bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Bean Pod Mottle Virus RNA2-Encoded 58-Kilodalton Protein P58 Is Required in
cis
for RNA2 Accumulation
Authors: Lin Junyan , Guo Jiangbo , Finer John , Dorrance Anne E. , Redinbaugh Margaret G. , Qu Feng 
Published: January 2014

ABSTRACT

Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus in the
Secoviridae
family. Its RNA1 encodes proteins required for genome replication, whereas RNA2 primarily encodes proteins needed for virion assembly and cell-to-cell movement. However, the function of a 58-kDa protein (P58) encoded by RNA2 has not been resolved. P58 and the movement protein (MP) of BPMV are two largely identical proteins differing only at their N termini, with P58 extending MP upstream by 102 amino acid residues. In this report, we unveil a unique role for P58. We show that BPMV RNA2 accumulation in infected cells was abolished when the start codon of P58 was eliminated. The role of P58 does not require the region shared by MP, as RNA2 accumulation in individual cells remained robust even when most of the MP coding sequence was removed. Importantly, the function of P58 required the P58 protein, rather than its coding RNA, as compensatory mutants could be isolated that restored RNA2 accumulation by acquiring new start codons upstream of the original one. Most strikingly, loss of P58 function could not be complemented by P58 provided in
trans
, suggesting that P58 functions in
cis
to selectively promote the accumulation of RNA2 copies that encode a functional P58 protein. Finally, we found that all RNA1-encoded proteins are
cis
-acting relative to RNA1. Together, our results suggest that P58 probably functions by recruiting the RNA1-encoded polyprotein to RNA2 to enable RNA2 reproduction.

IMPORTANCE
Bean pod mottle virus (BPMV) is one of the most important pathogens of the crop plant soybean, yet its replication mechanism is not well understood, hindering the development of knowledge-based control measures. The current study examined the replication strategy of BPMV RNA2, one of the two genomic RNA segments of this virus, and established an essential role for P58, one of the RNA2-encoded proteins, in the process of RNA2 replication. Our study demonstrates for the first time that P58 functions preferentially with the very RNA from which it is translated, thus greatly advancing our understanding of the replication mechanisms of this and related viruses. Furthermore, this study is important because it provides a potential target for BPMV-specific control, and hence could help to mitigate soybean production losses caused by this virus.
Toll-Like Receptor 7/8 (TLR7/8) and TLR9 Agonists Cooperate To Enhance HIV-1 Envelope Antibody Responses in Rhesus Macaques
Authors: Moody M. Anthony , Santra Sampa , Vandergrift Nathan A. , Sutherland Laura L. , Gurley Thaddeus C. , Drinker Mark S. , Allen Ashley A. , Xia Shi-Mao , Meyerhoff R. Ryan , Parks Robert , Lloyd Krissey E. , Easterhoff David , Alam S. Munir , Liao Hua-Xin , Ward Brandy M. , Ferrari Guido , Montefiori David C. , Tomaras Georgia D. , Seder Robert A. , Letvin Norman L. , Haynes Barton F. 
Published: January 2014

ABSTRACTThe development of a vaccine that can induce high titers of functional antibodies against HIV-1 remains a high priority. We have developed an adjuvant based on an oil-in-water emulsion that incorporates Toll-like receptor (TLR) ligands to test whether triggering multiple pathogen-associated molecular pattern receptors could enhance immunogenicity. Compared to single TLR agonists or other pairwise combinations, TLR7/8 and TLR9 agonists combined were able to elicit the highest titers of binding, neutralizing, and antibody-dependent cellular cytotoxicity-mediating antibodies against the protein immunogen, transmitted/founder HIV-1 envelope gp140 (B.63521). We further found that the combination of TLR7/8 and TLR9 agonists was associated with the release of CXCL10 (IP-10), suggesting that this adjuvant formulation may have optimally stimulated innate and adaptive immunity to elicit high titers of antibodies.IMPORTANCECombining TLR agonists in an adjuvant formulation resulted in higher antibody levels compared to an adjuvant without TLR agonists. Adjuvants that combine TLR agonists may be useful for enhancing antibody responses to HIV-1 vaccines.
HLA-B*57 Elite Suppressor and Chronic Progressor HIV-1 Isolates Replicate Vigorously and Cause CD4
+
T Cell Depletion in Humanized BLT Mice
Authors: Salgado Maria , Swanson Michael D. , Pohlmeyer Christopher W. , Buckheit Robert W. , Wu Jin , Archin Nancie M. , Williams Thomas M. , Margolis David M. , Siliciano Robert F. , Garcia J. Victor , Blankson Joel N. 
Published: January 2014

ABSTRACT

Elite controllers or suppressors (ES) are HIV-1-infected patients who maintain undetectable viral loads without antiretroviral therapy. The mechanism of control remains unclear, but the HLA-B*57 allele is overrepresented in cohorts of these patients. However, many HLA-B*57 patients develop progressive disease, and some studies have suggested that infection with defective viruses may be the cause of the lack of high levels of virus replication and disease progression in ES. We therefore performed a comprehensive comparative
in vivo
and
in vitro
characterization of viruses isolated from well-defined ES. For this purpose, we first performed full-genome sequence analysis and
in vitro
fitness assays on replication-competent isolates from HLA-B*57 ES and HLA-B*57 chronic progressors (CPs). Under our experimental conditions, we found that isolates from ES and CPs can replicate
in vitro
. However, since inherently these assays involve the use of unnaturally
in vitro
-activated cells, we also investigated the replication competence and pathogenic potential of these HIV isolates
in vivo
using humanized BLT mice. The results from these analyses demonstrate that virus isolates from ES are fully replication competent
in vivo
and can induce peripheral and systemic CD4 T cell depletion. These results provide the first direct
in vivo
evidence that viral fitness does not likely determine clinical outcome in HLA-B*57 patients and that elite suppressors can control replication-competent, fully pathogenic viruses. A better understanding of the immunological bases of viral suppression in ES will serve to inform novel approaches to preventive and therapeutic HIV vaccine design.

IMPORTANCE
Elite suppressors are HIV-1-infected patients who have undetectable levels of viremia despite not being on antiviral drugs. One of the most fundamental questions about this phenomenon involves the mechanism of control. To address this question, we isolated virus from elite suppressors and from HIV-1-infected patients who have the usual progressive disease course. We compared how well the isolates from the two groups of patients replicated in culture and in humanized mice. Our results suggest that elite suppressors are capable of controlling HIV-1 due to the possession of unique host factors rather than infection with defective virus.
Feline Immunodeficiency Virus Envelope Glycoproteins Antagonize Tetherin through a Distinctive Mechanism That Requires Virion Incorporation
Authors: Morrison James H. , Guevara Rebekah B. , Marcano Adriana C. , Saenz Dyana T. , Fadel Hind J. , Rogstad Daniel K. , Poeschla Eric M. 
Published: January 2014

ABSTRACT

BST2/tetherin inhibits the release of enveloped viruses from cells. Primate lentiviruses have evolved specific antagonists (Vpu, Nef, and Env). Here we characterized tetherin proteins of species representing both branches of the order Carnivora. Comparison of tiger and cat (Feliformia) to dog and ferret (Caniformia) genes demonstrated that the tiger and cat share a start codon mutation that truncated most of the tetherin cytoplasmic tail early in the Feliformia lineage (19 of 27 amino acids, including the dual tyrosine motif). Alpha interferon (IFN-α) induced tetherin and blocked feline immunodeficiency virus (FIV) replication in lymphoid and nonlymphoid feline cells. Budding of bald FIV and HIV particles was blocked by carnivore tetherins. However, infectious FIV particles were resistant, and spreading FIV replication was uninhibited. Antagonism mapped to the envelope glycoprotein (Env), which rescued FIV from carnivore tetherin restriction when expressed in
trans
but, in contrast to known antagonists, did not rescue noncognate particles. Also unlike the primate lentiviral antagonists, but similar to the Ebola virus glycoprotein, FIV Env did not reduce intracellular or cell surface tetherin levels. Furthermore, FIV-enveloped FIV particles actually required tetherin for optimal release from cells. The results show that FIV Envs mediate a distinctive tetherin evasion. Well adapted to a phylogenetically ancient tetherin tail truncation in the Felidae, it requires functional virion incorporation of Env, and it shields the budding particle without downregulating plasma membrane tetherin. Moreover, FIV has evolved dependence on this protein: particles containing FIV Env need tetherin for optimal release from the cell, while Env
−
particles do not.

IMPORTANCE
HIV-1 antagonizes the restriction factor tetherin with the accessory protein Vpu, while HIV-2 and the filovirus Ebola use their envelope (Env) glycoproteins for this purpose. It turns out that the FIV tetherin antagonist is also its Env protein, but the mechanism is distinctive. Unlike other tetherin antagonists, FIV Env cannot act in
trans
to rescue
vpu
-deficient HIV-1. It must be incorporated specifically into FIV virions to be active. Also unlike other retroviral antagonists, but similar to Ebola virus Env, it does not act by downregulating or degrading tetherin. FIV Env might exclude tetherin locally or direct assembly to tetherin-negative membrane domains. Other distinctive features are apparent, including evidence that this virus evolved an equilibrium in which tetherin is both restriction factor and cofactor, as FIV requires tetherin for optimal particle release.
Influence of Different Durations of Electroacupuncture Stimulation on Skin Blood Flow and Muscle Blood Volume
Authors: Mori Hidetoshi , Kuge Hiroshi , Tanaka Tim Hideaki , Taniwaki Eiichi 
Published: January 2014

Objective To determine whether skin blood flow (SBF) and muscle blood volume (MBV) responses differ according to the duration of electroacupuncture (EA) stimulation. Methods Two experiments were conducted. In Experiment 1, healthy male students (n=20) were randomly divided into two groups (an EA group and a no-stimulation group). In Experiment 2, healthy male students (n=37) were randomly divided into three groups with different stimulation durations of EA (5, 10 and 15 min). EA stimulation on the quadriceps femoris muscle was administered with a frequency of 1 Hz. SBF and MBV were estimated before, during and after stimulation. Results In Experiment 1 there was a significant difference between the groups (p=0.001). In the EA stimulation group, MBV increased immediately following EA (p=0.045) and 5 min (p=0.005) and 10 min (p=0.002) after EA compared with baseline. No significant change was observed in the no-stimulation group. In Experiment 2 there was no significant difference between the groups. All three stimulation durations (5, 10 and 15 min) yielded increases in MBV after stimulation compared with baseline. SBF following stimulation for 5 and 10 min was increased compared with baseline. Conclusions Based on these findings, we consider that 10 min EA stimulation could be a sufficient duration to induce a blood flow response in a clinical situation when increasing the blood flow is desirable.
Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers
Authors: Ye Ye , Tsui Fuchiang , Wagner Michael , Espino Jessi , Li Qi 
Published: January 2014

Abstract
Objectives To evaluate factors affecting performance of influenza detection, including accuracy of natural language processing (NLP), discriminative ability of Bayesian network (BN) classifiers, and feature selection.
Methods We derived a testing dataset of 124 influenza patients and 87 non-influenza (shigellosis) patients. To assess NLP finding-extraction performance, we measured the overall accuracy, recall, and precision of Topaz and MedLEE parsers for 31 influenza-related findings against a reference standard established by three physician reviewers. To elucidate the relative contribution of NLP and BN classifier to classification performance, we compared the discriminative ability of nine combinations of finding-extraction methods (expert, Topaz, and MedLEE) and classifiers (one human-parameterized BN and two machine-parameterized BNs). To assess the effects of feature selection, we conducted secondary analyses of discriminative ability using the most influential findings defined by their likelihood ratios.
Results The overall accuracy of Topaz was significantly better than MedLEE (with post-processing) (0.78 vs 0.71, p&lt;0.0001). Classifiers using human-annotated findings were superior to classifiers using Topaz/MedLEE-extracted findings (average area under the receiver operating characteristic (AUROC): 0.75 vs 0.68, p=0.0113), and machine-parameterized classifiers were superior to the human-parameterized classifier (average AUROC: 0.73 vs 0.66, p=0.0059). The classifiers using the 17 ‘most influential’ findings were more accurate than classifiers using all 31 subject-matter expert-identified findings (average AUROC: 0.76&gt;0.70, p&lt;0.05).
Conclusions Using a three-component evaluation method we demonstrated how one could elucidate the relative contributions of components under an integrated framework. To improve classification performance, this study encourages researchers to improve NLP accuracy, use a machine-parameterized classifier, and apply feature selection methods.
Sensitisation to mites in a group of patients with asthma in Yaounde, Cameroon: a cross-sectional study
Authors: Pefura-Yone Eric Walter , Kengne André Pascal , Kuaban Christopher 
Published: January 2014

ObjectivesSensitisation of asthmatic patients to mites in sub-Saharan Africa has been less described. The aim of this study was to assess the prevalence and determinants of sensitisation to mites in asthmatic adolescents and adults in Yaounde, Cameroon.DesignThis was a cross-sectional study. Logistic regression models were employed to investigate the determinants of sensitisation to mites.SettingThis study was carried out at the Jamot Hospital and CEDIMER private centre, in Yaounde, capital city of Cameroon.ParticipantsAll asthmatic patients received in consultations from January 2012 to June 2013 and in whom prick-skin tests for perennial aeroallergens were performed were included.Outcome measuresPrevalence of sensitisation to mites and associated factors.ResultsIn total, 201 patients (132 being women, 65.7%), with a median age of 36 (25th–75th centiles: 20–54) years were included, with 135 (67.2%) having a positive skin test for mites. Sensitisation toDermatophagoïdes pteronyssinus,Dermatophagoides farinaeandBlomia tropicaliswas found in 53.2%, 49.8% and 47.8% of the patients, respectively. Intermittent rhinitis (16.3% vs 7.6%) and persistent rhinitis (43.0% vs 22.7%) were more frequent in sensitised patients than in the non-sensitised ones (p<0.010). Independent allergological determinants of sensitisation to mites were sensitisation toAlternaria alternata(adjusted OR 14.98 (95% CIs 1.96 to 114.4)) and sensitisation toBlattella germanica(3.48 (1.34 to 9.00)).ConclusionsSensitisation to mites was found in about two-thirds of asthmatic patients in this setting, with a frequent multiple sensitisations toA alternataandBlattella germanica. Systematically investigating asthmatic patients for mites' sensitisation and determinants will help optimising the care in this setting by combining the aetiological treatment for the allergy with symptomatic treatment for asthma, in order to modify the natural course of the disease.
Investigating the bundle compliance of IVIG delivery in the Greater Manchester Neuroscience centre
Authors: Patel Neena , Woodall Amanda , Gow David 
Published: January 2014

AbstractSalford Royal Hospital is one of the largest users of IVIG for chronic neurological illnesses within the UK. The majority of patients are being treated for chronic inflammatory polyneuropathy and multifocal motor neuropathy. We hypothesised that the components of care being delivered to these patients differed to our stated standard of care (IVIG care bundle). We performed a service review exercise to identify shortcomings and improve quality of patient care. The aim was to measure overall bundle compliance being delivered to 75 patients with a view to improving the overall quality of care being delivered in the future. A retrospective case note study was carried out to measure compliance with the 17 areas of care, which constituted the IVIG bundle. Nine areas of care were being delivered to all 75 patients. This meant that all patients were receiving three monthly bloods, a documented cannula pathway, a filed prescription, a medical assessment, and the correct follow-up. Not all patients had a filed consent form, ECG or HAT assessment and an even smaller number of patients had a documented calculation for the amount of IVIG that needed to be given and few had a serum save. No patient in the group was receiving the intended complete bundle of care.The results led to the development of an electronic treatment dashboard for the delivery of chronic IVIG therapy to this group. A re-audit has shown that rates of individual areas of care being delivered has increased markedly but overall compliance has only increased a slightly due to a lack of serum saves for patients.
Endovascular reconstruction for progressively worsening carotid artery dissection
Authors: Asif Kaiz S , Lazzaro Marc A , Teleb Mohamed S , Fitzsimmons Brian-Fred , Lynch John , Zaidat Osama 
Published: January 2014

BackgroundCarotid artery dissection is an important cause of stroke in young patients. Selection criteria for endovascular repair have not been well defined and limited data exist on long-term outcomes of stent reconstruction.ObjectiveTo report the immediate and long-term clinical and radiographic outcomes of patients treated with stent placement for progressively worsening symptomatic carotid arterial dissection despite antithrombotic therapy.MethodsA single institution neuro-endovascular database was accessed to identify consecutive cases in which carotid artery dissection was treated with endovascular repair between 2006 and 2012. Clinical, demographic, radiographic, and procedural data were obtained through chart review.ResultsA total of 22 patients were identified and included 27 carotid artery dissection repairs with stent implantation. The mean age was 43 years (±8.7) with 13 patients being women. Traumatic dissections were seen in 9 (40.9%) patients and spontaneous dissections in 13 (59.1%) patients. All patients were symptomatic and were started on antithrombotic therapy on diagnosis. Most common indications for treatment included recurrent ischemia despite antithrombotic therapy in 15 (55.5%) arteries and enlarging dissecting aneurysm in 4 (14.8%) arteries. Mean degree of stenosis was 79.1%. Mean number of stents used was 1.88 (range 1–4). There was 1 (4.5%) asymptomatic peri-procedural thromboembolic event. Median clinical follow-up was 14 months (range 3–40) and median imaging follow-up was 14 months (range 3–38). There was 1 (4.5%) case of recurrent transient ischemic attack. There was no death, significant restenosis or stroke in the territory of the treated vessel during the duration of the follow-up.ConclusionsEndovascular stent reconstruction for the treatment of selected patients with progressively worsening carotid dissection despite medical management is feasible with acceptable immediate and long-term clinical and radiographic outcomes. To be able to draw more robust conclusions, further evaluation with larger number of patients and longer follow-up is needed.
Fixed Points of Two‐Degree of Freedom Systems
Authors: Abu-Hilal Mohammed 
Published: January 2014

The presence of fixed points in a frequency response of vibrating systems can greatly complicate the vibration reduction if these points are not recognized. In this paper, the fixed points of two‐degree of freedom systems are studied. The frequencies at which fixed points occur and their amplitudes are determined analytically.In this paper, the fixed points of two‐degree of freedom systems are studied. The frequencies at which fixed points occur and their amplitudes are determined analytically.
Self and Body Esteem Perception in Multiple Sclerosis
Authors: Barak Yoram , Lampl Yair , Sarova-Pinchas Ida , Achiron Anat 
Published: January 2014

Self esteem and body esteem were examined in a group of 35 relapsing‐remitting multiple sclerosis (MS) patients using the Body Esteem Scale (BES) and the Eysenck Self Esteem Scale (ESES) and compared to age and sex matched normal controls.There were 23 females and 12 males in the MS patient’s group; average age 38.9 years (range: 22–52). All participants completed the self‐rated BES evaluating the following subscales: females—sexual attractiveness, physical condition and weight concern; males—physical attractiveness, physical condition and upper body strength. In addition all participants were scored, following a semi‐structured interview, on the ESES. Psychiatric co‐morbidity was excluded using a semi‐structured interview by the consulting psychiatrist. All evaluations were carried out during the remitting phase. Statistical analysis, comparing patients to healthy controls, demonstrated lowered self‐rating of the physical condition (males < 0.05, females < 0.001). On the other hand, no significant differences were found in the physical (male) or sexual (female)—attractiveness subscales. The mean ESES score in the patients group was 23.2 ± 4.0, slightly above the reported average. The controls mean ESES was 28.4 ± 3.6, (P < 0.05). No correlation was found between self and body esteem amongst M.S. patients. This study emphasizes impaired perception of body esteem in multiple sclerosis patients even in remission. The preservation of physical and sexual attractiveness may be related to the non‐disfiguring nature of the disease. Preservation of self‐esteem in MS patients suggests that body‐esteem should be the focus of supportive treatment.
Laser Measurement of Building Vibration and Displacement
Authors: Bougard A.J. , Ellis B.R. 
Published: January 2014

This paper considers four laser systems used by the Building Research Establishment (BRE) to investigate the behaviour of structures. Lasers enable remote measurements of vibration and displacement to be taken where access to a structure is difficult or where fire, explosion or structural collapse creates a hazardous environment. Each system will be described, and its use illustrated using measurements taken on real structures.The four systems are:
1. Laser Interferometer: This is used to measure the velocity of vibration of a structure under ambient loading.
2. 3D‐Laser Survey System: This is used to track the movement of any number of targets on a structure under load.
3. VHS Laser System: This is used to measure displacement of a target moving at high velocities.
4. Tracking Lasers: This is used to track the angular displacements of a target.