bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrinsic limb morpho‐dynamics and the early development of interlimb coordination of walking in a quadrupedal primate
Authors: Druelle F. , Berillon G. , Aerts P. 
Published: December 2016

AbstractWe question the developmental changes of the temporal aspects of quadrupedal walking and how these relate to the intrinsic morphological (size, shape) and dynamical (inertia) properties of the limbs and body. Indeed, during ontogeny of altricial species, a dependent infant develops toward autonomy. Interlimb coordination is likely to be mediated by the neurological system (central pattern generators and/or supraspinal control), whereas the mechanical parameters of limbs and body appear to influence the locomotor optimization of gaits. We studied six captive baboons at two instants in their development, when they just begin foraging independently and when they are autonomous, in order to collect, in parallel, morphometrics and temporal parameters of voluntary quadrupedal walking. The natural pendular period (NPP) is put forward to represent the limb's intrinsic morpho‐dynamics; the position of the body center of mass as the morpho‐dynamics of the body. The main results reveal that fore‐ and hindlimbs, at the level of the convergence of the NPP, have a significant and positive impact on the interlimb coordination pattern. This probably facilitates, very early in development, the control of the coordination. Nevertheless, because an improved control of the interlimb coordination points at a proceeding neuromotor maturation as well, neuromotor control appears to become gradually important relatively to the intrinsic morpho‐dynamics of the limbs during infancy. These findings are of importance in the context of the evolution of the locomotor developmental processes in primates.
Early deterioration of iron status among a cohort of Bolivian infants
Authors: Burke Rachel M. , Rebolledo Paulina A. , Fabiszewski de Aceituno Anna M. , Revollo Rita , Iñiguez Volga , Klein Mitchel , Drews‐Botsch Carolyn , Leon Juan S. , Suchdev Parminder S. 
Published: December 2016

AbstractIron deficiency (ID) and iron deficiency anemia (IDA) are major contributors to infant and maternal morbidity worldwide. There is limited longitudinal data on iron status in young infants and on methods to adjust iron biomarkers for inflammation. We aimed to quantify the prevalence of inflammation‐adjusted ID, anemia, and IDA over the first year in a cohort of Bolivian infants and their mothers. Healthy mother‐infant dyads were recruited from two peri‐urban hospitals. Infants provided three blood draws (2, 6–8, and 12–18 months; N = 160); mothers provided two blood draws (1 and 6–8 months postpartum [plus third anemia measurement at 12–18 months]; N = 250). Blood was analyzed for hemoglobin, ferritin, soluble transferrin receptor, C‐reactive protein (CRP), and alpha(1)‐acid glycoprotein (AGP). Iron biomarkers were adjusted for inflammation using CRP and AGP; hemoglobin cutoffs were adjusted for altitude. Inflammation (elevated CRP or AGP) was 17% among toddlers 12–18 months of age. ID (inflammation‐adjusted ferritin) increased with age (<1%, 56%, and 79% at each blood draw), as did anemia and IDA (anemia: 70%, 76%, and 81%; IDA: <1%, 46%, and 68%). Maternal ID declined from the first to second assessment (39% vs. 27%). Inflammation‐adjusted ID prevalence was up to 15 percentage points higher than unadjusted estimates. The high prevalence of ID, anemia, and IDA in this cohort of Bolivian infants beginning at 6–8 months of age suggests that early interventions may be necessary in vulnerable populations.
Fusarium species causing eumycetoma: Report of two cases and comprehensive review of the literature
Authors: Al‐Hatmi Abdullah M. S. , Bonifaz Alexandro , Tirado‐Sánchez Andrés , Meis Jacques F. , de Hoog G. Sybren , Ahmed Sarah A. 
Published: December 2016

SummaryRecently, mycetoma was added to the World Health Organization's list of neglected tropical disease priorities. Fusarium as a genus has been reported to cause eumycetoma, but little is known about the species involved in this infection and their identification. In this study, molecular tools were applied to identify Fusarium agents from human eumycetoma cases. The partial translation elongation factor 1‐alpha (TEF‐1α) gene was used as diagnostic parameter. Two additional cases of eumycetoma, due to F. keratoplasticum and F. pseudensiforme, respectively, are presented. A systematic literature review was performed to assess general features, identification, treatment and outcome of eumycetoma infections due to Fusarium species. Of the 20 reviewed patients, the majority (75%) were male. Most agents belonged to the F. solani species complex, ie F. keratoplasticum, F. pseudensiforme, and an undescribed lineage of F. solani. In addition, F. thapsinum, a member of Fusarium fujikuroi species complex was encountered. The main antifungal drugs used were itraconazole, ketoconazole and amphotericin B, but cure rates were low (15%). Partial response or relapse was observed in some cases, and a case ended in amputation. Clinical management of eumycetoma due to Fusarium is complex and combination therapy might be required to increase cure rates.
Solanum tuberosum ZPR1 encodes a light‐regulated nuclear DNA‐binding protein adjusting the circadian expression of StBBX24 to light cycle
Authors: Kiełbowicz‐Matuk Agnieszka , Czarnecka Jagoda , Banachowicz Ewa , Rey Pascal , Rorat Tadeusz 
Published: December 2016

AbstractZPR1 proteins belong to the C4‐type of zinc finger coordinators known in animal cells to interact with other proteins and participate in cell growth and proliferation. In contrast, the current knowledge regarding plant ZPR1 proteins is very scarce. Here, we identify a novel potato nuclear factor belonging to this family and named StZPR1. StZPR1 is specifically expressed in photosynthetic organs during the light period, and the ZPR1 protein is located in the nuclear chromatin fraction. From modelling and experimental analyses, we reveal the StZPR1 ability to bind the circadian DNA cis motif ‘CAACAGCATC’, named CIRC and present in the promoter of the clock‐controlled double B‐box StBBX24 gene, the expression of which peaks in the middle of the day. We found that transgenic lines silenced for StZPR1 expression still display a 24 h period for the oscillation of StBBX24 expression but delayed by 4 h towards the night. Importantly, other BBX genes exhibit altered circadian regulation in these lines. Our data demonstrate that StZPR1 allows fitting of the StBBX24 circadian rhythm to the light period and provide evidence that ZPR1 is a novel clock‐associated protein in plants necessary for the accurate rhythmic expression of specific circadian‐regulated genes.
Mechanism for Missing Data Incorporated in Joint Modelling of Ordinal Responses
Authors: Ivanova Anna , Molenberghs Geert , Verbeke Geert 
Published: December 2016

SummaryWe analyse the problem of two clinically inseparable, repeatedly measured responses of ordinal type by also incorporating their missingness process. In our application these are the therapeutic effect and extent of side effects of fluvoxamine. In the case of a composite end point, the scientific questions addressed can be answered only when the responses are modelled jointly. As an extension of the methodology, several missingness not at random models were fitted to a set of observed data and shown to yield approximately the same result as their missingness at random counterparts, although it affects precision. In addition, the effect of various identifying restrictions on multiple imputation is investigated. An alternative numerical approximation method is suggested to reduce computational time.
A Meta‐Synthesis of Children's Experiences of Postoperative Pain Management
Authors: Sng Qian Wen , He Hong‐Gu , Wang Wenru , Taylor Beverley , Chow Aloysius , Klainin‐Yobas Piyanee , Zhu Lixia 
Published: December 2016

ABSTRACTBackgroundIneffective management of postoperative pain in children has been reported widely. To improve the effectiveness of postoperative pain management for children, it was necessary to conduct a systematic review to better understand the current knowledge of children's experiences of their postoperative pain management.AimsThe aim of this review was to update and synthesize current qualitative research of postoperative pain management based on children's experiences.MethodsQualitative studies published between January 1990 and July 2014 were searched from the electronic databases of CINAHL, MEDLINE, MedNar, ProQuest, PsycINFO, Scopus, ScienceDirect, Sociological Abstracts, and Web of Science. A broad range of search keywords and a three‐step search strategy were used. Meta‐syntheses were used to summarize the findings from the included studies.ResultsNine qualitative studies were included. Three meta‐syntheses from 22 categories based on 72 findings were generated: (a) Children experienced various negative emotions related to postoperative pain, and could assess and express their pain but need their parents as advocates; (b) apart from pain medication, various nonpharmacological strategies to relieve children's postoperative pain were employed by children, parents, and nurses; and (c) suggestions from children for their parents and nurses to better relieve postoperative pain.Linking Evidence to ActionThis review provided preliminary support for increasing the provision of information and education for children and their parents about postoperative conditions, pain, and pain relief strategies. Nurses should also be encouraged to employ more nonpharmacological pain‐relieving strategies and build rapport with children and their parents. Future intervention studies are needed to improve children's postoperative experiences.
Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing
Authors: Nieto-Aponte Leonardo , Quer Josep , Ruiz-Ripa Alicia , Tabernero David , Gonzalez Carolina , Gregori Josep , Vila Marta , Asensio Miriam , Garcia-Cehic Damir , Ruiz Gerardo , Chen Qian , Ordeig Laura , Llorens Meritxell , Saez Montserrat , Esteban Juan I. , Esteban Rafael , Buti Maria , Pumarola Tomas , Rodriguez-Frias Francisco 
Published: December 2016

ABSTRACT
The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by transferring non-1a/1b samples to a center where HRCS is available, if further characterization is needed.
High-Throughput Next-Generation Sequencing of Polioviruses
Authors: Montmayeur Anna M. , Ng Terry Fei Fan , Schmidt Alexander , Zhao Kun , Magaña Laura , Iber Jane , Castro Christina J. , Chen Qi , Henderson Elizabeth , Ramos Edward , Shaw Jing , Tatusov Roman L. , Dybdahl-Sissoko Naomi , Endegue-Zanga Marie Claire , Adeniji Johnson A. , Oberste M. Steven , Burns Cara C. 
Published: December 2016

ABSTRACT
The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance.
Toll-Like Receptor 2 Ligation Enhances HIV-1 Replication in Activated CCR6
+
CD4
+
T Cells by Increasing Virus Entry and Establishing a More Permissive Environment to Infection
Authors: Bolduc Jean-François , Ouellet Michel , Hany Laurent , Tremblay Michel J. 
Published: December 2016

ABSTRACT

In this study, we investigated the effect of Toll-like receptor 2 (TLR2) ligation on the permissiveness of activated CD4
+
T cells to HIV-1 infection by focusing our experiments on the relative susceptibility of cell subsets based on their expression of CCR6. Purified primary human CD4
+
T cells were first subjected to a CD3/CD28 costimulation before treatment with the TLR2 agonist Pam3CSK4. Finally, cells were inoculated with R5-tropic HIV-1 particles that permit us to study the effect of TLR2 triggering on virus production at both population and single-cell levels. We report here that HIV-1 replication is augmented in CD3/CD28-costimulated CCR6
+
CD4
+
T cells upon engagement of the cell surface TLR2. Additional studies indicate that a higher virus entry and polymerization of the cortical actin are seen in this cell subset following TLR2 stimulation. A TLR2-mediated increase in the level of phosphorylated NF-κB p65 subunit was also detected in CD3/CD28-costimulated CCR6
+
CD4
+
T cells. We propose that, upon antigenic presentation, an engagement of TLR2 acts specifically on CCR6
+
CD4
+
T cells by promoting virus entry in an intracellular milieu more favorable for productive HIV-1 infection.

IMPORTANCE
Following primary infection, HIV-1 induces an immunological and structural disruption of the gut mucosa, leading to bacterial translocation and release of microbial components in the bloodstream. These pathogen-derived constituents include several agonists of Toll-like receptors that may affect gut-homing CD4
+
T cells, such as those expressing the chemokine receptor CCR6, which are highly permissive to HIV-1 infection. We demonstrate that TLR2 ligation in CD3/CD28-costimulated CCR6
+
CD4
+
T cells leads to enhanced virus production. Our results highlight the potential impact of bacterial translocation on the overall permissiveness of CCR6
+
CD4
+
T cells to productive HIV-1 infection.
Increasing Type 1 Poliovirus Capsid Stability by Thermal Selection
Authors: Adeyemi Oluwapelumi O. , Nicol Clare , Stonehouse Nicola J. , Rowlands David J. 
Published: December 2016

ABSTRACT
Poliomyelitis is a highly infectious disease caused by poliovirus (PV). It can result in paralysis and may be fatal. Integrated global immunization programs using live-attenuated oral (OPV) and/or inactivated (IPV) PV vaccines have systematically reduced its spread and paved the way for eradication. Immunization will continue posteradication to ensure against reintroduction of the disease, but there are biosafety concerns for both OPV and IPV. They could be addressed by the production and use of virus-free virus-like particle (VLP) vaccines that mimic the “empty” capsids (ECs) normally produced in viral infection. Although ECs are antigenically indistinguishable from mature virus particles, they are less stable and readily convert into an alternative conformation unsuitable for vaccine purposes. Stabilized ECs, expressed recombinantly as VLPs, could be ideal candidate vaccines for a polio-free world. However, although genome-free PV ECs have been expressed as VLPs in a variety of systems, their inherent antigenic instability has proved a barrier to further development. In this study, we selected thermally stable ECs of type 1 PV (PV-1). The ECs are antigenically stable at temperatures above the conversion temperature of wild-type (wt) virions. We have identified mutations on the capsid surface and in internal networks that are responsible for EC stability. With reference to the capsid structure, we speculate on the roles of these residues in capsid stability and postulate that such stabilized VLPs could be used as novel vaccines.

IMPORTANCE
Poliomyelitis is a highly infectious disease caused by PV and is on the verge of eradication. There are biosafety concerns about reintroduction of the disease from current vaccines that require live virus for production. Recombinantly expressed virus-like particles (VLPs) could address these inherent problems. However, the genome-free capsids (ECs) of wt PV are unstable and readily change antigenicity to a form not suitable as a vaccine. Here, we demonstrate that the ECs of type 1 PV can be stabilized by selecting heat-resistant viruses. Our data show that some capsid mutations stabilize the ECs and could be applied as candidates to synthesize stable VLPs as future genome-free poliovirus vaccines.
Structural Insights into Reovirus σ1 Interactions with Two Neutralizing Antibodies
Authors: Dietrich Melanie H. , Ogden Kristen M. , Katen Sarah P. , Reiss Kerstin , Sutherland Danica M. , Carnahan Robert H. , Goff Matthew , Cooper Tracy , Dermody Terence S. , Stehle Thilo 
Published: December 2016

ABSTRACT
Reovirus attachment protein σ1 engages glycan receptors and junctional adhesion molecule-A (JAM-A) and is thought to undergo a conformational change during the proteolytic disassembly of virions to infectious subvirion particles (ISVPs) that accompanies cell entry. The σ1 protein is also the primary target of neutralizing antibodies. Here, we present a structural and functional characterization of two neutralizing antibodies that target σ1 of serotype 1 (T1) and serotype 3 (T3) reoviruses. The crystal structures revealed that each antibody engages its cognate σ1 protein within the head domain via epitopes distinct from the JAM-A-binding site. Surface plasmon resonance and cell-binding assays indicated that both antibodies likely interfere with JAM-A engagement by steric hindrance. To define the interplay between the carbohydrate receptor and antibody binding, we conducted hemagglutination inhibition assays using virions and ISVPs. The glycan-binding site of T1 σ1 is located in the head domain and is partly occluded by the bound Fab in the crystal structure. The T1-specific antibody inhibited hemagglutination by virions and ISVPs, probably via direct interference with glycan engagement. In contrast to T1 σ1, the carbohydrate-binding site of T3 σ1 is located in the tail domain, distal to the antibody epitope. The T3-specific antibody inhibited hemagglutination by T3 virions but not ISVPs, indicating that the antibody- and glycan-binding sites in σ1 are in closer spatial proximity on virions than on ISVPs. Our results provide direct evidence for a structural rearrangement of σ1 during virion-to-ISVP conversion and contribute new information about the mechanisms of antibody-mediated neutralization of reovirus.

IMPORTANCE
Virus attachment proteins mediate binding to host cell receptors, serve critical functions in cell and tissue tropism, and are often targeted by the neutralizing antibody response. The structural investigation of antibody-antigen complexes can provide valuable information for understanding the molecular basis of virus neutralization. Studies with enveloped viruses, such as HIV and influenza virus, have helped to define sites of vulnerability and guide vaccination strategies. By comparison, less is known about antibody binding to nonenveloped viruses. Here, we structurally investigated two neutralizing antibodies that bind the attachment protein σ1 of reovirus. Furthermore, we characterized the neutralization efficiency, the binding affinity for σ1, and the effect of the antibodies on reovirus receptor engagement. Our analysis defines reovirus interactions with two neutralizing antibodies, allows us to propose a mechanism by which they block virus infection, and provides evidence for a conformational change in the σ1 protein during viral cell entry.