bluuebunny/crossref_metadata_2025_split huggingface dataset:
Late Maturation Steps Preceding Selective Nuclear Export and Egress of Progeny Parvovirus
Authors: Wolfisberg Raphael , Kempf Christoph , Ros Carlos 
Published: March 2016

ABSTRACT
Although the mechanism is not well understood, growing evidence indicates that the nonenveloped parvovirus minute virus of mice (MVM) may actively egress before passive release through cell lysis. We have dissected the late maturation steps of the intranuclear progeny with the aims of confirming the existence of active prelytic egress and identifying critical capsid rearrangements required to initiate the process. By performing anion-exchange chromatography (AEX), we separated intranuclear progeny particles by their net surface charges. Apart from empty capsids (EC), two distinct populations of full capsids (FC) arose in the nuclei of infected cells. The earliest population of FC to appear was infectious but, like EC, could not be actively exported from the nucleus. Further maturation of this early population, involving the phosphorylation of surface residues, gave rise to a second, late population with nuclear export potential. While capsid surface phosphorylation was strictly associated with nuclear export capacity, mutational analysis revealed that the phosphoserine-rich N terminus of VP2 (N-VP2) was dispensable, although it contributed to passive release. The reverse situation was observed for the incoming particles, which were dephosphorylated in the endosomes. Our results confirm the existence of active prelytic egress and reveal a late phosphorylation event occurring in the nucleus as a selective factor for initiating the process.

IMPORTANCE
In general, the process of egress of enveloped viruses is active and involves host cell membranes. However, the release of nonenveloped viruses seems to rely more on cell lysis. At least for some nonenveloped viruses, an active process before passive release by cell lysis has been reported, although the underlying mechanism remains poorly understood. By using the nonenveloped model parvovirus minute virus of mice, we could confirm the existence of an active process of nuclear export and further characterize the associated capsid maturation steps. Following DNA packaging in the nucleus, capsids required further modifications, involving the phosphorylation of surface residues, to acquire nuclear export potential. Inversely, those surface residues were dephosphorylated on entering capsids. These spatially controlled phosphorylation-dephosphorylation events concurred with the nuclear export-import potential required to complete the infectious cycle.
The Respiratory Pathogen Moraxella catarrhalis Targets Collagen for Maximal Adherence to Host Tissues
Authors: Singh Birendra , Alvarado-Kristensson Maria , Johansson Martin , Hallgren Oskar , Westergren-Thorsson Gunilla , Mörgelin Matthias , Riesbeck Kristian 
Published: March 2016

ABSTRACT

Moraxella catarrhalis
is a human respiratory pathogen that causes acute otitis media in children and is associated with exacerbations in patients suffering from chronic obstructive pulmonary disease (COPD). The first step in
M. catarrhalis
colonization is adherence to the mucosa, epithelial cells, and extracellular matrix (ECM). The objective of this study was to evaluate the role of
M. catarrhalis
interactions with collagens from various angles. Clinical isolates (
n
= 43) were tested for collagen binding, followed by a detailed analysis of protein-protein interactions using recombinantly expressed proteins.
M. catarrhalis
-dependent interactions with collagen produced by human lung fibroblasts and tracheal tissues were studied by utilizing confocal immunohistochemistry and high-resolution scanning electron microscopy. A mouse smoke-induced chronic obstructive pulmonary disease (COPD) model was used to estimate the adherence of
M. catarrhalis
in vivo. We found that all
M. catarrhalis
clinical isolates tested adhered to fibrillar collagen types I, II, and III and network-forming collagens IV and VI. The trimeric autotransporter adhesins
u
biquitous
s
urface
p
rotein
A2
(UspA2) and UspA2H were identified as major collagen-binding receptors.
M. catarrhalis
wild type adhered to human tracheal tissue and collagen-producing lung fibroblasts, whereas UspA2 and UspA2H deletion mutants did not. Moreover, in the COPD mouse model, bacteria devoid of UspA2 and UspA2H had a reduced level of adherence to the respiratory tract compared to the adherence of wild-type bacteria. Our data therefore suggest that the
M. catarrhalis
UspA2 and UspA2H-dependent interaction with collagens is highly critical for adherence in the host and, furthermore, may play an important role in the establishment of disease.

IMPORTANCE
The respiratory tract pathogen
Moraxella catarrhalis
adheres to the host by interacting with several components, including the ECM. Collagen accounts for 30% of total body proteins, and therefore, bacterial adherence to abundant host collagens mediates bacterial persistence and colonization. In this study, we characterized previously unknown
M. catarrhalis
-dependent interactions with host collagens and found that the trimeric autotransporter adhesins
u
biquitous
s
urface
p
rotein
A2
(UspA2) and UspA2H are highly important. Our observations also suggested that collagen-mediated adherence of
M. catarrhalis
is indispensable for bacterial survival in the host, as exemplified by a mouse COPD model.
Interaction between Simian Virus 40 Major Capsid Protein VP1 and Cell Surface Ganglioside GM1 Triggers Vacuole Formation
Authors: Luo Yong , Motamedi Nasim , Magaldi Thomas G. , Gee Gretchen V. , Atwood Walter J. , DiMaio Daniel 
Published: March 2016

ABSTRACT
Simian virus 40 (SV40), a polyomavirus that has served as an important model to understand many aspects of biology, induces dramatic cytoplasmic vacuolization late during productive infection of monkey host cells. Although this activity led to the discovery of the virus in 1960, the mechanism of vacuolization is still not known. Pentamers of the major SV40 capsid protein VP1 bind to the ganglioside GM1, which serves as the cellular receptor for the virus. In this report, we show that binding of VP1 to cell surface GM1 plays a key role in SV40 infection-induced vacuolization. We previously showed that SV40 VP1 mutants defective for GM1 binding fail to induce vacuolization, even though they replicate efficiently. Here, we show that interfering with GM1-VP1 binding by knockdown of GM1 after infection is established abrogates vacuolization by wild-type SV40. Vacuole formation during permissive infection requires efficient virus release, and conditioned medium harvested late during SV40 infection rapidly induces vacuoles in a VP1- and GM1-dependent fashion. Furthermore, vacuolization can also be induced by a nonreplicating SV40 pseudovirus in a GM1-dependent manner, and a mutation in BK pseudovirus VP1 that generates GM1 binding confers vacuole-inducing activity. Vacuolization can also be triggered by purified pentamers of wild-type SV40 VP1, but not by GM1 binding-defective pentamers or by intracellular expression of VP1. These results demonstrate that SV40 infection-induced vacuolization is caused by the binding of released progeny viruses to GM1, thereby identifying the molecular trigger for the activity that led to the discovery of SV40.

IMPORTANCE
The DNA tumor virus SV40 was discovered more than a half century ago as a contaminant of poliovirus vaccine stocks, because it caused dramatic cytoplasmic vacuolization of permissive host cells. Although SV40 played a historically important role in the development of molecular and cellular biology, restriction mapping, molecular cloning, and whole-genome sequencing, the basis of this vacuolization phenotype was unknown. Here, we show that SV40-induced vacuolization is triggered by the binding of the major viral capsid protein, VP1, to a cell surface ganglioside receptor, GM1. No other viral proteins or virus replication is required for vacuole formation. Other polyomaviruses utilize different ganglioside receptors, but they do not induce vacuolization. This work identifies the molecular trigger for the phenotype that led to the discovery of this important virus and provides the first molecular insight into an unusual and enigmatic cytopathic effect due to virus infection.
Nonencapsulated Streptococcus pneumoniae: Emergence and Pathogenesis
Authors: Keller Lance E. , Robinson D. Ashley , McDaniel Larry S. 
Published: March 2016

ABSTRACT

While significant protection from pneumococcal disease has been achieved by the use of polysaccharide and polysaccharide-protein conjugate vaccines, capsule-independent protection has been limited by serotype replacement along with disease caused by nonencapsulated
Streptococcus pneumoniae
(NESp). NESp strains compose approximately 3% to 19% of asymptomatic carriage isolates and harbor multiple antibiotic resistance genes. Surface proteins unique to NESp enhance colonization and virulence despite the lack of a capsule even though the capsule has been thought to be required for pneumococcal pathogenesis. Genes for pneumococcal surface proteins replace the capsular polysaccharide (cps) locus in some NESp isolates, and these proteins aid in pneumococcal colonization and otitis media (OM). NESp strains have been isolated from patients with invasive and noninvasive pneumococcal disease, but noninvasive diseases, specifically, conjunctivitis (85%) and OM (8%), are of higher prevalence. Conjunctival strains are commonly of the so-called classical NESp lineages defined by multilocus sequence types (STs) ST344 and ST448, while sporadic NESp lineages such as ST1106 are more commonly isolated from patients with other diseases. Interestingly, sporadic lineages have significantly higher rates of recombination than classical lineages. Higher rates of recombination can lead to increased acquisition of antibiotic resistance and virulence factors, increasing the risk of disease and hindering treatment. NESp strains are a significant proportion of the pneumococcal population, can cause disease, and may be increasing in prevalence in the population due to effects on the pneumococcal niche caused by pneumococcal vaccines. Current vaccines are ineffective against NESp, and further research is necessary to develop vaccines effective against both encapsulated and nonencapsulated pneumococci.
The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species
Authors: Schmoll Monika , Dattenböck Christoph , Carreras-Villaseñor Nohemí , Mendoza-Mendoza Artemio , Tisch Doris , Alemán Mario Ivan , Baker Scott E. , Brown Christopher , Cervantes-Badillo Mayte Guadalupe , Cetz-Chel José , Cristobal-Mondragon Gema Rosa , Delaye Luis , Esquivel-Naranjo Edgardo Ulises , Frischmann Alexa , Gallardo-Negrete Jose de Jesus , García-Esquivel Monica , Gomez-Rodriguez Elida Yazmin , Greenwood David R. , Hernández-Oñate Miguel , Kruszewska Joanna S. , Lawry Robert , Mora-Montes Hector M. , Muñoz-Centeno Tania , Nieto-Jacobo Maria Fernanda , Nogueira Lopez Guillermo , Olmedo-Monfil Vianey , Osorio-Concepcion Macario , Piłsyk Sebastian , Pomraning Kyle R. , Rodriguez-Iglesias Aroa , Rosales-Saavedra Maria Teresa , Sánchez-Arreguín J. Alejandro , Seidl-Seiboth Verena , Stewart Alison , Uresti-Rivera Edith Elena , Wang Chih-Li , Wang Ting-Fang , Zeilinger Susanne , Casas-Flores Sergio , Herrera-Estrella Alfredo 
Published: March 2016

SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.
Protocol for the development and validation of a questionnaire to assess concerning behaviours and mental health in individuals with autism spectrum disorders: the Assessment of Concerning Behaviour (ACB) scale
Authors: Santosh Paramala , Tarver Joanne , Gibbons Felicity , Vitoratou Silia , Simonoff Emily 
Published: March 2016

IntroductionCo-occurring psychiatric conditions and concerning behaviours are prevalent in individuals with autism spectrum disorders (ASD), and are likely to be detrimental to functioning and long-term outcomes. The cognitive rigidity and deficits in emotional literacy and verbal behaviour that commonly occur in ASD can adversely affect clinicians’ confidence to identify concerning behaviours and mental health problems. There is a need to develop a measure that is tailored towards individuals with ASD, and differentiates between symptoms of psychopathology and core ASD symptoms. Furthermore, it should be modified to capture internalising symptoms that individuals with ASD may find difficult or be unable to verbalise. This protocol describes the intended development and validation of the Assessment of Concerning Behaviour (ACB) scale. The ACB will aim to be a multidimensional measure of concerning behaviours in ASD incorporating self-report, parent/carer, teacher/employer and clinician report versions that can be used across the lifespan and spectrum of intellectual ability.Methods and analysisThis study will be guided by the methods described in the US Food and Drug Administration Guidance for Industry Patient-reported Outcome Measures. A literature review, cognitive interviews and focus groups with individuals who have experience of working or living with ASDs will be used for item generation. A sample of children and adults with ASD will complete the ACB, in addition to other gold standard measures of concerning behaviour in order to establish the initial psychometric properties of the scale.Ethics and disseminationThis study has received ethical approval from the NHS Research Ethics Committee: London-Camden and King's Cross (ref: 15/LO/0085). Study findings will be disseminated to healthcare professionals and scientists in the field through publication in peer-reviewed journals and conference presentations.
Value of systematic detection of physical child abuse at emergency rooms: a cross-sectional diagnostic accuracy study
Authors: Sittig Judith S , Uiterwaal Cuno S P M , Moons Karel G M , Russel Ingrid M B , Nievelstein Rutger A J , Nieuwenhuis Edward E S , van de Putte Elise M 
Published: March 2016

ObjectivesThe aim of our diagnostic accuracy study Child Abuse Inventory at Emergency Rooms (CHAIN-ER) was to establish whether a widely used checklist accurately detects or excludes physical abuse among children presenting to ERs with physical injury.DesignA large multicentre study with a 6-month follow-up.Setting4 ERs in The Netherlands.Participants4290 children aged 0–7 years attending the ER because of physical injury. All children were systematically tested with an easy-to-use child abuse checklist (index test). A national expert panel (reference standard) retrospectively assessed all children with positive screens and a 15% random sample of the children with negative screens for physical abuse, using additional information, namely, an injury history taken by a paediatrician, information provided by the general practitioner, youth doctor and social services by structured questionnaires, and 6-month follow-up information.Main outcome measurePhysical child abuse.Secondary outcome measureInjury due to neglect and need for help.Results4253/4290 (99%) parents agreed to follow-up. At a prevalence of 0.07% (3/4253) for inflicted injury by expert panel decision, the positive predictive value of the checklist was 0.03 (95% CI 0.006 to 0.085), and the negative predictive value 1.0 (0.994 to 1.0). There was 100% (93 to 100) agreement about inflicted injury in children, with positive screens between the expert panel and child abuse experts.ConclusionsRare cases of inflicted injury among preschool children presenting at ERs for injury are very likely captured by easy-to-use checklists, but at very high false-positive rates. Subsequent assessment by child abuse experts can be safely restricted to children with positive screens at very low risk of missing cases of inflicted injury. Because of the high false positive rate, we do advise careful prior consideration of cost-effectiveness and clinical and societal implications before de novo implementation.
Validation of a metered dose inhaler electronic monitoring device: implications for asthma clinical trial use
Authors: Pilcher Janine , Holliday Mark , Ebmeier Stefan , McKinstry Steve , Messaoudi Fatiha , Weatherall Mark , Beasley Richard 
Published: March 2016

BackgroundThe SmartTouch Ventolin monitor (Adherium, Auckland, New Zealand) is an electronic monitor for use with a Ventolin metered dose inhaler, which records the date and time of inhaler actuations. This technology has the potential to allow in-depth analysis of patterns of inhaler use in clinical trial settings. The aim of this study was to determine the accuracy of the SmartTouch Ventolin monitor in recording Ventolin actuations.Methods20 SmartTouch Ventolin monitors were attached to Ventolin metered dose inhalers. Bench testing was performed over a 10-week period, to reflect the potential time frame between visits in a clinical trial. Inhaler actuations were recorded in a paper diary, which was compared with data uploaded from the monitors.Results2560 actuations were performed during the 10-week study period. Monitor sensitivity for diary-recorded actuations was 99.9% with a lower 97.5% confidence bound of 99.7%. The positive predictive value for diary-recorded actuations was 100% with a 97.5% lower confidence bound of 99.9%.ConclusionsThe SmartTouch Ventolin monitor is highly accurate in recording and retaining electronic data. It can be recommended for use in clinical trial settings in which training and quality control systems are incorporated into study protocols to ensure accurate data acquisition.
Immunochemical faecal occult blood testing to screen for colorectal cancer: can the screening interval be extended?
Authors: Haug Ulrike , Grobbee Esmée J , Lansdorp-Vogelaar Iris , Spaander Manon C W , Kuipers Ernst J 
Published: March 2016

ObjectiveColorectal cancer (CRC) screening programmes based on faecal immunochemical testing for haemoglobin (FIT) typically use a screening interval of 2 years. We aimed to estimate how alternative FIT strategies that use a lower than usual positivity threshold followed by a longer screening interval compare with conventional strategies.MethodsWe analysed longitudinal data of 4523 Dutch individuals (50–74 years at baseline) participating in round I of a one-sample FIT screening programme, of which 3427 individuals also participated in round II after 1–3 years. The cohort was followed until 2 years after round II. In both rounds, a cut-off level of ≥50 ng haemoglobin (Hb)/mL buffer (corresponding to 10 µg Hb/g faeces) was used, representing the standard scenario. We determined the cumulative positivity rate (PR) and the numbers of subjects diagnosed with advanced adenomas (N_AdvAd) and early stage CRC (N_earlyCRC) in the cohort over two rounds of screening (standard scenario) and compared it with hypothetical single-round screening with use of a lower cut-off and omission of the second round (alternative scenario).ResultsIn the standard scenario, the cumulative (ie, round I and II combined) PR, N_AdvAd and N_earlyCRC were 13%, 180% and 26%, respectively. In alternative scenarios using a cut-off level of respectively ≥11 and ≥22 ng/HbmL buffer (corresponding to 2 and 4 µg Hb/g faeces), the PRs were 18% and 13%, the N_AdvAd were 180 and 162 and the N_earlyCRC ranged between 22–27 and 22–26.ConclusionsThe diagnostic yield of FIT screening using a lowered positivity threshold in combination with an extended screening interval (up to 5 years) may be similar to conventional FIT strategies. This justifies and motivates further research steps in this direction.
Magnetic and optical properties in the 1D TM–O chain compounds Sr2TMO3 (TM = Ni, Co): A first-principle investigation
Authors: Gui Hong , Li Xin , Zhao Zhenjie , Xie Wenhui 
Published: March 2016

In this paper, we have calculated the structural, electronic, magnetic and optical properties of Sr2NiO3 and Sr2CoO3 using density functional theory (DFT) within generalized gradient approximation (GGA). The crystal structure of both materials is well described with Immm (No. 71) symmetry which are isostructural with Sr2CuO3 and both are quasi-one-dimensional (1D) rectangular lattice G-type antiferromagnets, in consistent with the experimental data. Due to a distortion, Sr2CoO3 lifts the near-degeneracy [Formula: see text] and [Formula: see text] states of the local Co electronic configuration, which demonstrates a strong coupling between the structural lattice and the electronic configuration. The calculated band structure shows a band gap of 1.376 eV for Sr2NiO3 and a band gap of 1.735 eV for Sr2CoO3. Ni and Co ions are in the high-spin [Formula: see text] and [Formula: see text] configurations with the magnetic moments of 1.585 [Formula: see text] and 2.587 [Formula: see text], respectively. Based on the Heisenberg Hamiltonian model, we conclude that the superexchange intrachain TM–O–TM superexchange interaction is predominant and interaction between the 1D chains is weak. According to the calculated dielectric function, absorption spectrum and electron energy loss spectrum, the optical responses suggest that Sr2NiO3 shows the unique anisotropic structure and interaction of the application in optoelectronics.