bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA‐directed DNA methylation efficiency depends on trigger and target sequence identity
Authors: Dalakouras Athanasios , Dadami Elena , Wassenegger Michèle , Krczal Gabi , Wassenegger Michael 
Published: April 2016

SummaryRNA‐directed DNA methylation (RdDM) in plants has been extensively studied, but the RNA molecules guiding the RdDM machinery to their targets are still to be characterized. It is unclear whether these molecules require full complementarity with their target. In this study, we have generated Nicotiana tabacum (Nt) plants carrying an infectious tomato apical stunt viroid (TASVd) transgene (Nt‐TASVd) and a non‐infectious potato spindle tuber viroid (PSTVd) transgene (Nt‐SB2). The two viroid sequences exhibit 81% sequence identity. Nt‐TASVd and Nt‐SB2 plants were genetically crossed. In the progeny plants (Nt‐SB2/TASVd), deep sequencing of small RNAs (sRNAs) showed that TASVd infection was associated with the accumulation of abundant small interfering RNAs (siRNAs) that mapped along the entire TASVd but only partially matched the SB2 transgene. TASVd siRNAs efficiently targeted SB2 RNA for degradation, but no transitivity was detectable. Bisulfite sequencing in the Nt‐SB2/TASVd plants revealed that the TASVd transgene was targeted for dense cis‐RdDM along its entire sequence. In the same plants, the SB2 transgene was targeted for trans‐RdDM. The SB2 methylation pattern, however, was weak and heterogeneous, pointing to a positive correlation between trigger–target sequence identity and RdDM efficiency. Importantly, trans‐RdDM on SB2 was also detected at sites where no homologous siRNAs were detected. Our data indicate that RdDM efficiency depends on the trigger–target sequence identity, and is not restricted to siRNA occupancy. These findings support recent data suggesting that RNAs with sizes longer than 24 nt (>24‐nt RNAs) trigger RdDM.
Solanum pennelliibackcross inbred lines (BILs) link small genomic bins with tomato traits
Authors: Ofner Itai , Lashbrooke Justin , Pleban Tzili , Aharoni Asaph , Zamir Dani 
Published: April 2016

SummaryWe present a resource for fine mapping of traits derived from the wild tomato speciesSolanum pennellii(LA0716). The population of backcross inbred lines (BILs) is composed of 446 lines derived after a few generations of backcrosses of the wild species with cultivated tomato (cultivar M82;LA3475), followed by more than seven generations of self‐pollination. TheBILs were genotyped using the 10KSOL‐CAPsingle nucleotide polymorphism (SNP) ‐Chip, and 3700 polymorphic markers were used to map recombination break points relative to the physical map ofSolanum lycopersicum. TheBILs carry, on average, 2.7 introgressions per line, with a mean introgression length of 11.7 Mbp. Whereas the classic 76 introgression lines (ILs) partitioned the genome into 106 mapping bins, theBILs generated 633 bins, thereby enhancing the mapping resolution of traits derived from the wild species. We demonstrate the power of theBILs for rapid fine mapping of simple and complex traits derived from the wild tomato species.
Cerebrovascular disorders caused by hyperfibrinogenaemia
Authors: Muradashvili Nino , Tyagi Reeta , Tyagi Neetu , Tyagi Suresh C. , Lominadze David 
Published: April 2016

Key points
Hyperfibrinogenaemia (HFg) results in vascular remodelling, and fibrinogen (Fg) and amyloid β (Aβ) complex formation is a hallmark of Alzheimer's disease. However, the interconnection of these effects, their mechanisms and implications in cerebrovascular diseases are not known.
Using a mouse model of HFg, we showed that at an elevated blood level, Fg increases cerebrovascular permeability via mainly caveolar protein transcytosis.
This enhances deposition of Fg in subendothelial matrix and interstitium making the immobilized Fg a readily accessible substrate for binding Aβ and cellular prion protein (PrPC), the protein that is thought to have a greater effect on memory than Aβ.
We showed that enhanced formation of Fg–Aβ and Fg–PrPC complexes are associated with reduction in short‐term memory.
The present study delineates a new mechanistic pathway for vasculo‐neuronal dysfunctions found in inflammatory cardiovascular and cerebrovascular diseases associated with an elevated blood level of Fg.
AbstractMany cardiovascular diseases are associated with inflammation and as such are accompanied by an increased blood level of fibrinogen (Fg). Besides its well‐known prothrombotic effects Fg seems to have other destructive roles in developing microvascular dysfunction that include changes in vascular reactivity and permeability. Increased permeability of brain microvessels has the most profound effects as it may lead to cerebrovascular remodelling and result in memory reduction. The goal of the present study was to define mechanisms of cerebrovascular permeability and associated reduction in memory induced by elevated blood content of Fg. Genetically modified, transgenic hyperfibrinogenic (HFg) mice were used to study cerebrovascular transcellular and paracellular permeability in vivo. The extent of caveolar formation and the role of caveolin‐1 signalling were evaluated by immunohistochemistry (IHC) and Western blot (WB) analysis in brain samples from experimental animals. Formation of Fg complexes with amyloid β (Aβ) and with cellular prion protein (PrPC) were also assessed with IHC and WB analysis. Short‐term memory of mice was assessed by novel object recognition and Y‐maze tests. Caveolar protein transcytosis was found to have a prevailing role in overall increased cerebrovascular permeability in HFg mice. These results were associated with enhanced formation of caveolae. Increased formation of Fg–PrPC and Fg–Aβ complexes were correlated with reduction in short‐term memory in HFg mice. Using the model of hyperfibrinogenaemia, the present study shows a novel mechanistic pathway of inflammation‐induced and Fg‐mediated reduction in short‐term memory.
Monoclonal Antibodies to Different Components of the Human Cytomegalovirus (HCMV) Pentamer gH/gL/pUL128L and Trimer gH/gL/gO as well as Antibodies Elicited during Primary HCMV Infection Prevent Epithelial Cell Syncytium Formation
Authors: Gerna Giuseppe , Percivalle Elena , Perez Laurent , Lanzavecchia Antonio , Lilleri Daniele 
Published: April 2016

ABSTRACT
Human cytomegalovirus (HCMV) may cause disseminated/end-organ disease in congenitally infected newborns and immunosuppressed transplant recipients. Two glycoprotein complexes, gH/gL/gO and gH/gL/pUL128/pUL130/pUL131 (gH/gL/pUL128L; referred to as the pentamer), are required for HCMV entry into fibroblasts and endothelial/epithelial cells, respectively, in the presence of the viral fusion protein gB. In addition, gH/gL/gO was recently reported to also be required for infection of endothelial/epithelial cells. Virus entry into human fibroblasts involves fusion of the virus envelope with the plasma membrane, whereas entry into endothelial/epithelial cells involves macropinocytosis or endocytosis and low-pH-dependent fusion with endosomes. A large set of neutralizing monoclonal antibodies (MAbs), directed to gH, gB, and multiple components of the pentamer, was developed. In addition, novel anti-gO human monoclonal antibodies were recently isolated. It is known that epithelial cell infection with a wild HCMV strain at a high multiplicity of infection produces a large number of syncytia. Incubation of heavily HCMV VR1814-infected ARPE-19 epithelial cells with neutralizing MAbs to one, two, or three components of the pUL128L portion of the pentamer blocked syncytium formation at an antibody concentration of 10 μg/ml, whereas only a partial inhibitory effect was displayed for MAbs to gO, gH, or gB at the same concentration. A blocking effect was also exhibited by convalescent-phase sera from primary HCMV infections. These findings indicate that the pentamer is required for syncytium formation in epithelial cells.

IMPORTANCE
Human cytomegalovirus (HCMV) mostly infects epithelial and endothelial cells
in vivo
. Recently, the pentamer protein complex (gH/gL/pUL128L) was identified as being required for infection of these cells, in association with the other protein complex, gH/gL/gO. In primary infections, HCMV migrates to endothelial cells and then to leukocytes, which disseminate the infection throughout the body. The virus then spreads to organs and tissues, mostly infecting either single cells or multinucleated epithelial giant cells (syncytia), depending on the viral load. Potent neutralizing human MAbs directed to distinct binding sites of the pUL128L portion of the pentamer were shown in the past to block virus dissemination. In the present study, MAbs to pUL128L were shown to block syncytium formation with a higher potency than that of MAbs to gO, gH, or gB, thus suggesting their role in limiting virus dissemination. This finding provides additional information useful for the development of anti-HCMV therapeutic antibodies and subunit vaccines.
Migration of Nucleocapsids in Vesicular Stomatitis Virus-Infected Cells Is Dependent on both Microtubules and Actin Filaments
Authors: Yacovone Shalane K. , Smelser Amanda M. , Macosko Jed C. , Holzwarth George , Ornelles David A. , Lyles Douglas S. 
Published: April 2016

ABSTRACT
The distribution of vesicular stomatitis virus (VSV) nucleocapsids in the cytoplasm of infected cells was analyzed by scanning confocal fluorescence microscopy using a newly developed quantitative approach called the border-to-border distribution method. Nucleocapsids were located near the cell nucleus at early times postinfection (2 h) but were redistributed during infection toward the edges of the cell. This redistribution was inhibited by treatment with nocodazole, colcemid, or cytochalasin D, indicating it is dependent on both microtubules and actin filaments. The role of actin filaments in nucleocapsid mobility was also confirmed by live-cell imaging of fluorescent nucleocapsids of a virus containing P protein fused to enhanced green fluorescent protein. However, in contrast to the overall redistribution in the cytoplasm, the incorporation of nucleocapsids into virions as determined in pulse-chase experiments was dependent on the activity of actin filaments with little if any effect on inhibition of microtubule function. These results indicate that the mechanisms by which nucleocapsids are transported to the farthest reaches of the cell differ from those required for incorporation into virions. This is likely due to the ability of nucleocapsids to follow shorter paths to the plasma membrane mediated by actin filaments.

IMPORTANCE
Nucleocapsids of nonsegmented negative-strand viruses like VSV are assembled in the cytoplasm during genome RNA replication and must migrate to the plasma membrane for assembly into virions. Nucleocapsids are too large to diffuse in the cytoplasm in the time required for virus assembly and must be transported by cytoskeletal elements. Previous results suggested that microtubules were responsible for migration of VSV nucleocapsids to the plasma membrane for virus assembly. Data presented here show that both microtubules and actin filaments are responsible for mobility of nucleocapsids in the cytoplasm, but that actin filaments play a larger role than microtubules in incorporation of nucleocapsids into virions.
Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions
Authors: Greening Chris , Ahmed F. Hafna , Mohamed A. Elaaf , Lee Brendon M. , Pandey Gunjan , Warden Andrew C. , Scott Colin , Oakeshott John G. , Taylor Matthew C. , Jackson Colin J. 
Published: April 2016

SUMMARY5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420in methanogenic archaea in processes such as substrate oxidation, C1pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid byMycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Foand F420are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
Investigation of bias in meta-analyses due to selective inclusion of trial effect estimates: empirical study
Authors: Page Matthew J , Forbes Andrew , Chau Marisa , Green Sally E , McKenzie Joanne E 
Published: April 2016

ObjectiveTo explore whether systematic reviewers selectively include trial effect estimates in meta-analyses when multiple are available, and what impact this may have on meta-analytic effects.DesignCross-sectional study.Data sourcesWe randomly selected systematic reviews of interventions from 2 clinical specialties published between January 2010 and 2012. The first presented meta-analysis of a continuous outcome in each review was selected (index meta-analysis), and all trial effect estimates that were eligible for inclusion in the meta-analysis (eg, from multiple scales or time points) were extracted from trial reports.AnalysisWe calculated a statistic (the Potential Bias Index (PBI)) to quantify and test for evidence of selective inclusion. The PBI ranges from 0 to 1; values above or below 0.5 are suggestive of selective inclusion of effect estimates more or less favourable to the intervention, respectively. The impact of any potential selective inclusion was investigated by comparing the index meta-analytic standardised mean difference (SMD) to the median of a randomly constructed distribution of meta-analytic SMDs (representing the meta-analytic SMD expected when there is no selective inclusion).Results31 reviews (250 trials) were included. The estimated PBI was 0.57 (95% CI 0.50 to 0.63), suggesting that trial effect estimates that were more favourable to the intervention were included in meta-analyses slightly more often than expected under a process consistent with random selection; however, the 95% CI included the null hypothesis of no selective inclusion. Any potential selective inclusion did not have an important impact on the meta-analytic effects.ConclusionThere was no clear evidence that selective inclusion of trial effect estimates occurred in this sample of meta-analyses. Further research on selective inclusion in other clinical specialties is needed. To enable readers to assess the risk of selective inclusion bias, we recommend that systematic reviewers report the methods used to select effect estimates to include in meta-analyses.
Rapid identification and antimicrobial susceptibility testing of positive blood cultures using MALDI-TOF MS and a modification of the standardised disc diffusion test: a pilot study
Authors: Fitzgerald C , Stapleton P , Phelan E , Mulhare P , Carey B , Hickey M , Lynch B , Doyle M 
Published: April 2016

AimsIn an era when clinical microbiology laboratories are under increasing financial pressure, there is a need for inexpensive, yet effective, rapid microbiology tests. The aim of this study was to evaluate a novel modification of standard methodology for the identification and antimicrobial susceptibility testing (AST) of pathogens in positive blood cultures, reducing the turnaround time of laboratory results by 24 h.Methods277 positive blood cultures had a Gram stain performed and were subcultured and incubated at 37°C in a CO2atmosphere for 4–6 h. Identification of the visible growth was performed using matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS). Taking a modified approach to the Clinical and Laboratory Standards Institute-standardised AST methodology, an inoculum density of 0.5 McFarland was prepared from the early growth for disc diffusion testing. The standard AST method was also performed on the 18–24 h culture.Results96% (n=73/76) of gram-negative organisms were correctly identified by MALDI-TOF MS. Comparative analysis of the rapid and standard AST results showed an overall interpretive category error rate of 7.7% (6.7% minor errors, 0.6% major errors and 0.4% very major errors). 100% ofStaphylococcus aureus(n=41) and enterococcus isolates (n=9) were correctly identified after 4–6 h incubation. The overall AST categorical agreement was also 100% for these isolates.ConclusionsAn incubation of 4–6 h directly from positive blood cultures allowed for both a rapid species identification and an antimicrobial susceptibility result approximately 24 h earlier than is possible using standard methodology.
Diurnal Climatology of the Boundary Layer in Southern California Using AMDAR Temperature and Wind Profiles
Authors: Rahn David A. , Mitchell Christopher J. 
Published: April 2016

AbstractObservations from commercial aircraft [e.g., the Aircraft Meteorological Data Relay (AMDAR) automated weather reports] have been increasing dramatically. Two main applications of the aircraft data are use in short-term forecasts and assimilation into numerical weather prediction models. Now that more than 10 years of measurements exist, using this dataset to construct a description of the long-term climatological behavior (a “climatology”) of the lower atmosphere is explored with two main objectives. The first objective is to examine strengths and weaknesses of using the dataset to construct a climatology of the lower atmosphere. Unlike the traditional twice-daily radiosonde launches, the high frequency of observations at major airports allows for an unprecedented set of diurnal information at many locations globally. The second objective is to obtain a climatology of the lower atmosphere of Southern California, specifically at Los Angeles, San Diego, and Ontario, during the spring and summer when the boundary layer is well defined and easily detected. The June 2001–14 climatology reveals that the deepening of the boundary layer overnight is consistent with a cloud-topped boundary layer. Whereas the average boundary layer height decreases right after sunrise at San Diego, at Los Angeles the deeper boundary layer persists about 4 h after sunrise and then decreases rapidly over 2 h as the onshore sea breeze strengthens. Morning intrusions of the marine air inland are easily detected at Ontario in some months but are practically nonexistent during July and August.
Behavioural improvement in a minimally conscious state after caloric vestibular stimulation: evidence from two single case studies
Authors: Vanzan Serena , Wilkinson David , Ferguson Heather , Pullicino Patrick , Sakel Mohamed 
Published: April 2016

Objective: To investigate whether caloric vestibular stimulation, a non-invasive form of neuro-modulation, alters the level of awareness in people residing in a minimally conscious state. Design: Single-case ( n = 2), prospective, controlled (ABAB) efficacy study. Setting: Tertiary, neuro-rehabilitation inpatient ward within a university hospital. Participants: Two individuals in a minimally conscious state. Intervention: Left ear caloric vestibular stimulation was performed in two four/five-week blocks interleaved with two four/five-week blocks of sham stimulation. Session duration and frequency gradually increased within each block from once per day for 10 minutes (Week 1) to once per day for 20 minutes (Week 2) to 20 minutes twice per day in the remaining weeks. Measures: Wessex Head Injury Matrix, JFK Coma Recovery Scale – Revised. Results: Both participants’ Wessex Head Injury Matrix scores indicated a transition from involuntary (i.e. mechanical vocalization) to voluntary (i.e. gesture making, selective responses to family members) behaviour that was time-locked to the onset of active stimulation. In one participant, this improvement persisted for at least four weeks after active stimulation, while in the other it diminished two weeks after stimulation. Allied, although less dramatic, changes were seen on the arousal and auditory subscales of the JFK Coma Recovery Scale – Revised. Conclusion: The data provide the first evidence that vestibular stimulation may help improve outcome in a low awareness state, although further studies are needed to replicate effect and determine longer-term benefit.
Effects of Remnant Tissue Preservation on the Tendon Graft in Anterior Cruciate Ligament Reconstruction
Authors: Takahashi Tsuneari , Kondo Eiji , Yasuda Kazunori , Miyatake Shin , Kawaguchi Yasuyuki , Onodera Jun , Kitamura Nobuto 
Published: April 2016

Background: There is controversy regarding the efficacy of remnant tissue preservation on graft healing in anterior cruciate ligament (ACL) reconstruction. Hypothesis: The preserved remnant tissue will (1) adhere to the graft surface and undergo a remodeling process, (2) accelerate graft revascularization, (3) increase the number of graft mechanoreceptors by 4 weeks, and (4) improve anteroposterior knee laxity and structural properties of the graft by 12 weeks. Study Design: Controlled laboratory study. Methods: Forty-two sheep were randomly divided into 2 groups of 21 animals. In group I, the ACL was completely removed. In group II, the ACL was transected at the midsubstance but not debrided. ACL reconstruction was performed using a semitendinosus tendon autograft in both groups. Histological changes of the grafted tendon and the remnant tissue were evaluated at 4 and 12 weeks after surgery. Biomechanically, anterior translation and knee joint stiffness under an anterior drawer force and the structural properties of the femur-graft-tibia complex were evaluated. Results: The preserved remnant tissue was histologically distinct from the graft at 4 weeks, while the tissue partially adhered to the graft surface at 12 weeks. The ACL remnant tissue significantly accelerated revascularization in the grafted tendon at 4 weeks and significantly increased the number of mechanoreceptors at 4 and 12 weeks. In addition, remnant preservation significantly improved anterior translation (9.3 ± 2.1 mm and 5.4 ± 1.7 mm at 60° of knee flexion in groups I and II, respectively) and knee joint stiffness at 12 weeks. However, there were no significant differences in the structural properties between the 2 groups at 4 and 12 weeks after surgery. Conclusion: Preservation of the ACL remnant tissue in ACL reconstruction enhanced cell proliferation, revascularization, and regeneration of proprioceptive organs in the reconstructed ACL and reduced anterior translation. However, remnant preservation did not improve the structural properties of the graft. Clinical Relevance: These results imply that preservation of the ACL remnant tissue may improve graft healing after ACL reconstruction.