bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical and physical weathering in a hot‐arid, tectonically active alluvial system of Anza Borrego Desert, California
Authors: Joo Young Ji , Elwood Madden Megan E. , Soreghan Gerilyn S. 
Published: October 2015

AbstractInvestigation of chemical and physical weathering of bedrock and alluvial sediment in the Anza Borrego Desert, California, sheds light on weathering processes in hot‐arid systems and clarifies interpretations of climate from alluvial sediment. All of the alluvial sediment in the study area emanates from Cretaceous tonalite of the Peninsular Range, enabling exploration of the effects of external variables – climate, transport distance and tectonics – on the physical and chemical properties of the sediment. Chemical weathering in this area is dominated by plagioclase alteration observed in both bedrock outcrops and sediment, evinced most clearly by changes in the Eu anomaly. Biotite chemical weathering, manifested by interlayer K+ loss, is not evident in bedrock, but clearly observed in the sediment. Despite the weak intensity of chemical weathering (Chemical Index of Alteration = 56 to 62), fine‐grained (<63 μm) sediment displays a clear weathering trend in A–CN–K space and contains up to 25% clay minerals. Physical abrasion and grain‐size reduction in biotite during transport predominates in the sediment, whereas physical (insolation) weathering affecting bedrock is inferred from estimates of differential thermal expansion of mineral phases in response to extreme temperature changes in the study area. Chemical alteration and Brunauer–Emmett–Teller surface area both increase within the active Elsinore fault zone at the distal end of the depositional transect, reflecting tectonic‐induced fracturing and associated accelerated weathering. Extensive fracturing, together with a more humid Pleistocene climate, probably facilitated in situ bedrock weathering, preceding arid alluvial deposition in the Holocene. This study demonstrates that both climate and tectonic processes can affect chemical and physical weathering, resulting in alteration of plagioclase, leaching of K+ from biotite in the sediment and formation of clay minerals, even in hot, arid systems.
Coastal lagoons and beach ridges as complementary sedimentary archives for the reconstruction of Holocene relative sea‐level changes
Authors: Sander Lasse , Hede Mikkel U. , Fruergaard Mikkel , Nielsen Lars , Clemmensen Lars B. , Kroon Aart , Johannessen Peter N. , Nielsen Lars H. , Pejrup Morten 
Published: October 2015

AbstractCoastal lagoons and beach ridges are genetically independent, though non‐continuous, sedimentary archives. We here combine the results from two recently published studies in order to produce an 8000‐year‐long record of Holocene relative sea‐level changes on the island of Samsø, southern Kattegat, Denmark. The reconstruction of the initial mid‐Holocene sea‐level rise is based on the sedimentary infill from topography‐confined coastal lagoons (Sander et al., Boreas, 2015b). Sea‐level index points over the mid‐ to late Holocene period of sea‐level stability and fall are retrieved from the internal structures of a wide beach‐ridge system (Hede et al., The Holocene, 2015). Data from sediment coring, georadar and absolute dating are thus combined in an inter‐disciplinary approach that is highly reproducible in micro‐tidal environments characterised by high sediment supply. We show here that the commonly proximate occurrence of coastal lagoons and beach ridges allows us to produce seamless time series of relative sea‐level changes from field sites in SW Scandinavia and in similar coastal environments.
Naturally Acquired HMW1- and HMW2-Specific Serum Antibodies in Adults and Children Mediate Opsonophagocytic Killing of Nontypeable Haemophilus influenzae
Authors: Winter Linda E. , Barenkamp Stephen J. 
Published: October 2015

ABSTRACTThe HMW1 and HMW2 proteins are highly immunogenic adhesins expressed by approximately 75% of nontypeableHaemophilus influenzae(NTHi) strains, and HMW1- and HMW2-specific antibodies can mediate opsonophagocytic killing of NTHi. In this study, we assessed the ability of HMW1- and HMW2-specific antibodies in sera from healthy adults and convalescent-phase sera from children with NTHi otitis media to mediate killing of homologous and heterologous NTHi. The serum samples were examined pre- and postadsorption on HMW1 and HMW2 affinity columns, and affinity-purified antibodies were assessed for ability to mediate killing of homologous and heterologous strains. Adult serum samples mediated the killing of six prototype NTHi strains at titers of <1:10 to 1:1,280. HMW1- and HMW2-adsorbed sera demonstrated unchanged to 8-fold decreased opsonophagocytic titers against the homologous strains. Each affinity-purified antibody preparation mediated the killing of the respective homologous strain at titers of <1:10 to 1:320 and of the five heterologous strains at titers of <1:10 to 1:320, with most preparations killing most heterologous strains to some degree. None of the acute-phase serum samples from children mediated killing, but each convalescent-phase serum sample mediated killing of the infecting strain at titers of 1:40 to 1:640. HMW1- and HMW2-adsorbed convalescent-phase serum samples demonstrated ≥4-fold decreases in titer. Three of four affinity-purified antibody preparations mediated killing of the infecting strain at titers of 1:20 to 1:320, but no killing of representative heterologous strains was observed. HMW1- and HMW2-specific antibodies capable of mediating opsonophagocytic killing are present in the serum from normal adults and develop in convalescent-phase sera of children with NTHi otitis media. Continued investigation of the HMW1 and HMW2 proteins as potential vaccine candidates for the prevention of NTHi disease is warranted.
Enumeration of Gut-Homing β7-Positive, Pathogen-Specific Antibody-Secreting Cells in Whole Blood from Enterotoxigenic Escherichia coli- and Vibrio cholerae-Infected Patients, Determined Using an Enzyme-Linked Immunosorbent Spot Assay Technique
Authors: Bhuiyan Taufiqur Rahman , Hoq Mohammad Rubel , Nishat Naoshin Sharmin , Al Mahbuba Deena , Rashu Rasheduzzaman , Islam Kamrul , Hossain Lazina , Dey Ayan , Harris Jason B. , Ryan Edward T. , Calderwood Stephen B. , Svennerholm Ann-Mari , Qadri Firdausi 
Published: October 2015

ABSTRACTVibrio choleraeand enterotoxigenicEscherichia coli(ETEC) are noninvasive mucosal pathogens that cause acute watery diarrhea in people in developing countries. Direct assessment of the mucosal immune responses to these pathogens is problematic. Surrogate markers of local mucosal responses in blood are increasingly being studied to determine the mucosal immune responses after infection. However, the volume of blood available in children and infants has limited this approach. We assessed whether an approach that first isolates β7-positive cells from a small volume of blood would allow measurement of the antigen-specific immune responses in patients with cholera and ETEC infection. β7 is a cell surface marker associated with mucosal homing. We isolated β7-expressing cells from blood on days 2, 7, and 30 and used an enzyme-linked immunosorbent spot (ELISPOT) assay to assess the gut-homing antibody-secreting cells (ASCs) specific to pathogen antigens. Patients with ETEC diarrhea showed a significant increase in toxin-specific gut-homing ASCs at day 7 compared to the levels at days 2 and 30 after onset of illness and to the levels in healthy controls. Similar elevations of responses to the ETEC colonization factors (CFs) CS6 and CFA/I were observed in patients infected with CS6- and CFA/I-positive ETEC strains. Antigen-specific gut-homing ASCs to the B subunit of cholera toxin and cholera-specific lipopolysaccharides (LPS) were also observed on day 7 after the onset of cholera using this approach. This study demonstrates that a simple ELISPOT assay can be used to study the mucosal immunity to specific antigens using a cell-sorting protocol to isolate mucosal homing cells, facilitating measurement of mucosal responses in children following infection or vaccination.
Meningitis and Bacteremia Due to Neisseria cinerea following a Percutaneous Rhizotomy of the Trigeminal Ganglion
Authors: von Kietzell M. , Richter H. , Bruderer T. , Goldenberger D. , Emonet S. , Strahm C. 
Published: October 2015

ABSTRACT

Neisseria cinerea
is a human commensal. The first known case of meningitis and bacteremia due to
Neisseria cinerea
following percutaneous glycerol instillation of the trigeminal ganglion is reported. Conventional phenotypic methods and complete 16S RNA gene sequencing accurately identified the pathogen. Difficulties in differentiation from pathogenic neisseriae are discussed.
An Update on Clostridium difficile Toxinotyping
Authors: Rupnik Maja , Janezic Sandra 
Published: October 2015

ABSTRACT

Toxinotyping is a PCR-restriction fragment length polymorphism (RFLP)-based method for differentiation of
Clostridium difficile
strains according to the changes in the pathogenicity locus (PaLoc), a region coding for toxins A and B. Toxinotypes are a heterogenous group of strains that are important in the development of molecular diagnostic tests and vaccines and are a good basis for
C. difficile
phylogenetic studies. Here we describe an overview of the 34 currently known toxinotypes (I to XXXIV) and some changes in nomenclature.
Laboratory-Acquired Infection with Salmonella enterica Serovar Typhimurium Exposed by Whole-Genome Sequencing
Authors: Alexander David C. , Fitzgerald Stephen F. , DePaulo Rachel , Kitzul Rosanne , Daku Dawn , Levett Paul N. , Cameron Andrew D. S. 
Published: October 2015

ABSTRACT
Despite advances in laboratory design, professional training, and workplace biosafety guidelines, laboratory-acquired infections continue to occur. Effective tools are required to investigate cases and prevent future illness. Here, we demonstrate the value of whole-genome sequencing as a tool for the identification and source attribution of laboratory-acquired salmonellosis.
Microbiological Characteristics of Chlamydia trachomatis and Neisseria gonorrhoeae Infections in South African Women
Authors: Dubbink Jan Henk , de Waaij Dewi J. , Bos Myrte , van der Eem Lisette , Bébéar Cécile , Mbambazela Nontembeko , Ouburg Sander , Peters Remco P. H. , Morré Servaas A. 
Published: October 2015

ABSTRACT

We analyzed data of 263 women with at least one genital or anorectal sexually transmitted infection from a cross-sectional study conducted in rural South Africa. We provide new insights concerning the concurrence of
Chlamydia trachomatis
,
Neisseria gonorrhoeae
,
Mycoplasma genitalium
, and
Trichomonas vaginalis
infections as well as the characteristics of bacterial loads.
Elucidation of the Molecular Mechanism Driving Duplication of the HIV-1 PTAP Late Domain
Authors: Martins Angelica N. , Waheed Abdul A. , Ablan Sherimay D. , Huang Wei , Newton Alicia , Petropoulos Christos J. , Brindeiro Rodrigo D. M. , Freed Eric O. 
Published: October 2015

ABSTRACTHIV-1 uses cellular machinery to bud from infected cells. This cellular machinery is comprised of several multiprotein complexes known as endosomal sorting complexes required for transport (ESCRTs). A conserved late domain motif, Pro-Thr-Ala-Pro (PTAP), located in the p6 region of Gag (p6Gag), plays a central role in ESCRT recruitment to the site of virus budding. Previous studies have demonstrated that PTAP duplications are selected in HIV-1-infected patients during antiretroviral therapy; however, the consequences of these duplications for HIV-1 biology and drug resistance are unclear. To address these questions, we constructed viruses carrying a patient-derived PTAP duplication with and without drug resistance mutations in the viral protease. We evaluated the effect of the PTAP duplication on viral release efficiency, viral infectivity, replication capacity, drug susceptibility, and Gag processing. In the presence of protease inhibitors, we observed that the PTAP duplication in p6Gagsignificantly increased the infectivity and replication capacity of the virus compared to those of viruses bearing only resistance mutations in protease. Our biochemical analysis showed that the PTAP duplication, in combination with mutations in protease, enhances processing between the nucleocapsid and p6 domains of Gag, resulting in more complete Gag cleavage in the presence of protease inhibitors. These results demonstrate that duplication of the PTAP motif in p6Gagconfers a selective advantage in viral replication by increasing Gag processing efficiency in the context of protease inhibitor treatment, thereby enhancing the drug resistance of the virus. These findings highlight the interconnected role of PTAP duplications and protease mutations in the development of resistance to antiretroviral therapy.IMPORTANCEResistance to current drug therapy limits treatment options in many HIV-1-infected patients. Duplications in a Pro-Thr-Ala-Pro (PTAP) motif in the p6 domain of Gag are frequently observed in viruses derived from patients on protease inhibitor (PI) therapy. However, the reason that these duplications arise and their consequences for virus replication remain to be established. In this study, we examined the effect of PTAP duplication on PI resistance in the context of wild-type protease or protease bearing PI resistance mutations. We observe that PTAP duplication markedly enhances resistance to a panel of PIs. Biochemical analysis reveals that the PTAP duplication reverses a Gag processing defect imposed by the PI resistance mutations in the context of PI treatment. The results provide a long-sought explanation for why PTAP duplications arise in PI-treated patients.
Dengue Virus prM-Specific Human Monoclonal Antibodies with Virus Replication-Enhancing Properties Recognize a Single Immunodominant Antigenic Site
Authors: Smith Scott A. , Nivarthi Usha K. , de Alwis Ruklanthi , Kose Nurgun , Sapparapu Gopal , Bombardi Robin , Kahle Kristen M. , Pfaff Jennifer M. , Lieberman Sherri , Doranz Benjamin J. , de Silva Aravinda M. , Crowe James E. 
Published: October 2015

ABSTRACT
The proposed antibody-dependent enhancement (ADE) mechanism for severe dengue virus (DENV) disease suggests that non-neutralizing serotype cross-reactive antibodies generated during a primary infection facilitate entry into Fc receptor bearing cells during secondary infection, resulting in enhanced viral replication and severe disease. One group of cross-reactive antibodies that contributes considerably to this serum profile target the premembrane (prM) protein. We report here the isolation of a large panel of naturally occurring human monoclonal antibodies (MAbs) obtained from subjects following primary DENV serotype 1, 2, or 3 or secondary natural DENV infections or following primary DENV serotype 1 live attenuated virus vaccination to determine the antigenic landscape on the prM protein that is recognized by human antibodies. We isolated 25 prM-reactive human MAbs, encoded by diverse antibody-variable genes. Competition-binding studies revealed that all of the antibodies bound to a single major antigenic site on prM. Alanine scanning-based shotgun mutagenesis epitope mapping studies revealed diverse patterns of fine specificity of various clones, suggesting that different antibodies use varied binding poses to recognize several overlapping epitopes within the immunodominant site. Several of the antibodies interacted with epitopes on both prM and E protein residues. Despite the diverse genetic origins of the antibodies and differences in the fine specificity of their epitopes, each of these prM-reactive antibodies was capable of enhancing the DENV infection of Fc receptor-bearing cells.

IMPORTANCE
Antibodies may play a critical role in the pathogenesis of enhanced DENV infection and disease during secondary infections. A substantial proportion of enhancing antibodies generated in response to natural dengue infection are directed toward the prM protein. The fine specificity of human prM antibodies is not understood. Here, we isolated a panel of dengue prM-specific human monoclonal antibodies from individuals after infection in order to define the mode of molecular recognition by enhancing antibodies. We found that only a single antibody molecule can be bound to each prM protein at any given time. Distinct overlapping epitopes were mapped, but all of the epitopes lie within a single major antigenic site, suggesting that this antigenic domain forms an immunodominant region of the protein. Neutralization and antibody-dependent enhanced replication experiments showed that recognition of any of the epitopes within the major antigenic site on prM was sufficient to cause enhanced infection of target cells.
Extracellular Vesicles Mediate Receptor-Independent Transmission of Novel Tick-Borne Bunyavirus
Authors: Silvas Jesus A. , Popov Vsevolod L. , Paulucci-Holthauzen Adriana , Aguilar Patricia V. 
Published: October 2015

ABSTRACT

Severe fever with thrombocytopenia syndrome (SFTS) virus is a newly recognized member of the genus
Phlebovirus
in the family
Bunyaviridae
. The virus was isolated from patients presenting with hemorrhagic manifestations and an initial case fatality rate of 12 to 30% was reported. Due to the recent emergence of this pathogen, there is limited knowledge on the molecular virology of SFTS virus. Recently, we reported that the SFTS virus NSs protein inhibited the activation of the beta interferon (IFN-β) promoter. Furthermore, we also found that SFTS virus NSs relocalizes key components of the IFN response into NSs-induced cytoplasmic structures. Due to the important role these structures play during SFTS virus replication, we conducted live cell imaging studies to gain further insight into the role and trafficking of these cytoplasmic structures during virus infection. We found that some of the SFTS virus NSs-positive cytoplasmic structures were secreted to the extracellular space and endocytosed by neighboring cells. We also found that these secreted structures isolated from NSs-expressing cells and SFTS virus-infected cells were positive for the viral protein NSs and the host protein CD63, a protein associated with extracellular vesicles. Electron microscopy studies also revealed that the isolated CD63-immunoprecipitated extracellular vesicles produced during SFTS virus infection contained virions. The virions harbored within these structures were efficiently delivered to uninfected cells and were able to sustain SFTS virus replication. Altogether, these results suggest that SFTS virus exploits extracellular vesicles to mediate virus receptor-independent transmission to host cells and open the avenue for novel therapeutic strategies against SFTS virus and related pathogens.

IMPORTANCE
SFTS virus is novel bunyavirus associated with hemorrhagic fever illness. Currently, limited information is available about SFTS virus. In the present study, we demonstrated that extracellular vesicles produced by SFTS virus-infected cells harbor infectious virions. We sought to determine whether these “infectious” extracellular vesicles can mediate transmission of the virus and confirmed that the SFTS virions were efficiently transported by these secreted structures into uninfected cells and were able to sustain efficient replication of SFTS virus. These results have significant impact on our understanding of how the novel tick-borne phleboviruses hijack cellular machineries to establish infection and point toward a novel mechanism for virus replication among arthropod-borne viruses.
Infectious Risks of Air Travel
Authors: Mangili Alexandra , Vindenes Tine , Gendreau Mark 
Published: October 2015

ABSTRACT
Infectious diseases are still among the leading causes of death worldwide due to their persistence, emergence, and reemergence. As the recent Ebola virus disease and MERS-CoV outbreaks demonstrate, the modern epidemics and large-scale infectious outbreaks emerge and spread quickly. Air transportation is a major vehicle for the rapid spread and dissemination of communicable diseases, and there have been a number of reported outbreaks of serious airborne diseases aboard commercial flights including tuberculosis, severe acute respiratory syndrome, influenza, smallpox, and measles, to name a few. In 2014 alone, over 3.3 billion passengers (a number equivalent to 42% of the world population) and 50 million metric tons of cargo traveled by air from 41,000 airports and 50,000 routes worldwide, and significant growth is anticipated, with passenger numbers expected to reach 5.9 billion by 2030. Given the increasing numbers of travelers, the risk of infectious disease transmission during air travel is a significant concern, and this chapter focuses on the current knowledge about transmission of infectious diseases in the context of both transmissions within the aircraft passenger cabin and commercial aircraft serving as vehicles of worldwide infection spread.
The Exosporium Layer of Bacterial Spores: a Connection to the Environment and the Infected Host
Authors: Stewart George C. 
Published: October 2015

SUMMARY

Much of what we know regarding bacterial spore structure and function has been learned from studies of the genetically well-characterized bacterium
Bacillus subtilis
. Molecular aspects of spore structure, assembly, and function are well defined. However, certain bacteria produce spores with an outer spore layer, the exosporium, which is not present on
B. subtilis
spores. Our understanding of the composition and biological functions of the exosporium layer is much more limited than that of other aspects of the spore. Because the bacterial spore surface is important for the spore's interactions with the environment, as well as being the site of interaction of the spore with the host's innate immune system in the case of spore-forming bacterial pathogens, the exosporium is worthy of continued investigation. Recent exosporium studies have focused largely on members of the
Bacillus cereus
family, principally
Bacillus anthracis
and
Bacillus cereus
. Our understanding of the composition of the exosporium, the pathway of its assembly, and its role in spore biology is now coming into sharper focus. This review expands on a 2007 review of spore surface layers which provided an excellent conceptual framework of exosporium structure and function (A. O. Henriques and C. P. Moran, Jr., Annu Rev Microbiol
61
:555–588, 2007,
http://dx.doi.org/10.1146/annurev.micro.61.080706.093224
). That review began a process of considering outer spore layers as an integrated, multilayered structure rather than simply regarding the outer spore components as independent parts.
An observational study to evaluate three pilot programmes of retesting chlamydia-positive individuals within 6 months in the South West of England
Authors: Angel Georgina , Horner Paddy J , O'Brien Norah , Sharp Matt , Pye Karl , Priestley Cecilia , Macleod John , Looker Katharine J , Turner Katherine M E 
Published: October 2015

ObjectivesTo evaluate 3 pilot chlamydia retesting programmes in South West England which were initiated prior to the release of new National Chlamydia Screening Programme (NCSP) guidelines recommending retesting in 2014.MethodsIndividuals testing positive between August 2012 and July 2013 in Bristol (n=346), Cornwall (n=252) and Dorset (n=180) programmes were eligible for inclusion in the retesting pilots. The primary outcomes were retest within 6 months (yes/no) and repeat diagnosis at retest (yes/no), adjusted for area, age and gender.ResultsOverall 303/778 (39.0%) of participants were retested within 6 months and 31/299 (10.4%) were positive at retest. Females were more likely to retest than males and Dorset had higher retesting rates than the other areas.ConclusionsMore than a third of those eligible were retested within the time frame of the study. Chlamydia retesting programmes appear feasible within the context of current programmes to identify individuals at continued risk of infection with relatively low resource and time input.