bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular phylogeny of Sericostomatoidea (Trichoptera) with the establishment of three new families
Authors: JOHANSON KJELL ARNE , MALM TOBIAS , ESPELAND MARIANNE 
Published: October 2016

AbstractWe inferred the phylogenetic relationships among 58 genera of Sericostomatoidea, representing all previously accepted families as well as genera that were not placed in established families. The analyses were based on five fragments of the protein coding genes carbamoylphosphate synthetase (CPSase of CAD), isocitrate dehydrogenase (IDH), Elongation factor 1a (EF‐1a), RNA polymerase II (POL II) and cytochrome oxidase I (COI). The data set was analysed using Bayesian methods with a mixed model, raxml, and parsimony. The various methods generated slightly different results regarding relationships among families, but the shared results comprise support for: (i) a monophyletic Sericostomatoidea; (ii) a paraphyletic Parasericostoma due to inclusion of Myotrichia murina, leading to synonymization of Myotrichia with Parasericostoma; (iii) a polyphyletic Sericostomatidae, which is divided into two families, Sericostomatidae sensu stricto and Parasericostomatidae fam.n.; (iv) a polyphyletic Helicophidae which is divided into Helicophidae sensu stricto and Heloccabucidae fam.n.; (v) hypothesized phylogenetic placement of the former incerta sedis genera Ngoya, Seselpsyche and Karomana; (vi) a paraphyletic Costora (Conoesucidae) that should be divided into several genera after more careful examination of morphological data; (vii) reinstatement of Gyrocarisa as a valid genus within Petrothrincidae. A third family, Ceylanopsychidae fam.n., is established based on morphological characters alone. A hypothesis of the relationship among 14 of the 15 families in the superfamily is presented. A key to the families is presented based on adults (males). Taxonomic history, diagnosis, habitat preference and distribution data for all sericostomatoid families are presented.This published work has been registered in ZooBank,
http://zoobank.org/urn:lsid:zoobank.org:pub:CF6A6B9F‐6A72‐4265‐BD09‐3A710DFCD7B1.
Screening for Human Immunodeficiency Virus, Hepatitis B Virus, Hepatitis C Virus, and Treponema pallidum by Blood Testing Using a Bio-Flash Technology-Based Algorithm before Gastrointestinal Endoscopy
Authors: Jun Zhou , Zhen Chen , QuiuLi Zhang , YuanQi An , Casado Verónica Vocero , Fan Yuan 
Published: October 2016

ABSTRACT

Currently, conventional enzyme immunoassays which use manual gold immunoassays and colloidal tests (GICTs) are used as screening tools to detect
Treponema pallidum
(syphilis), hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus type 1 (HIV-1), and HIV-2 in patients undergoing surgery. The present observational, cross-sectional study compared the sensitivity, specificity, and work flow characteristics of the conventional algorithm with manual GICTs with those of a newly proposed algorithm that uses the automated Bio-Flash technology as a screening tool in patients undergoing gastrointestinal (GI) endoscopy. A total of 956 patients were examined for the presence of serological markers of infection with HIV-1/2, HCV, HBV, and
T. pallidum
. The proposed algorithm with the Bio-Flash technology was superior for the detection of all markers (100.0% sensitivity and specificity for detection of anti-HIV and anti-HCV antibodies, HBV surface antigen [HBsAg], and
T. pallidum
) compared with the conventional algorithm based on the manual method (80.0% sensitivity and 98.6% specificity for the detection of anti-HIV, 75.0% sensitivity for the detection of anti-HCV, 94.7% sensitivity for the detection of HBsAg, and 100% specificity for the detection of anti-HCV and HBsAg) in these patients. The automated Bio-Flash technology-based screening algorithm also reduced the operation time by 85.0% (205 min) per day, saving up to 24 h/week. In conclusion, the use of the newly proposed screening algorithm based on the automated Bio-Flash technology can provide an advantage over the use of conventional algorithms based on manual methods for screening for HIV, HBV, HCV, and syphilis before GI endoscopy.
Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1
Authors: Luque Daniel , Mata Carlos P. , González-Camacho Fernando , González José M. , Gómez-Blanco Josué , Alfonso Carlos , Rivas Germán , Havens Wendy M. , Kanematsu Satoko , Suzuki Nobuhiro , Ghabrial Said A. , Trus Benes L. , Castón José R. 
Published: October 2016

ABSTRACT

Most double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids help to organize the viral genome and replicative complex(es). They also act as molecular sieves that isolate the virus genome from host defense mechanisms and allow the passage of nucleotides and viral transcripts. Rosellinia necatrix quadrivirus 1 (RnQV1), the type species of the family
Quadriviridae
, is a dsRNA fungal virus with a multipartite genome consisting of four monocistronic segments (segments 1 to 4). dsRNA-2 and dsRNA-4 encode two CPs (P2 and P4, respectively), which coassemble into ∼450-Å-diameter capsids. We used three-dimensional cryo-electron microscopy combined with complementary biophysical techniques to determine the structures of RnQV1 virion strains W1075 and W1118. RnQV1 has a quadripartite genome, and the capsid is based on a single-shelled T=1 lattice built of P2-P4 dimers. Whereas the RnQV1-W1118 capsid is built of full-length CP, P2 and P4 of RnQV1-W1075 are cleaved into several polypeptides, maintaining the capsid structural organization. RnQV1 heterodimers have a quaternary organization similar to that of homodimers of reoviruses and other dsRNA mycoviruses. The RnQV1 capsid is the first T=1 capsid with a heterodimer as an asymmetric unit reported to date and follows the architectural principle for dsRNA viruses that a 120-subunit capsid is a conserved assembly that supports dsRNA replication and organization.

IMPORTANCE
Given their importance to health, members of the family
Reoviridae
are the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of bacterial, protozoal, and fungal dsRNA viruses has improved our understanding of their structure, function, and evolution, as well. Here, we studied a dsRNA virus that infects the fungus
Rosellinia necatrix
, an ascomycete that is pathogenic to a wide range of plants. Using three-dimensional cryo-electron microscopy and analytical ultracentrifugation analysis, we determined the structure and stoichiometry of Rosellinia necatrix quadrivirus 1 (RnQV1). The RnQV1 capsid is a T=1 capsid with 60 heterodimers as the asymmetric units. The large amount of genetic information used by RnQV1 to construct a simple T=1 capsid is probably related to the numerous virus-host and virus-virus interactions that it must face in its life cycle, which lacks an extracellular phase.
Phosphorylation Requirement of Murine Leukemia Virus p12
Authors: Brzezinski Jonathon D. , Felkner Roland , Modi Apexa , Liu Mengdan , Roth Monica J. 
Published: October 2016

ABSTRACT

The p12 protein of murine leukemia virus (MLV) Gag is associated with the preintegration complex (PIC), and mutants of p12 (PM14) exhibit defects in nuclear entry/retention. Mutants of the phosphorylated serine 61 also have been reported to have defects in the early life cycle. Here we show that a phosphorylated peptide motif derived from human papillomavirus 8 (HPV-8), the E2 hinge region including residues 240 to 255, can functionally replace the main phosphorylated motif of MLV p12 and can rescue the viral titer of a strain with the lethal p12-PM14 mutation. Complementation with the HPV-8 E2 hinge motif generated multiple second-site mutations in live viral passage assays. Additional p12 phosphorylation sites were detected, including the late domain of p12 (PPPY) as well as the late domain/protease cleavage site of matrix (LYPAL), by mass spectrometry and Western blotting. Chromatin binding of p12-green fluorescent protein (GFP) fusion protein and functional complementation of p12-PM14 occurred in a manner independent of the E2 hinge region phosphorylation. Replacement of serine 61 by alanine within the minimal tethering domain (
61
SPMASRLRGRR
71
) maintained tethering, but in the context of the full-length p12, mutants with substitutions in S61 remained untethered and lost infectivity, indicating phosphorylation of p12 serine 61 functions to temporally regulate early and late p12 functions.

IMPORTANCE
The p12 protein, required for both early and late viral functions, is the predominant phosphorylated viral protein of Moloney MLV and is required for virus viability. Our studies indicate that the N terminus of p12 represses the early function of the chromatin binding domain and that deletion of the N terminus activates chromatin binding in the wild-type Moloney MLV p12 protein. Mass spectrometry and mutagenesis studies suggest that phosphorylation of both the repression domain and the chromatin binding domain acts to temporally regulate this process at the appropriate stages during infection.
Simian Immunodeficiency Virus-Producing Cells in Follicles Are Partially Suppressed by CD8+CellsIn Vivo
Authors: Li Shengbin , Folkvord Joy M. , Rakasz Eva G. , Abdelaal Hadia M. , Wagstaff Reece K. , Kovacs Katalin J. , Kim Hyeon O. , Sawahata Ryoko , MaWhinney Samantha , Masopust David , Connick Elizabeth , Skinner Pamela J. 
Published: October 2016

ABSTRACTHuman immunodeficiency virus (HIV)- and simian immunodeficiency virus (SIV)-specific CD8+T cells are typically largely excluded from lymphoid B cell follicles, where HIV- and SIV-producing cells are most highly concentrated, indicating that B cell follicles are somewhat of an immunoprivileged site. To gain insights into virus-specific follicular CD8+T cells, we determined the location and phenotype of follicular SIV-specific CD8+T cellsin situ, the local relationship of these cells to Foxp3+cells, and the effects of CD8 depletion on levels of follicular SIV-producing cells in chronically SIV-infected rhesus macaques. We found that follicular SIV-specific CD8+T cells were able to migrate throughout follicular areas, including germinal centers. Many expressed PD-1, indicating that they may have been exhausted. A small subset was in direct contact with and likely inhibited by Foxp3+cells, and a few were themselves Foxp3+. In addition, subsets of follicular SIV-specific CD8+T cells expressed low to medium levels of perforin, and subsets were activated and proliferating. Importantly, after CD8 depletion, the number of SIV-producing cells increased in B cell follicles and extrafollicular areas, suggesting that follicular and extrafollicular CD8+T cells have a suppressive effect on SIV replication. Taken together, these results suggest that during chronic SIV infection, despite high levels of exhaustion and likely inhibition by Foxp3+cells, a subset of follicular SIV-specific CD8+T cells are functional and suppress viral replicationin vivo. These findings support HIV cure strategies that augment functional follicular virus-specific CD8+T cells to enhance viral control.IMPORTANCEHIV- and SIV-specific CD8+T cells are typically largely excluded from lymphoid B cell follicles, where virus-producing cells are most highly concentrated, suggesting that B cell follicles are somewhat of an immunoprivileged site where virus-specific CD8+T cells are not able to clear all follicular HIV- and SIV-producing cells. To gain insights into follicular CD8+T cell function, we characterized follicular virus-specific CD8+T cellsin situby using an SIV-infected rhesus macaque model of HIV. We found that subsets of follicular SIV-specific CD8+T cells are able to migrate throughout the follicle, are likely inhibited by Foxp3+cells, and are likely exhausted but that, nonetheless, subsets are likely functional, as they express markers consistent with effector function and show signs of suppressing viral replicationin vivo. These findings support HIV cure strategies that increase the frequency of functional follicular virus-specific CD8+T cells.
Rationally Designed Immunogens Targeting HIV-1 gp120 V1V2 Induce Distinct Conformation-Specific Antibody Responses in Rabbits
Authors: Jiang Xunqing , Totrov Max , Li Wei , Sampson Jared M. , Williams Constance , Lu Hong , Wu Xueling , Lu Shan , Wang Shixia , Zolla-Pazner Susan , Kong Xiang-Peng 
Published: October 2016

ABSTRACT
The V1V2 region of HIV-1 gp120 harbors a major vulnerable site targeted by a group of broadly neutralizing monoclonal antibodies (MAbs) such as PG9 through strand-strand recognition. However, this epitope region is structurally polymorphic as it can also form a helical conformation recognized by RV144 vaccine-induced MAb CH58. This structural polymorphism is a potential mechanism for masking the V1V2 vulnerable site. Designing immunogens that can induce conformation-specific antibody (Ab) responses may lead to vaccines targeting this vulnerable site. We designed a panel of immunogens engrafting the V1V2 domain into trimeric and pentameric scaffolds in structurally constrained conformations. We also fused V1V2 to an Fc fragment to mimic the unconstrained V1V2 conformation. We tested these V1V2-scaffold proteins for immunogenicity in rabbits and assessed the responses by enzyme-linked immunosorbent assay (ELISA) and competition assays. Our V1V2 immunogens induced distinct conformation-specific Ab responses. Abs induced by structurally unconstrained immunogens reacted preferentially with unconstrained V1V2 antigens, suggesting recognition of the helical configuration, while Abs induced by the structurally constrained immunogens reacted preferentially with constrained V1V2 antigens, suggesting recognition of the β-strand conformation. The Ab responses induced by the structurally constrained immunogens were more broadly reactive and had higher titers than those induced by the structurally unconstrained immunogens. Our results demonstrate that immunogens presenting the different structural conformations of the gp120 V1V2 vulnerable site can be designed and that these immunogens induce distinct Ab responses with epitope conformation specificity. Therefore, these structurally constrained V1V2 immunogens are vaccine prototypes targeting the V1V2 domain of the HIV-1 envelope.

IMPORTANCE
The correlates analysis of the RV144 HIV-1 vaccine trial suggested that the presence of antibodies to the V1V2 region of HIV-1 gp120 was responsible for the modest protection observed in the trial. In addition, V1V2 harbors one of the key vulnerable sites of HIV-1 Env recognized by a family of broadly neutralizing MAbs such as PG9. Thus, V1V2 is a key target for vaccine development. However, this vulnerable site is structurally polymorphic, and designing immunogens that present different conformations is crucial for targeting this site. We show here that such immunogens can be designed and that they induced conformation-specific antibody responses in rabbits. Our immunogens are therefore prototypes of vaccine candidates targeting the V1V2 region of HIV-1 Env.
Identification of Interferon-Stimulated Gene Proteins That Inhibit Human Parainfluenza Virus Type 3
Authors: Rabbani M. A. G. , Ribaudo Michael , Guo Ju-Tao , Barik Sailen 
Published: October 2016

ABSTRACT

A major arm of cellular innate immunity is type I interferon (IFN), represented by IFN-α and IFN-β. Type I IFN transcriptionally induces a large number of cellular genes, collectively known as IFN-stimulated gene (ISG) proteins, which act as antivirals. The IFIT (interferon-induced proteins with tetratricopeptide repeats) family proteins constitute a major subclass of ISG proteins and are characterized by multiple tetratricopeptide repeats (TPRs). In this study, we have interrogated IFIT proteins for the ability to inhibit the growth of human parainfluenza virus type 3 (PIV3), a nonsegmented negative-strand RNA virus of the
Paramyxoviridae
family and a major cause of respiratory disease in children. We found that IFIT1 significantly inhibited PIV3, whereas IFIT2, IFIT3, and IFIT5 were less effective or not at all. In further screening a set of ISG proteins we discovered that several other such proteins also inhibited PIV3, including IFITM1, IDO (indoleamine 2,3-dioxygenase), PKR (protein kinase, RNA activated), and viperin (virus inhibitory protein, endoplasmic reticulum associated, interferon inducible)/Cig5. The antiviral effect of IDO, the enzyme that catalyzes the first step of tryptophan degradation, could be counteracted by tryptophan. These results advance our knowledge of diverse ISG proteins functioning as antivirals and may provide novel approaches against PIV3.

IMPORTANCE
The innate immunity of the host, typified by interferon (IFN), is a major antiviral defense. IFN inhibits virus growth by inducing a large number of IFN-stimulated gene (ISG) proteins, several of which have been shown to have specific antiviral functions. Parainfluenza virus type 3 (PIV3) is major pathogen of children, and no reliable vaccine or specific antiviral against it currently exists. In this article, we report several ISG proteins that strongly inhibit PIV3 growth, the use of which may allow a better antiviral regimen targeting PIV3.
Exercise to prevent falls in older adults: an updated systematic review and meta-analysis
Authors: Sherrington Catherine , Michaleff Zoe A , Fairhall Nicola , Paul Serene S , Tiedemann Anne , Whitney Julie , Cumming Robert G , Herbert Robert D , Close Jacqueline C T , Lord Stephen R 
Published: October 2016

ObjectivePrevious meta-analyses have found that exercise prevents falls in older people. This study aimed to test whether this effect is still present when new trials are added, and it explores whether characteristics of the trial design, sample or intervention are associated with greater fall prevention effects.DesignUpdate of a systematic review with random effects meta-analysis and meta-regression.Data sourcesCochrane Library, CINAHL, MEDLINE, EMBASE, PubMed, PEDro and SafetyLit were searched from January 2010 to January 2016.Study eligibility criteriaWe included randomised controlled trials that compared fall rates in older people randomised to receive exercise as a single intervention with fall rates in those randomised to a control group.Results99 comparisons from 88 trials with 19 478 participants were available for meta-analysis. Overall, exercise reduced the rate of falls in community-dwelling older people by 21% (pooled rate ratio 0.79, 95% CI 0.73 to 0.85, p<0.001, I247%, 69 comparisons) with greater effects seen from exercise programmes that challenged balance and involved more than 3 hours/week of exercise. These variables explained 76% of the between-trial heterogeneity and in combination led to a 39% reduction in falls (incident rate ratio 0.61, 95% CI 0.53 to 0.72, p<0.001). Exercise also had a fall prevention effect in community-dwelling people with Parkinson's disease (pooled rate ratio 0.47, 95% CI 0.30 to 0.73, p=0.001, I265%, 6 comparisons) or cognitive impairment (pooled rate ratio 0.55, 95% CI 0.37 to 0.83, p=0.004, I221%, 3 comparisons). There was no evidence of a fall prevention effect of exercise in residential care settings or among stroke survivors or people recently discharged from hospital.Summary/conclusionsExercise as a single intervention can prevent falls in community-dwelling older people. Exercise programmes that challenge balance and are of a higher dose have larger effects. The impact of exercise as a single intervention in clinical groups and aged care facility residents requires further investigation, but promising results are evident for people with Parkinson's disease and cognitive impairment.
Experiences of long-term life-limiting conditions among patients and carers: what can we learn from a meta-review of systematic reviews of qualitative studies of chronic heart failure, chronic obstructive pulmonary disease and chronic kidney disease?
Authors: May Carl R , Cummings Amanda , Myall Michelle , Harvey Jonathan , Pope Catherine , Griffiths Peter , Roderick Paul , Arber Mick , Boehmer Kasey , Mair Frances S , Richardson Alison 
Published: October 2016

ObjectivesTo summarise and synthesise published qualitative studies to characterise factors that shape patient and caregiver experiences of chronic heart failure (CHF), chronic obstructive pulmonary disease (COPD) and chronic kidney disease (CKD).DesignMeta-review of qualitative systematic reviews and metasyntheses. Papers analysed using content analysis.Data sourcesCINAHL, EMBASE, MEDLINE, PsychINFO, Scopus and Web of Science were searched from January 2000 to April 2015.Eligibility criteria for selecting studiesSystematic reviews and qualitative metasyntheses where the participants were patients, caregivers and which described experiences of care for CHF, COPD and CKD in primary and secondary care who were aged ≥18 years.ResultsSearches identified 5420 articles, 53 of which met inclusion criteria. Reviews showed that patients' and caregivers' help seeking and decision-making were shaped by their degree of structural advantage (socioeconomic status, spatial location, health service quality); their degree of interactional advantage (cognitive advantage, affective state and interaction quality) and their degree of structural resilience (adaptation to adversity, competence in managing care and caregiver response to demands).ConclusionsTo the best of our knowledge, this is the first synthesis of qualitative systematic reviews in the field. An important outcome of this overview is an emphasis on what patients and caregivers value and on attributes of healthcare systems, relationships and practices that affect the distressing effects and consequences of pathophysiological deterioration in CHF, COPD and CKD. Interventions that seek to empower individual patients may have limited effectiveness for those who are most affected by the combined weight of structural, relational and practical disadvantage identified in this overview. We identify potential targets for interventions that could address these disadvantages.Systematic review registration numberPROSPERO CRD42014014547.
Symptoms in patients with takotsubo syndrome: a qualitative interview study
Authors: Wallström Sara , Ulin Kerstin , Omerovic Elmir , Ekman Inger 
Published: October 2016

ObjectiveThe aim of the study was to investigate the meaning of narrated symptoms in connection to takotsubo syndrome.Design, method, participants and settingQualitative study consisting of 25 interviews, 23 women and 2 men aged 39–84 and living in Region Västra Götaland, Sweden. The transcribed text was analysed with phenomenological hermeneutics.ResultsThe interviewees reported a large number of symptoms before, during and after the acute onset of takotsubo syndrome, including pain, affected breathing, lassitude, malaise and nausea. Several of these have not been reported previously. Symptoms before the acute onset were, even if they had been prominent, ignored by the interviewees for various reasons. During the acute phase, the symptoms could no longer be ignored and the interviewees sought healthcare. The remaining residual symptom after discharge from hospital caused a great deal of worry because the interviewees feared that they would be permanent and they felt they could not live this way. On the whole, becoming ill and having a large number of symptoms greatly impacted the lives of the interviewees and made them re-evaluate how they had been living. Furthermore, they reported feeling alone and lost regarding their symptom burden, especially in relation to their residual symptoms, which affected their health and ability to return to daily life.ConclusionsAcute symptoms, and symptoms before and after the acute ones, are a major part of the illness experience for patients with takotsubo syndrome and affect their health and well-being. Assessment of symptoms should be an integrated part of care to promote health. One way of achieving this is through the patients’ own narratives of their experiences, which are an important component in person-centred care.