| 1. |
- Kazemi Rashed, Salma, et al.
(author)
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English dictionaries, gold and silver standard corpora for biomedical natural language processing related to SARS-CoV-2 and COVID-19
- 2020
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Other publication (other academic/artistic)abstract
- Here we present a toolbox for natural language processing tasks related to SARS-CoV-2. It comprises English dictionaries of synonyms for SARS-CoV-2 and COVID-19, a silver standard corpus generated with the dictionaries and a gold standard corpus of 10 Pubmed abstracts manually annotated for disease, virus, symptom and protein/gene terms. This toolbox is freely available on github and can be used for text analytics in a variety of settings related to the COVID-19 crisis. It will be expanded and applied in NLP tasks over the next weeks and the community is invited to contribute.
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| 2. |
- Roswall, Josefine, et al.
(author)
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Developmental trajectory of the healthy human gut microbiota during the first 5 years of life
- 2021
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In: Cell Host & Microbe. - : Elsevier BV. - 1931-3128 .- 1934-6069. ; 29:5, s. 765-
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Journal article (peer-reviewed)abstract
- The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyze the microbiota from 471 Swedish children followed from birth to 5 years of age, collecting samples after 4 and 12 months and at 3 and 5 years of age as well as from their mothers at birth using 16S rRNA gene profiling. We also compare their microbiota to an adult Swedish population. Genera follow 4 different colonization patterns during establishment where Methanobrevibacter and Christensenellaceae colonize late and do not reached adult levels at 5 years. These late colonizers correlate with increased alpha diversity in both children and adults. By following the children through age-specific community types, we observe that children have individual dynamics in the gut microbiota development trajectory.
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| 3. |
- Wold, Agnes E, 1955, et al.
(author)
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Breast feeding and the intestinal microflora of the infant--implications for protection against infectious diseases.
- 2000
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In: Advances in experimental medicine and biology. - Boston : Kluwer Academic Publishers. - 0065-2598. ; 478, s. 77-93
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Research review (peer-reviewed)abstract
- Human breast milk contains an array of factors with anti-infectious potential, such as immunoglobulins (especially secretory IgA), oligosaccharides and glycoproteins with anti-adhesive capacity, and cytokines. Breast-feeding is associated with protection from the following infections or infection-related conditions: gastroenteritis, upper and lower respiratory tract infection, acute otitis media, urinary tract infection, neonatal septicaemia and necrotizing enterocolitis. Some of the protective effects may derive from an altered mucosal colonization pattern in the breast-fed infant. In other instances breast-fed infants develop less symptoms to the same microbe which causes disease in the bottle-fed infant. An example of an altered colonization pattern is that breast-fed infants have less P-fimbriated, but more type 1-fimbriated E. coli. This may protect against urinary tract infection in the breast-fed infant since P. fimbriae are the major virulence factor for urinary tract infection. An example of changed consequences of the same microbial colonization is that secretory IgA in the breast-milk protects very efficiently from translocation of intestinal bacteria across the gut mucosa by coating intestinal bacteria and blocking their interaction with the epithelium. This mechanism may protect the infant from septicaemia of gut origin and, possibly, necrotizing enterocolitis. Breast-milk is also highly anti-inflammatogenic and contains hormone like factors which counteract diarrhea. Thus, breast-fed infants may be colonized by recognized diarrheal pathogens and still remain healthy. Due to a less virulent intestinal microflora and decreased translocation breast-fed infants will obtain less stimuli for the gut immune system, resulting, in e.g., lower salivary IgA antibody titres.
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| 4. |
- Khamzeh, Arsham, et al.
(author)
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High levels of short-chain fatty acids secreted by Candida albicans hyphae induce neutrophil chemotaxis via free fatty acid receptor 2
- 2024
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In: Journal of Leukocyte Biology. - : Oxford University Press. - 1938-3673 .- 0741-5400. ; 115:3, s. 536-546
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Journal article (peer-reviewed)abstract
- Candida albicans belongs to our commensal mucosal flora and in immune-competent individuals in the absence of epithelial damage, this fungus is well tolerated and controlled by our immune defense. However, C. albicans is an opportunistic microorganism that can cause different forms of infections, ranging from superficial to life-threatening systemic infections. C. albicans is polymorphic and switches between different phenotypes (e.g. from yeast form to hyphal form). C. albicans hyphae are invasive and can grow into tissues to eventually reach circulation. During fungal infections, neutrophils in particular play a critical role for the defense, but how neutrophils are directed toward the invasive forms of fungi is less well understood. We set out to investigate possible neutrophil chemoattractants released by C. albicans into culture supernatants. We found that cell-free culture supernatants from the hyphal form of C. albicans induced both neutrophil chemotaxis and concomitant intracellular calcium transients. Size separation and hydrophobic sorting of supernatants indicated small hydrophilic factors as responsible for the activity. Further analysis showed that the culture supernatants contained high levels of short-chain fatty acids with higher levels from hyphae as compared to yeast. Short-chain fatty acids are known neutrophil chemoattractants acting via the neutrophil free fatty acid receptor 2. In line with this, the calcium signaling in neutrophils induced by hyphae culture supernatants was blocked by a free fatty acid receptor 2 antagonist and potently increased in the presence of a positive allosteric modulator. Our data imply that short-chain fatty acids may act as a recruitment signal whereby neutrophils can detect C. albicans hyphae.
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| 5. |
- Zilg, Brita, et al.
(author)
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A Rapid Method for Postmortem Vitreous Chemistry - Deadside Analysis
- 2022
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In: Biomolecules. - : MDPI. - 2218-273X. ; 12:1
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Journal article (peer-reviewed)abstract
- Vitreous fluid is commonly collected for toxicological analysis during forensic postmortem investigations. Vitreous fluid is also often analyzed for potassium, sodium, chloride and glucose for estimation of time since death, and for the evaluation of electrolyte imbalances and hyperglycemia, respectively. Obtaining such results in the early phase of a death investigation is desirable both in regard to assisting the police and in the decision-making prior to the autopsy. We analyzed vitreous fluid with blood gas instruments to evaluate/examine the possible impact of different sampling and pre-analytical treatment. We found that samples from the right and left eye, the center of the eye as well as whole vitreous samples gave similar results. We also found imprecision to be very low and that centrifugation and dilution were not necessary when analyzing vitreous samples with blood gas instruments. Similar results were obtained when analyzing the same samples with a regular multi-analysis instrument, but we found that such instruments could require dilution of samples with high viscosity, and that such dilution might impact measurement accuracy. In conclusion, using a blood gas instrument, the analysis of postmortem vitreous fluid for electrolytes and glucose without sample pretreatment produces rapid and reliable results.
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| 6. |
- Singh, Birendra, et al.
(author)
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Crystallization and X-ray diffraction analysis of a novel surface-adhesin protein: protein E from Haemophilus influenzae.
- 2012
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In: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications. - 2053-230X. ; 68:Pt 2, s. 222-226
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Journal article (peer-reviewed)abstract
- Protein E (PE) is a ubiquitous multifunctional surface protein of Haemophilus spp. and other bacterial pathogens of the Pasteurellaceae family. H. influenzae utilizes PE for attachment to respiratory epithelial cells. In addition, PE interacts directly with plasminogen and the extracellular matrix (ECM) components vitronectin and laminin. Vitronectin is a complement regulator that inhibits the formation of the membrane-attack complex (MAC). PE-mediated vitronectin recruitment at the H. influenzae surface thus inhibits MAC and protects against serum bactericidal activity. Laminin is an abundant ECM protein and is present in the basement membrane that helps in adherence of H. influenzae during colonization. Here, the expression, purification and crystallization of and the collection of high-resolution data for this important H. influenzae adhesin are reported. To solve the phase problem for PE, Met residues were introduced and an SeMet variant was expressed and crystallized. Both native and SeMet-containing PE gave plate-like crystals in space group P2(1), with unit-cell parameters a = 44, b = 57, c = 61 Å, β = 96°. Diffraction data collected from native and SeMet-derivative crystals extended to resolutions of 1.8 and 2.6 Å, respectively.
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| 7. |
- Aabenhus, Rune, et al.
(author)
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Lectin Typing of Campylobacter concisus
- 2002
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In: Journal of Clinical Microbiology. - 1098-660X. ; 40:2, s. 715-717
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Journal article (peer-reviewed)abstract
- A total of 44 clinical isolates and the type strain of the putative pathogen Campylobacter concisus were grouped based on their reactions with plant lectins. The optimized lectin typing system used C. concisus strains proteolytically pretreated and subsequently typed by using a panel of four lectins. The system grouped all 45 strains into 13 lectin reaction patterns, leaving no strain untypeable due to autoagglutination. Lectin types were both stable and reproducible.
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| 8. |
- Aaseth, Jan, et al.
(author)
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The Aging Kidney-As Influenced by Heavy Metal Exposure and Selenium Supplementation
- 2021
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In: Biomolecules. - : MDPI. - 2218-273X. ; 11:8
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Journal article (peer-reviewed)abstract
- The aging process in the kidneys has been well studied. It is known that the glomerular filtration rate (GFR) declines with age in subjects older than 50-60 years. However, there is still insufficient knowledge regarding the response of the aged kidney to environmental toxicants such as mercury, cadmium, and lead. Here, we present a review on the functional decline and proposed mechanisms in the aging kidney as influenced by metal pollutants. Due to the prevalence of these toxicants in the environment, human exposure is nearly unavoidable. Further, it is well known that acute and chronic exposures to toxic metals may be detrimental to kidneys of normal adults, thus it may be hypothesized that exposure of individuals with reduced GFR will result in additional reductions in renal function. Individuals with compromised renal function, either from aging or from a combination of aging and disease, may be particularly susceptible to environmental toxicants. The available data appear to show an association between exposure to mercury, cadmium and/or lead and an increase in incidence and severity of renal disease in elderly individuals. Furthermore, some physiological thiols, as well as adequate selenium status, appear to exert a protective action. Further studies providing improved insight into the mechanisms by which nephrotoxic metals are handled by aging kidneys, as well as possibilities of therapeutic protection, are of utmost importance.
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| 9. |
- Abarenkov, Kessy, et al.
(author)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Journal article (peer-reviewed)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 10. |
- Abate, Ebba, et al.
(author)
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Asymptomatic Helminth Infection in Active Tuberculosis Is Associated with Increased Regulatory and Th-2 Responses and a Lower Sputum Smear Positivity
- 2015
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In: PLoS Neglected Tropical Diseases. - : PUBLIC LIBRARY SCIENCE. - 1935-2727 .- 1935-2735. ; 9:8
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Journal article (peer-reviewed)abstract
- Background The impact of intestinal helminth infection on the clinical presentation and immune response during active tuberculosis (TB) infection is not well characterized. Our aim was to investigate whether asymptomatic intestinal helminth infection alters the clinical signs and symptoms as well as the cell mediated immune responses in patients with active TB.Methodology Consecutive, newly diagnosed TB patients and healthy community controls (CCs) were recruited in North-west Ethiopia. TB-score, body mass index and stool samples were analyzed. Cells from HIV-negative TB patients (HIV-/TB) and from CCs were analyzed for regulatory T-cells (Tregs) and cytokine responses using flow cytometry and ELISPOT, respectively.Results A significantly higher ratio of helminth co-infection was observed in TB patients without HIV (Helm+/HIV-/TB) compared to HIV negative CCs, (40% (121/306) versus 28% (85/306), p = 0.003). Helm+/HIV-/TB patients showed significantly increased IL-5 secreting cells compared to Helm-/HIV-/TB (37 SFU (IQR:13-103) versus 2 SFU (1-50); p = 0.02, n = 30). Likewise, levels of absolute Tregs (9.4 (3.2-16.7) cells/mu l versus 2.4 (1.1-4.0) cells/mu l; p = 0.041) and IL-10 secreting cells (65 SFU (7-196) versus 1 SFU (0-31); p = 0.014) were significantly higher in Helm+/HIV-/TB patients compared to Helm-/HIV-/TB patients. In a multivariate analysis, a lower rate of sputum smear positivity for acid fast bacilli, lower body temperature, and eosinophilia were independently associated with helminth infection in TB patients.Conclusions Asymptomatic helminth infection is associated with increased regulatory T-cell and Th2-type responses and a lower rate of sputum smear positivity. Further studies are warranted to investigate the clinical and immunological impact of helminth infection in TB patients.
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