bluuebunny/crossref_metadata_2025_split huggingface dataset:
A molecular gut content study of Themisto abyssorum (Amphipoda) from Arctic hydrothermal vent and cold seep systems
Authors: Olsen Bernt Rydland , Troedsson Christofer , Hadziavdic Kenan , Pedersen Rolf B. , Rapp Hans Tore 
Published: September 2013

AbstractThe use of DNA as a marker for prey inside the gut of predators has been instrumental in further understanding of known and unknown interactions. Molecular approaches are in particular useful in unavailable environments like the deep sea. Trophic interactions in the deep sea are difficult to observe in situ, correct deep‐sea experimental laboratory conditions are difficult to obtain, animals rarely survive the sampling, or the study organisms feed during the sampling due to long hauls. Preliminary studies of vent and seep systems in the Nordic Seas have identified the temperate‐cold‐water pelagic amphipod Themisto abyssorum as a potentially important predator in these chemosynthetic habitats. However, the prey of this deep‐sea predator is poorly known, and we applied denaturing high performance liquid chromatography (DHPLC) to investigate the predator–prey interactions of T. abyssorum in deep‐water vent and seep systems. Two deep‐water hydrothermally active localities (The Jan Mayen and Loki's Castle vent fields) and one cold seep locality (The Håkon Mosby mud volcano) in the Nordic Seas were sampled, genomic DNA of the stomachs of T. abyssorum was extracted, and 18S rDNA gene was amplified and used to map the stomach content. We found a wide range of organisms including micro‐eukaryotes, metazoans and detritus. Themisto abyssorum specimens from Loki's Castle had the highest diversity of prey. The wide range of prey items found suggests that T. abyssorum might be involved in more than one trophic level and should be regarded as an omnivore and not a strict carnivore as have previously been suggested.
Unlocking the vault: next‐generation museum population genomics
Authors: Bi Ke , Linderoth Tyler , Vanderpool Dan , Good Jeffrey M. , Nielsen Rasmus , Moritz Craig 
Published: September 2013

AbstractNatural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome‐scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here, we circumvent these challenges by using custom, multiplexed, exon capture to enrich and sequence ~11 000 exons (~4 Mb) from early 20th‐century museum skins. We used this approach to test for changes in genomic diversity accompanying a climate‐related range retraction in the alpine chipmunks (Tamias alpinus) in the high Sierra Nevada area of California, USA. We developed robust bioinformatic pipelines that rigorously detect and filter out base misincorporations in DNA derived from skins, most of which likely resulted from postmortem damage. Furthermore, to accommodate genotyping uncertainties associated with low‐medium coverage data, we applied a recently developed probabilistic method to call single‐nucleotide polymorphisms and estimate allele frequencies and the joint site frequency spectrum. Our results show increased genetic subdivision following range retraction, but no change in overall genetic diversity at either nonsynonymous or synonymous sites. This case study showcases the advantages of integrating emerging genomic and statistical tools in museum collection‐based population genomic applications. Such technical advances greatly enhance the value of museum collections, even where a pre‐existing reference is lacking and points to a broad range of potential applications in evolutionary and conservation biology.
Discrepancies between explicit and implicit self‐esteem and their relationship to symptoms of depression and mania
Authors: Pavlickova Hana , Turnbull Oliver H. , Bentall Richard P. 
Published: September 2013

ObjectivesSelf‐esteem is a key feature of bipolar symptomatology. However, so far no study has examined the interaction between explicit and implicit self‐esteem in individuals vulnerable to bipolar disorder.DesignCross‐sectional design was employed.MethodsThirty children of parents with bipolar disorder and 30 offspring of control parents completed Hamilton Rating Scale for Depression, the Bech‐Rafaelson Mania Scale, the Self‐esteem Rating Scale and the Implicit Association Test.ResultsNo differences between groups were revealed in levels of explicit or implicit self‐esteem. However, bipolar offspring showed increased levels of symptoms of depression and mania. Furthermore, depressive symptoms were associated with low explicit self‐esteem, whilst symptoms of mania were associated with low implicit self‐esteem. When self‐esteem discrepancies were examined, damaged self‐esteem (i.e., low explicit but high implicit self‐esteem) was associated with depression, whilst no associations between mania and self‐esteem discrepancies were found.ConclusionsNot only explicit, but also implicit self‐esteem, and the interactions between the two are of relevance in bipolar symptoms. Clinical implications and future research directions are discussed.Practitioner points

Explicit as well as implicit SE, and particularly their relationship, are relevant for mental health.

Fluctuations in implicit SE may serve as an early indicator for risk of bipolarity.

Psychotherapeutic approaches may be more suitable for one kind of SE challenge than the other.
Overnight storage of whole blood: cooling and transporting blood at room temperature under extreme temperature conditions
Authors: Thibault L. , Beauséjour A. , Jacques A. , Ducas É. , Tremblay M. 
Published: September 2013

Background and ObjectivesMany countries allow the overnight storage of whole blood (WB) at ambient temperature. Some countries, such as Canada, also require a rapid cooling of WB with an active cooling system. Given the significant operational constraints associated with current cooling systems, an alternative method for cooling and transporting WB at 20–24°C was evaluated.Materials and MethodsPhase 22 cooling packs (TCP Reliable Inc., USA) were used in combination with vacuum‐insulated panel (VIP) boxes. Temperature profiles of simulated WB units were studied in extreme temperatures (−35 and 40°C). The quality of blood components prepared using Phase 22 packs and CompoCool‐WB (Fresenius HemoCare, Germany) was studied.ResultsPhase 22 packs reduced the temperature of simulated WB bags from 37 to 24°C in 1·7 ± 0·2 h. Used in combination with VIP boxes, Phase 22 packs maintain the temperature of bags between 20 and 24°C for 15 and 24 h, compared to 2 and 11 h with CompoCool‐WB, when exposed at −35 and 40°C, respectively. The quality of platelet concentrates and plasma was comparable, regardless of the cooling system used. For red blood cell units, per cent haemolysis on day 42 was slightly higher in products prepared after cooling with Phase 22 packs compared to CompoCool‐WB (0·33 ± 0·15% vs. 0·21 ± 0·06%; P < 0·05).ConclusionsPhase 22 packs combined with VIP boxes are an acceptable alternative to butane‐1,4‐diol cooling systems. This system allows blood manufacturers to transport WB to processing facilities in a broad range of environmental conditions.
A novel approach for direct reconstruction of parametric images for myocardial blood flow from PET imaging
Authors: Su Kuan‐Hao , Yen Tzu‐Chen , Fang Yu‐Hua Dean 
Published: September 2013

Purpose:The aim of this study is to develop and evaluate a novel direct reconstruction method to improve the signal‐to‐noise ratio (SNR) of parametric images in dynamic positron‐emission tomography (PET), especially for applications in myocardial perfusion studies.Methods:Simulation studies were used to test the performance in SNR and computational efficiency for different methods. The NCAT phantom was used to generate simulated dynamic data. Noise realization was performed in the sinogram domain and repeated for 30 times with four different noise levels by varying the injection dose (ID) from standard ID to 1/8 of it. The parametric images were calculated by (1) three direct methods that compute the kinetic parameters from the sinogram and (2) an indirect method, which computes the kinetic parameter with pixel‐by‐pixel curve fitting in image space using weighted least‐squares. The first direct reconstruction maximizes the likelihood function using trust‐region‐reflective (TRR) algorithm. The second approach uses tabulated parameter sets to generate precomputed time‐activity curves for maximizing the likelihood functions. The third approach, as a newly proposed method, assumes separable complete data to derive the M‐step for maximizing the likelihood.Results:The proposed method with the separable complete data performs similarly to the other two direct reconstruction methods in terms of the SNR, providing a 5%–10% improvement as compared to the indirect parametric reconstruction under the standard ID. The improvement of SNR becomes more obvious as the noise level increases, reaching more than 30% improvement under 1/8 ID. Advantage of the proposed method lies in the computation efficiency by shortening the time requirement to 25% of the indirect approach and 3%–6% of other direct reconstruction methods.Conclusions:With results provided from this simulation study, direct reconstruction of myocardial blood flow shows a high potential for improving the parametric image quality for clinical use.
Risk Factors for Campylobacteriosis in Two Washington State Counties with High Numbers of Dairy Farms
Authors: Davis Margaret A. , Moore Danna L. , Baker Katherine N. K. , French Nigel P. , Patnode Marianne , Hensley Joni , MacDonald Kathryn , Besser Thomas E. 
Published: September 2013

ABSTRACT

Campylobacteriosis is a frequently reported, food-borne, human bacterial disease that can be associated with ruminant reservoirs, although public health messages primarily focus on poultry. In Washington State, the two counties with the highest concentrations of dairy cattle also report the highest incidences of campylobacteriosis. Conditional logistic regression analysis of case-control data from both counties found living or working on a dairy farm (odds ratio [OR], 6.7 [95% confidence interval [CI], 1.7 to 26.4]) and Hispanic ethnicity (OR, 6.4 [95% CI, 3.1 to 13.1]) to have the strongest significant positive associations with campylobacteriosis. When the analysis was restricted to residents of one county, Hispanic ethnicity (OR, 9.3 [95% CI, 3.9 to 22.2]), contact with cattle (OR, 5.0 [95% CI, 1.3 to 19.5]), and pet ownership (OR, 2.6 [95% CI, 1.1 to 6.3]) were found to be independent risk factors for disease.
Campylobacter jejuni
isolates from human (
n
= 65), bovine (
n
= 28), and retail poultry (
n
= 27) sources from the same counties were compared using multilocus sequence typing. These results indicated that sequence types commonly found in human isolates were also commonly found in bovine isolates. These findings suggest that, in areas with high concentrations of dairy cattle, exposure to dairy cattle may be more important than food-borne exposure to poultry products as a risk for campylobacteriosis.
Evaluation of Pneumococcal Serotyping by Multiplex PCR and Quellung Reactions
Authors: Richter Sandra S. , Heilmann Kristopher P. , Dohrn Cassie L. , Riahi Fathollah , Diekema Daniel J. , Doern Gary V. 
Published: September 2013

ABSTRACT
Screening of 1,750 pneumococcal isolates for common serotypes by PCR was followed by Quellung reaction analysis of PCR-negative isolates with a comparison to the conventional (Quellung reaction only) approach. PCR agreed with Quellung reaction results for 99% of isolates. The sequential PCR/Quellung reaction algorithm is accurate and more cost-effective than the conventional approach.
Incidence of Inducible Clindamycin Resistance in Staphylococcus pseudintermedius from Dogs
Authors: Gold Randi M. , Lawhon Sara D. 
Published: September 2013

ABSTRACTClindamycin is increasingly used to treat canine pyoderma. Eight of 608Staphylococcus pseudintermediusisolates were positive for inducible clindamycin resistance by double-disk diffusion testing and PCR detection ofermB.Staphylococcus pseudintermediusisolates that are erythromycin resistant but clindamycin susceptible byin vitroantimicrobial susceptibility testing should be tested for inducible clindamycin resistance.
Identification of Novel Host Factors via Conserved Domain Search: Cns1 Cochaperone Is a Novel Restriction Factor of Tombusvirus Replication in Yeast
Authors: Lin Jing-Yi , Nagy Peter D. 
Published: September 2013

ABSTRACT

A large number of host-encoded proteins affect the replication of plus-stranded RNA viruses by acting as susceptibility factors. Many other cellular proteins are known to function as restriction factors of viral infections. Previous studies with tomato bushy stunt tombusvirus (TBSV) in a yeast model host have revealed the inhibitory function of TPR (tetratricopeptide repeat) domain-containing cyclophilins, which are members of the large family of host prolyl isomerases, in TBSV replication. In this paper, we tested additional TPR-containing yeast proteins in a cell-free TBSV replication assay and identified the Cns1p cochaperone for heat shock protein 70 (Hsp70) and Hsp90 chaperones as a strong inhibitor of TBSV replication. Cns1p interacted with the viral replication proteins and inhibited the assembly of the viral replicase complex and viral RNA synthesis
in vitro
. Overexpression of Cns1p inhibited TBSV replication in yeast. The use of a temperature-sensitive (TS) mutant of Cns1p in yeast revealed that at a semipermissive temperature, TS Cns1p could not inhibit TBSV replication. Interestingly, Cns1p and the TPR-containing Cpr7p cyclophilin have similar inhibitory functions during TBSV replication, although some of the details of their viral restriction mechanisms are different. Our observations indicate that TPR-containing cellular proteins could act as virus restriction factors.
High-Avidity and Potently Neutralizing Cross-Reactive Human Monoclonal Antibodies Derived from Secondary Dengue Virus Infection
Authors: Tsai Wen-Yang , Lai Chih-Yun , Wu Yi-Chieh , Lin Hong-En , Edwards Carolyn , Jumnainsong Amonrat , Kliks Srisakul , Halstead Scott , Mongkolsapaya Juthathip , Screaton Gavin R. , Wang Wei-Kung 
Published: September 2013

ABSTRACT
The envelope (E) protein of dengue virus (DENV) is the major target of neutralizing antibodies (Abs) and vaccine development. Previous studies of human dengue-immune sera reported that a significant proportion of anti-E Abs, known as group-reactive (GR) Abs, were cross-reactive to all four DENV serotypes and to one or more other flaviviruses. Based on studies of mouse anti-E monoclonal antibodies (MAbs), GR MAbs were nonneutralizing or weakly neutralizing compared with type-specific MAbs; a GR response was thus not regarded as important for vaccine strategy. We investigated the epitopes, binding avidities, and neutralization potencies of 32 human GR anti-E MAbs. In addition to fusion loop (FL) residues in E protein domain II, human GR MAbs recognized an epitope involving both FL and bc loop residues in domain II. The neutralization potencies and binding avidities of GR MAbs derived from secondary DENV infection were stronger than those derived from primary infection. GR MAbs derived from primary DENV infection primarily blocked attachment, whereas those derived from secondary infection blocked DENV postattachment. Analysis of the repertoire of anti-E MAbs derived from patients with primary DENV infection revealed that the majority were GR, low-avidity, and weakly neutralizing MAbs, whereas those from secondary infection were primarily GR, high-avidity, and potently neutralizing MAbs. Our findings suggest that the weakly neutralizing GR anti-E Abs generated from primary DENV infection become potently neutralizing MAbs against the four serotypes after secondary infection. The observation that the dengue immune status of the host affects the quality of the cross-reactive Abs generated has implications for new strategies for DENV vaccination.
Gamma Interferon Regulates Contraction of the Influenza Virus-Specific CD8 T Cell Response and Limits the Size of the Memory Population
Authors: Prabhu Nayana , Ho Adrian W. , Wong Kenneth H. S. , Hutchinson Paul Edward , Chua Yen Leong , Kandasamy Matheswaran , Lee Debbie C. P. , Sivasankar Baalasubramanian , Kemeny David Michael 
Published: September 2013

ABSTRACTThe factors that regulate the contraction of the CD8 T cell response and the magnitude of the memory cell population against localized mucosal infections such as influenza are important for generation of efficient vaccines but are currently undefined. In this study, we used a mouse model of influenza to demonstrate that the absence of gamma interferon (IFN-γ) or IFN-γ receptor 1 (IFN-γR1) leads to aberrant contraction of antigen-specific CD8 T cell responses. The increased accumulation of the effector CD8 T cell population was independent of viral load. Reduced contraction was associated with an increased fraction of CD8 T cells expressing the interleukin-7 receptor (IL-7R) at the peak of the response, resulting in enhanced numbers of memory/memory precursor cells in IFN-γ−/−and IFN-γR−/−compared to wild-type (WT) mice. Blockade of IL-7 within the lungs of IFN-γ−/−mice restored the contraction of influenza virus-specific CD8 T cells, indicating that IL-7R is important for survival and is not simply a consequence of the lack of IFN-γ signaling. Finally, enhanced CD8 T cell recall responses and accelerated viral clearance were observed in the IFN-γ−/−and IFN-γR−/−mice after rechallenge with a heterologous strain of influenza virus, confirming that higher frequencies of memory precursors are formed in the absence of IFN-γ signaling. In summary, we have identified IFN-γ as an important regulator of localized viral immunity that promotes the contraction of antigen-specific CD8 T cells and inhibits memory precursor formation, thereby limiting the size of the memory cell population after an influenza virus infection.
Mechanistic Insights into the Enhancement of Adeno-Associated Virus Transduction by Proteasome Inhibitors
Authors: Mitchell Angela M. , Samulski R. Jude 
Published: September 2013

ABSTRACT
Proteasome inhibitors (e.g., bortezomib, MG132) are known to enhance adeno-associated virus (AAV) transduction; however, whether this results from pleotropic proteasome inhibition or off-target serine and/or cysteine protease inhibition remains unresolved. Here, we examined recombinant AAV (rAAV) effects of a new proteasome inhibitor, carfilzomib, which specifically inhibits chymotrypsin-like proteasome activity and no other proteases. We determined that proteasome inhibitors act on rAAV through proteasome inhibition and not serine or cysteine protease inhibition, likely through positive changes late in transduction.
Chandipura Virus Induces Neuronal Death through Fas-Mediated Extrinsic Apoptotic Pathway
Authors: Ghosh Sourish , Dutta Kallol , Basu Anirban 
Published: September 2013

ABSTRACTChandipura virus (CHPV; genusVesiculovirus, familyRhabdoviridae) is an emerging tropical pathogen with a case fatality rate of 55 to 75% that predominantly affects children in the age group of 2 to 16 years. Although it has been established as a neurotropic virus causing encephalitis, the molecular pathology leading to neuronal death is unknown. The present study elucidates for the first time the mechanism of cell death in neurons after CHPV infection that answers the basic cause of CHPV-mediated neurodegeneration. Through various cell death assaysin vitroandin vivo, a relationship between viral replication within neuron and neuronal apoptosis has been established. We report that expression of CHPV phosphoprotein increases up to 6 h postinfection and diminishes thereafter in neuronal cell lines, signifying the replicative phase of CHPV. Various analyses conducted during the investigation established that CHPV-infected neurons are undergoing apoptosis through an extrinsic pathway mediated through the Fas-associated death domain (FADD) following activation of caspase-8 and -3 and prominent cleavage of poly(ADP-ribose) polymerase (PARP). Knocking down the expression of caspase-3, the final executioner of apoptosis, in a neuronal cell line by endoribonuclease-prepared small interfering RNA (siRNA) validated its pivotal role in CHPV-mediated neurodegeneration by showing reduction in apoptosis after CHPV infection.
A Mutant Influenza Virus That Uses an N1 Neuraminidase as the Receptor-Binding Protein
Authors: Hooper Kathryn A. , Bloom Jesse D. 
Published: September 2013

ABSTRACT
In the vast majority of influenza A viruses characterized to date, hemagglutinin (HA) is the receptor-binding and fusion protein, whereas neuraminidase (NA) is a receptor-cleaving protein that facilitates viral release but is expendable for entry. However, the NAs of some recent human H3N2 isolates have acquired receptor-binding activity via the mutation D151G, although these isolates also appear to retain the ability to bind receptors via HA. We report here the laboratory generation of a mutation (G147R) that enables an N1 NA to completely co-opt the receptor-binding function normally performed by HA. Viruses with this mutant NA grow to high titers even in the presence of extensive mutations to conserved residues in HA's receptor-binding pocket. When the receptor-binding NA is paired with this binding-deficient HA, viral infectivity and red blood cell agglutination are blocked by NA inhibitors. Furthermore, virus-like particles expressing only the receptor-binding NA agglutinate red blood cells in an NA-dependent manner. Although the G147R NA receptor-binding mutant virus that we characterize is a laboratory creation, this same mutation is found in several natural clusters of H1N1 and H5N1 viruses. Our results demonstrate that, at least in tissue culture, influenza virus receptor-binding activity can be entirely shifted from HA to NA.
Middle East Respiratory Syndrome Coronavirus Infection Mediated by the Transmembrane Serine Protease TMPRSS2
Authors: Shirato Kazuya , Kawase Miyuki , Matsuyama Shutoku 
Published: September 2013

ABSTRACT

The Middle East respiratory syndrome coronavirus (MERS-CoV) utilizes host proteases for virus entry into lung cells. In the current study, Vero cells constitutively expressing type II transmembrane serine protease (Vero-TMPRSS2 cells) showed larger syncytia at 18 h after infection with MERS-CoV than after infection with other coronaviruses. Furthermore, the susceptibility of Vero-TMPRSS2 cells to MERS-CoV was 100-fold higher than that of non-TMPRSS2-expressing parental Vero cells. The serine protease inhibitor camostat, which inhibits TMPRSS2 activity, completely blocked syncytium formation but only partially blocked virus entry into Vero-TMPRSS2 cells. Importantly, the coronavirus is thought to enter cells via two distinct pathways, one mediated by TMPRSS2 at the cell surface and the other mediated by cathepsin L in the endosome. Simultaneous treatment with inhibitors of cathepsin L and TMPRSS2 completely blocked virus entry into Vero-TMPRSS2 cells, indicating that MERS-CoV employs both the cell surface and the endosomal pathway to infect Vero-TMPRSS2 cells. In contrast, a single camostat treatment suppressed MERS-CoV entry into human bronchial submucosal gland-derived Calu-3 cells by 10-fold and virus growth by 270-fold, although treatment with both camostat and (23,25)-
trans
-epoxysuccinyl-
l
-leucylamindo-3-methylbutane ethyl ester, a cathepsin inhibitor, or treatment with leupeptin, an inhibitor of cysteine, serine, and threonine peptidases, was no more efficacious than treatment with camostat alone. Further, these inhibitors were not efficacious against MERS-CoV infection of MRC-5 and WI-38 cells, which were derived from lung, but these characters differed from those of mature pneumocytes. These results suggest that a single treatment with camostat is sufficient to block MERS-CoV entry into a well-differentiated lung-derived cell line.