cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7936958.v1
title: An update on the human and animal enteric pathogen <i>Clostridium perfringens</i>

description: <i>Clostridium perfringens</i>, a rapid-growing pathogen known to secrete an arsenal of &gt;20 virulent toxins, has been associated with intestinal diseases in both animals and humans throughout the past century. Recent advances in genomic analysis and experimental systems make it timely to re-visit this clinically and veterinary important pathogen. This Review will summarise our understanding of the genomics and virulence-linked factors, including antimicrobial potentials and secreted toxins of this gut pathogen, and then its up-to-date clinical epidemiology and biological role in the pathogenesis of several important human and animal-associated intestinal diseases, including pre-term necrotising enterocolitis. Finally, we highlight some of the important unresolved questions in relation to <i>C. perfringens</i>-mediated infections, and implications for future research directions.
DOI: 10.6084/m9.figshare.7937117
title: Seroepidemiological investigation of HAdV-4 infection among healthy adults in China and in Sierra Leone, West Africa

description: An apparent increase in the frequency of human adenovirus type 4 (HAdV-4) infections among general populations has been observed over the past 10 years. However, available epidemiological data that may reflect previous viral circulation and assist in predicting potential outbreaks are sparse, particularly in mainland China and Africa. In this study, a convenient neutralization assay for use in the surveillance of historical HAdV-4 infections was established based on a recombinant luciferase-expressing virus. Subsequently, the neutralizing antibodies (nAbs) of 1013 healthy adult serum samples from China and Sierra Leone were evaluated. Our results showed that over 50% of the participants from China and nearly 70% of donors from Sierra Leone had detectable nAbs against HAdV-4 despite the few infection cases officially reported in these regions. Furthermore, the prevalence of nAbs to HAdV-4 is lower than that to HAdV-5, and both varied by geographic location. In addition, the seropositive rates of both HAdV-4 and HAdV-5 nAbs increased with age. However, the nAbs stimulated by HAdV-4 remained stable at low (≤200) levels among the different age groups, whereas moderate (201–1000) or high (&gt;1000) nAb levels were produced by HAdV-5 and tended to decrease with age. These results elucidate the human humoral immune response against HAdV-4 and revealed that this virus may be an underestimated causative agent of respiratory disease among adults in China and West Africa, demonstrating the importance of HAdV-4 surveillance and providing useful insights for the future development of HAdV-4-based vaccines.
DOI: 10.6084/m9.figshare.7937117.v1
title: Seroepidemiological investigation of HAdV-4 infection among healthy adults in China and in Sierra Leone, West Africa

description: An apparent increase in the frequency of human adenovirus type 4 (HAdV-4) infections among general populations has been observed over the past 10 years. However, available epidemiological data that may reflect previous viral circulation and assist in predicting potential outbreaks are sparse, particularly in mainland China and Africa. In this study, a convenient neutralization assay for use in the surveillance of historical HAdV-4 infections was established based on a recombinant luciferase-expressing virus. Subsequently, the neutralizing antibodies (nAbs) of 1013 healthy adult serum samples from China and Sierra Leone were evaluated. Our results showed that over 50% of the participants from China and nearly 70% of donors from Sierra Leone had detectable nAbs against HAdV-4 despite the few infection cases officially reported in these regions. Furthermore, the prevalence of nAbs to HAdV-4 is lower than that to HAdV-5, and both varied by geographic location. In addition, the seropositive rates of both HAdV-4 and HAdV-5 nAbs increased with age. However, the nAbs stimulated by HAdV-4 remained stable at low (≤200) levels among the different age groups, whereas moderate (201–1000) or high (&gt;1000) nAb levels were produced by HAdV-5 and tended to decrease with age. These results elucidate the human humoral immune response against HAdV-4 and revealed that this virus may be an underestimated causative agent of respiratory disease among adults in China and West Africa, demonstrating the importance of HAdV-4 surveillance and providing useful insights for the future development of HAdV-4-based vaccines.
DOI: 10.6084/m9.figshare.7936940
title: Multiple domains of bacterial and human Lon proteases define substrate selectivity

description: The Lon protease selectively degrades abnormal proteins or certain normal proteins in response to environmental and cellular conditions in many prokaryotic and eukaryotic organisms. However, the mechanism(s) behind the substrate selection of normal proteins remains largely unknown. In this study, we identified 10 new substrates of <i>F. tularensis</i> Lon from a total of 21 candidate substrates identified in our previous work, the largest number of novel Lon substrates from a single study. Cross-species degradation of these and other known Lon substrates revealed that human Lon is unable to degrade many bacterial Lon substrates, suggestive of a “organism-adapted” substrate selection mechanism for the natural Lon variants. However, individually replacing the N, A, and P domains of human Lon with the counterparts of bacterial Lon did not enable the human protease to degrade the same bacterial Lon substrates. This result showed that the “organism-adapted” substrate selection depends on multiple domains of the Lon proteases. Further in vitro proteolysis and mass spectrometry analysis revealed a similar substrate cleavage pattern between the bacterial and human Lon variants, which was exemplified by predominant representation of leucine, alanine, and other hydrophobic amino acids at the P(−1) site within the substrates. These observations suggest that the Lon proteases select their substrates at least in part by fine structural matching with the proteins in the same organisms.
DOI: 10.6084/m9.figshare.7936940.v1
title: Multiple domains of bacterial and human Lon proteases define substrate selectivity

description: The Lon protease selectively degrades abnormal proteins or certain normal proteins in response to environmental and cellular conditions in many prokaryotic and eukaryotic organisms. However, the mechanism(s) behind the substrate selection of normal proteins remains largely unknown. In this study, we identified 10 new substrates of <i>F. tularensis</i> Lon from a total of 21 candidate substrates identified in our previous work, the largest number of novel Lon substrates from a single study. Cross-species degradation of these and other known Lon substrates revealed that human Lon is unable to degrade many bacterial Lon substrates, suggestive of a “organism-adapted” substrate selection mechanism for the natural Lon variants. However, individually replacing the N, A, and P domains of human Lon with the counterparts of bacterial Lon did not enable the human protease to degrade the same bacterial Lon substrates. This result showed that the “organism-adapted” substrate selection depends on multiple domains of the Lon proteases. Further in vitro proteolysis and mass spectrometry analysis revealed a similar substrate cleavage pattern between the bacterial and human Lon variants, which was exemplified by predominant representation of leucine, alanine, and other hydrophobic amino acids at the P(−1) site within the substrates. These observations suggest that the Lon proteases select their substrates at least in part by fine structural matching with the proteins in the same organisms.
DOI: 10.6084/m9.figshare.7937144
title: ZIKA virus infection causes persistent chorioretinal lesions

description: Zika-infected patients can have eye involvement ranging from mild conjunctivitis to severe chorioretinal lesions, however the possible long-term sequelae of infection and timeline to recovery remain unknown. Here we describe the partial recovery of chorioretinal lesions in an immunocompetent patient diagnosed with bilateral posterior uveitis associated with Zika infection and show that some lesions resolved with focal atrophy evident as pigmentary changes on funduscopy. To better understand the progression of the lesions and correlate the changes in fundus imaging with local viral load, immune responses, and retinal damage, we developed a symptomatic mouse model of ocular Zika virus infection. Imaging of the fundus revealed multiple hypopigmentary patches indicative of chorioretinal degeneration as well as thinning of the retina that mirror the lesions in patients. Microscopically, the virus primarily infected the optic nerve, retinal ganglion cells, and inner nuclear layer cells, showing thinning of the outer plexiform layer. During acute infection, the eyes showed retinal layer disorganization, retinitis, vitritis, and focal choroiditis, with mild cellular infiltration and increased expression of tumor necrosis factor, interferon-γ, granzyme B, and perforin. Focal areas of gliosis and retinal degeneration persisted 60 dpi. The model recapitulates features of ZIKA infections in patients and should help elucidate the mechanisms underlying the damage to the eyes and aid in the development of effective therapeutics.
DOI: 10.6084/m9.figshare.7937144.v2
title: ZIKA virus infection causes persistent chorioretinal lesions

description: Zika-infected patients can have eye involvement ranging from mild conjunctivitis to severe chorioretinal lesions, however the possible long-term sequelae of infection and timeline to recovery remain unknown. Here we describe the partial recovery of chorioretinal lesions in an immunocompetent patient diagnosed with bilateral posterior uveitis associated with Zika infection and show that some lesions resolved with focal atrophy evident as pigmentary changes on funduscopy. To better understand the progression of the lesions and correlate the changes in fundus imaging with local viral load, immune responses, and retinal damage, we developed a symptomatic mouse model of ocular Zika virus infection. Imaging of the fundus revealed multiple hypopigmentary patches indicative of chorioretinal degeneration as well as thinning of the retina that mirror the lesions in patients. Microscopically, the virus primarily infected the optic nerve, retinal ganglion cells, and inner nuclear layer cells, showing thinning of the outer plexiform layer. During acute infection, the eyes showed retinal layer disorganization, retinitis, vitritis, and focal choroiditis, with mild cellular infiltration and increased expression of tumor necrosis factor, interferon-γ, granzyme B, and perforin. Focal areas of gliosis and retinal degeneration persisted 60 dpi. The model recapitulates features of ZIKA infections in patients and should help elucidate the mechanisms underlying the damage to the eyes and aid in the development of effective therapeutics.
DOI: 10.15468/dl.2tmqtv
title: Occurrence Download

description: A dataset containing 516 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Yersinia pestis (Lehmann & Neumann, 1896) van Loghem, 1944, Pomacea maculata Perry, 1810, Pomacea canaliculata (Lamarck, 1822), Pomacea bridgesii (Reeve, 1856), Phytophthora cinnamomi Rands, Lissachatina fulica (Bowdich, 1822), Cherax quadricarinatus (von Martens, 1868), Salvinia cucullata Roxb. ex Bory, Hedychium gardnerianum Sheph. ex Ker Gawl., Banana bunchy top virus, Eichhornia crassipes (Mart.) Solms, Brontispa longissima (Gestro, 1885), Callisia fragrans (Lindl.) Woodson, Trachemys scripta elegans (Wied, 1838), Phragmites australis subsp. americanus Saltonst., P.M.Peterson & Soreng, Crocodylus rhombifer (Cuvier, 1807), Pennisetum polystachion (L.) Schult., Panicum repens L., Myocastor coypus (Molina, 1782), Pygocentrus nattereri Kner, 1858, Poecilia reticulata Peters, 1859, Gambusia holbrooki Girard, 1859, Gambusia affinis (Baird & Girard, 1853), Pistia stratiotes L., Micropterus salmoides (Lacepède, 1802), Stachytarpheta jamaicensis (L.) Vahl, Lantana camara L., Hypophthalmichthys molitrix (Valenciennes, 1844), Hypophthalmichthys nobilis (Richardson, 1845), Cyprinus carpio Linnaeus, 1758, Cirrhinus cirrhosus (Bloch, 1795), Pterygoplichthys pardalis (Castelnau, 1855), Hypostomus punctatus Valenciennes, 1840, Clarias gariepinus (Burchell, 1822), Passiflora foetida L., Argemone mexicana L., Cuscuta chinensis Lam., Opuntia stricta (Haw.) Haw., Amaranthus spinosus L., Xanthium strumarium Lour., 1790, Parthenium hysterophorus L., Chromolaena odorata (L.) R.M.King & H.Rob., Bidens pilosa L., Mimosa pigra L., Mimosa diplotricha C.Wright ex Sauvalle)",
 "HasCoordinate is true",
 "Country is Viet Nam"
 ]
}

 The dataset includes 516 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085925-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-64258
title: Redemption tidings, vol. 44, nos. 1-52, 4 Jan. - 26 Dec. 1968

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7937144.v1
title: ZIKA virus infection causes persistent chorioretinal lesions

description: Zika-infected patients can have eye involvement ranging from mild conjunctivitis to severe chorioretinal lesions, however the possible long-term sequelae of infection and timeline to recovery remain unknown. Here we describe the partial recovery of chorioretinal lesions in an immunocompetent patient diagnosed with bilateral posterior uveitis associated with Zika infection and show that some lesions resolved with focal atrophy evident as pigmentary changes on funduscopy. To better understand the progression of the lesions and correlate the changes in fundus imaging with local viral load, immune responses, and retinal damage, we developed a symptomatic mouse model of ocular Zika virus infection. Imaging of the fundus revealed multiple hypopigmentary patches indicative of chorioretinal degeneration as well as thinning of the retina that mirror the lesions in patients. Microscopically, the virus primarily infected the optic nerve, retinal ganglion cells, and inner nuclear layer cells, showing thinning of the outer plexiform layer. During acute infection, the eyes showed retinal layer disorganization, retinitis, vitritis, and focal choroiditis, with mild cellular infiltration and increased expression of tumor necrosis factor, interferon-γ, granzyme B, and perforin. Focal areas of gliosis and retinal degeneration persisted 60 dpi. The model recapitulates features of ZIKA infections in patients and should help elucidate the mechanisms underlying the damage to the eyes and aid in the development of effective therapeutics.
DOI: 10.15468/dl.b88v8m
title: Occurrence Download

description: A dataset containing 379 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gossypium arboreum L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 379 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073494-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7937156
title: The molecular basis of antigenic variation among A(H9N2) avian influenza viruses

description: Avian influenza A(H9N2) viruses are an increasing threat to global poultry production and, through zoonotic infection, to human health where they are considered viruses with pandemic potential. Vaccination of poultry is a key element of disease control in endemic countries, but vaccine effectiveness is persistently challenged by the emergence of antigenic variants. Here we employed a combination of techniques to investigate the genetic basis of H9N2 antigenic variability and evaluate the role of different molecular mechanisms of immune escape. We systematically tested the influence of published H9N2 monoclonal antibody escape mutants on chicken antisera binding, determining that many have no significant effect. Substitutions introducing additional glycosylation sites were a notable exception, though these are relatively rare among circulating viruses. To identify substitutions responsible for antigenic variation in circulating viruses, we performed an integrated meta-analysis of all published H9 haemagglutinin sequences and antigenic data. We validated this statistical analysis experimentally and allocated several new residues to H9N2 antigenic sites, providing molecular markers that will help explain vaccine breakdown in the field and inform vaccine selection decisions. We find evidence for the importance of alternative mechanisms of immune escape, beyond simple modulation of epitope structure, with substitutions increasing glycosylation or receptor-binding avidity, exhibiting the largest impacts on chicken antisera binding. Of these, meta-analysis indicates avidity regulation to be more relevant to the evolution of circulating viruses, suggesting that a specific focus on avidity regulation is required to fully understand the molecular basis of immune escape by influenza, and potentially other viruses.
DOI: 10.6084/m9.figshare.7937156.v1
title: The molecular basis of antigenic variation among A(H9N2) avian influenza viruses

description: Avian influenza A(H9N2) viruses are an increasing threat to global poultry production and, through zoonotic infection, to human health where they are considered viruses with pandemic potential. Vaccination of poultry is a key element of disease control in endemic countries, but vaccine effectiveness is persistently challenged by the emergence of antigenic variants. Here we employed a combination of techniques to investigate the genetic basis of H9N2 antigenic variability and evaluate the role of different molecular mechanisms of immune escape. We systematically tested the influence of published H9N2 monoclonal antibody escape mutants on chicken antisera binding, determining that many have no significant effect. Substitutions introducing additional glycosylation sites were a notable exception, though these are relatively rare among circulating viruses. To identify substitutions responsible for antigenic variation in circulating viruses, we performed an integrated meta-analysis of all published H9 haemagglutinin sequences and antigenic data. We validated this statistical analysis experimentally and allocated several new residues to H9N2 antigenic sites, providing molecular markers that will help explain vaccine breakdown in the field and inform vaccine selection decisions. We find evidence for the importance of alternative mechanisms of immune escape, beyond simple modulation of epitope structure, with substitutions increasing glycosylation or receptor-binding avidity, exhibiting the largest impacts on chicken antisera binding. Of these, meta-analysis indicates avidity regulation to be more relevant to the evolution of circulating viruses, suggesting that a specific focus on avidity regulation is required to fully understand the molecular basis of immune escape by influenza, and potentially other viruses.
DOI: 10.6084/m9.figshare.7937849
title: The concordance between upper and lower respiratory microbiota in children with <i>Mycoplasma pneumoniae</i> pneumonia

description: In recent years, the morbidity of <i>Mycoplasma pneumoniae</i> pneumonia (MPP) has dramatically increased in China. An increasing number of studies indicate that an imbalance in the respiratory microbiota is associated with respiratory infection. We selected 28 hospitalized patients infected with <i>M. pneumoniae</i> and 32 healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from healthy children, whereas NP, OP and bronchoalveolar lavage (BAL) specimens were collected from patients. Microbiota analysis was performed on all microbial samples using 16 S ribosomal RNA (16 S rRNA) sequencing. The NP microbial samples in healthy children were divided into two groups, which were dominated by either <i>Staphylococcus</i> or mixed microbial components. The respiratory microbiota in pneumonia patients harbored a lower microbial diversity compared to healthy children, and both the NP and OP microbiota of patients differed significantly from that of healthy children. Hospitalized MPP children with a higher abundance of <i>Mycoplasma</i> in the BAL fluid (BALF) microbiota tended to suffer longer hospitalization lengths and higher peak fevers and serum C-reactive protein levels. Concordance analysis explained the succession of imbalanced NP microbiota to the OP and lung in diseased children. However, the association of the abundance of <i>Mycoplasma</i> in BALF microbiota with that in NP or OP microbiota varied among individuals, which suggested the sensitivity of BALF in MPP diagnostics, mirroring MPP severity.
DOI: 10.6084/m9.figshare.7937849.v1
title: The concordance between upper and lower respiratory microbiota in children with <i>Mycoplasma pneumoniae</i> pneumonia

description: In recent years, the morbidity of <i>Mycoplasma pneumoniae</i> pneumonia (MPP) has dramatically increased in China. An increasing number of studies indicate that an imbalance in the respiratory microbiota is associated with respiratory infection. We selected 28 hospitalized patients infected with <i>M. pneumoniae</i> and 32 healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from healthy children, whereas NP, OP and bronchoalveolar lavage (BAL) specimens were collected from patients. Microbiota analysis was performed on all microbial samples using 16 S ribosomal RNA (16 S rRNA) sequencing. The NP microbial samples in healthy children were divided into two groups, which were dominated by either <i>Staphylococcus</i> or mixed microbial components. The respiratory microbiota in pneumonia patients harbored a lower microbial diversity compared to healthy children, and both the NP and OP microbiota of patients differed significantly from that of healthy children. Hospitalized MPP children with a higher abundance of <i>Mycoplasma</i> in the BAL fluid (BALF) microbiota tended to suffer longer hospitalization lengths and higher peak fevers and serum C-reactive protein levels. Concordance analysis explained the succession of imbalanced NP microbiota to the OP and lung in diseased children. However, the association of the abundance of <i>Mycoplasma</i> in BALF microbiota with that in NP or OP microbiota varied among individuals, which suggested the sensitivity of BALF in MPP diagnostics, mirroring MPP severity.
DOI: 10.15468/dl.uxg6a4
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((19.5293 37.0201,29.79492 37.0201,29.79492 44.3647,19.5293 44.3647,19.5293 37.0201))",
 "HasCoordinate is true",
 "TaxonKey is Gymnocephalus cernua (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 25 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054756-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.