
Published: March 2010

AbstractThe classical problem of the Hebrew consecutive tenses is here attacked from a different angle: that of comparative language typology. The article explores parallel typological developments between West Semitic and early Indo-European as pertains to the creation of verbal forms by means of adding an “augment” or temporalizing particle to otherwise Aktionsart- or aspect-based morphological constructs. A typological comparison between the consecutive Wāw and the Indo-European augment is used to highlight some of the factors which may have been involved in the genesis of the consecutive forms, as well as to illustrate some of the typological similarities in verbal syntax in the two phyla.
A Philological Approach to the Problem of King So (2 Kgs 17:4)
Authors: Kang Seung Il 
Published: March 2010

AbstractThis paper supports Kitchen’s identification of with Osorkon IV and supplements it with philological details. The results of this study, however, demand a modification of Kitchen’s suggestion by proposing that the Hebrew word should be seen as a transcription of s3-r in Osorkon’s name w3-s3-r-kn, and not just of s3.
The Duplicity of the Theoretical: On Heidegger’s First Freiburg Lectures
Authors: Gasché Rodolphe 
Published: March 2010

AbstractAt first sight, “theory” does not seem to be a major issue in Heidegger’s thought. Yet, as his early Freiburg lectures from 1919 demonstrate, Heidegger’s development of a phenomenological method of his own required a systematic debate with the neo-Kantians and the philosophical privilege they accorded to theoretization. While laying the foundation for a phenomenological method whose prime object is the lived experience of the surrounding world, Heidegger sketches out a double concept of theorization, one which, through a process of successive stages of un-living, culminates in the objectified conception of an empty “something,” and another concept of theoretization for which the “something” is “the experienceable in general,” and which guides the a-theoretical encounter of phenomenology as an “archontic form of life” with the world, the other, and the “not yet.”
The Endangerment of Moses: Towards a New Reading of Exodus 4:24-26
Authors: Embry B. 
Published: March 2010

AbstractMoses’ endangerment in Exodus 4:24-26 in which Yahweh sought to kill him has perplexed scholarship as to its rationale: why kill Moses, the one chosen to deliver Israel out of slavery? Scholarly responses to this pericope tend to identify causality for Moses’ endangerment that is both Moses’ doing and external to the call and journey. The following article suggests that Moses’ endangerment is a formalized rite of passage which is part of a wider, literary unit. As such, Moses is endangered precisely because he has undertaken this journey and for no other reason; his jeopardy is both internal to the narrative and a functional component of his mission. The paper proposes that this wider, literary unit is also the framework around which the story of Balaam’s journey in Numbers 22 is built. As such, Exodus 4 and Numbers 22 are read, and best understood, in conversation with one another.
Poetic Line Structure in Qoheleth 3:1
Authors: Tod Linafelt , Dobbs-Allsopp F. W. 
Published: March 2010

AbstractIn this note we argue for understanding Qoh 3:1 as verse (the opening to the poem that follows in 3:2-8) and consider possible lineation options, proposing in the process a new way of under-standing its structure as a couplet. With only limited and erratic early manuscript evidence for lineation and no explicit, contemporary comment on this topic, the line structure of biblical Hebrew poems will always be in need of (re)construction. The exercise undertaken here exemplifies the kind of (re)constructive endeavor we believe necessary for thinking seriously about line structure in biblical verse.
Restructuring the Public Sphere for Social Order in the Niger Delta through Polycentric Planning: What Lessons for Africa?
Authors: Akinola Dr. Samson Ranti 
Published: March 2010

AbstractThe increasing deprivation, neglect and orchestrated politics of exclusion by the Nigerian-state against the people of the Niger Delta can be traced to the structurally-defective and centralized governance arrangements in the Niger Delta. The consequent stiff resistance, violent reactions, militancy and hostage taking triggered by this politics of exclusion in the region have confirmed that people matter in politics. This paper argues that in some ways, the weakness of centralized and structurally-defective governance in the Niger Delta provides an opportunity for community self-governing institutions to play the role that governments and their agencies have abandoned. Using the Institutional Analysis and Development (IAD) framework, this paper engages in problem solving and solution seeking strategies that could help restructure the public sphere in the Niger Delta. This paper demonstrates principles and practices needed to make polycentric planning, self-governance and adaptive development strategies resolve socio-economic and political crisis. It is in light of this exigency that this paper develops an African Public Sphere Restructuring Model (APSRM) that derives inspirations and workability mechanisms from twelve (12) African development models that cut across several sectors of the economy in the Niger Delta.