| 1. |
- Ameur, Adam, et al.
(author)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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In: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Journal article (peer-reviewed)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 2. |
- Bátori, Veronika, 1980-, et al.
(author)
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The effect of glycerol, sugar and maleic anhydride on pectin-cellulose biofilms prepared from orange waste
- 2019
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In: Polymers. - : MDPI AG. - 2073-4360.
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Journal article (peer-reviewed)abstract
- This study was conducted to improve the properties of thin films prepared from orange waste by the solution casting method. The main focus was the elimination of holes in the film structure by establishing better cohesion between the major cellulosic and pectin fractions. For this, a previously developed method was improved first by the addition of sugar to promote pectin gelling, then by the addition of maleic anhydride. Principally, maleic anhydride was introduced to the films to induce cross-linking within the film structure. The effects of concentrations of sugar and glycerol as plasticizers and maleic anhydride as a cross-linking agent on the film characteristics were studied. Maleic anhydride improved the structure, resulting in a uniform film, and morphology studies showed better adhesion between components. However, it did not act as a cross-linking agent, but rather as a compatibilizer. The middle level (0.78%) of maleic anhydride content resulted in the highest tensile strength (26.65 ± 3.20 MPa) at low (7%) glycerol and high (14%) sugar levels and the highest elongation (28.48% ± 4.34%) at high sugar and glycerol levels. To achieve a uniform film surface with no holes present, only the lowest (0.39%) level of maleic anhydride was necessary.
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| 3. |
- Bivik, Caroline, et al.
(author)
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Novel Genes Involved in Controlling Specification of Drosophila FMRFamide Neuropeptide Cells
- 2015
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In: Genetics. - : Genetics Society of America. - 0016-6731 .- 1943-2631. ; 200:4, s. 1229-1244
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Journal article (peer-reviewed)abstract
- The expression of neuropeptides is often extremely restricted in the nervous system, making them powerful markers for addressing cell specification . In the developing Drosophila ventral nerve cord, only six cells, the Ap4 neurons, of some 10,000 neurons, express the neuropeptide FMRFamide (FMRFa). Each Ap4/FMRFa neuron is the last-born cell generated by an identifiable and well-studied progenitor cell, neuroblast 5-6 (NB5-6T). The restricted expression of FMRFa and the wealth of information regarding its gene regulation and Ap4 neuron specification makes FMRFa a valuable readout for addressing many aspects of neural development, i.e., spatial and temporal patterning cues, cell cycle control, cell specification, axon transport, and retrograde signaling. To this end, we have conducted a forward genetic screen utilizing an Ap4-specific FMRFa-eGFP transgenic reporter as our readout. A total of 9781 EMS-mutated chromosomes were screened for perturbations in FMRFa-eGFP expression, and 611 mutants were identified. Seventy-nine of the strongest mutants were mapped down to the affected gene by deficiency mapping or whole-genome sequencing. We isolated novel alleles for previously known FMRFa regulators, confirming the validity of the screen. In addition, we identified novel essential genes, including several with previously undefined functions in neural development. Our identification of genes affecting most major steps required for successful terminal differentiation of Ap4 neurons provides a comprehensive view of the genetic flow controlling the generation of highly unique neuronal cell types in the developing nervous system.
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| 4. |
- Dahlström, Örjan, et al.
(author)
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Cognitive training and effects on speech-in noise performance in normal hearing and hearing impaired individuals
- 2015
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In: CHSCOM2015. - : Linköping University Electronic Press. ; , s. 127-127
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Conference paper (other academic/artistic)abstract
- Cognitive training might have potential to improve speech understanding under adverse listening conditions. Here, we have examined the effects of a 5-week computer-based cognitive training program on speech-in-noise-performance, in normal hearing (NH) participants and in participants with mild-to-moderate sensorineural hearing loss (HI).Two groups, matched on gender and age (45-65 years), of 20 participants each (HI and NH respectively) are recruited. Participants perform four test-sessions; inclusion (t0), five weeks (t1), ten weeks (t2) and six months (t3). Training is performed either between t0 and t1, or between t1 and t2 (using a cross-over design), using the computer-based Cogmed training program, approximately 30-40 minutes per day, five days per week, during five weeks. At each session participants are tested in three different ways: (a) cognitive testing (KIPS, SICSPAN, TRT); (b) auditory performance (pure tone-audiometry (air- and bone-conduction) and speech audiometry (HINT, Swedish SPIN-test (SNR +4dB))); (c) cortical activation (MR sessions where participants performed a speech-in-noise task using Hagerman-sentences with steady-state speech-spectrum noise (SSN) and with two competing talkers). MR imaging is performed on a Philips Achieva 1.5 Tesla scanner using a sparse imaging technique in which stimuli are presented during the silent period between successive scans. Participants listen to auditory stimuli under eight different conditions: clear speech, SSN or two competing talkers (each at 90%, 50% and 0% intelligibility), and silent rest. Pre- and post-training, hearing disability is assessed by the Speech-Spatial-Qualities-Questionnaire.The study is on-going and behavioral results as well as results from fMRI will be presented.
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| 5. |
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| 6. |
- Hammarström, Lars G. J., et al.
(author)
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The Oncolytic Efficacy and in Vivo Pharmacokinetics of [2-(4-Chlorophenyl)quinolin-4-yl](piperidine-2-yl)methanol (Vacquinol-1) Are Governed by Distinct Stereochemical Features
- 2016
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In: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 59:18, s. 8577-8592
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Journal article (peer-reviewed)abstract
- Glioblastoma remains an incurable brain cancer. Drugs developed in the past 20 years have not improved the prognosis for patients, necessitating the development of new treatments. We have previously reported the therapeutic potential of the quinoline methanol Vacquinol-1 (1) that targets glioblastoma cells and induces cell death by catastrophic vacuolization. Compound 1 is a mixture of four stereoisomers due to the two adjacent stereogenic centers in the molecule, complicating further development in the preclinical setting. This work describes the isolation and characterization of the individual isomers of 1 and shows that these display stereospecific pharmacokinetic and pharmacodynamic features. In addition, we present a stereoselective synthesis of the active isomers, providing a basis for further development of this compound series into a novel experimental therapeutic for glioblastoma.
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| 7. |
- Krite Svanberg, Emilie, et al.
(author)
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Diode laser spectroscopy for non-invasive monitoring of oxygen in the lungs of newborn infants.
- 2016
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In: Pediatric Research. - : Springer Science and Business Media LLC. - 1530-0447 .- 0031-3998. ; 79, s. 621-628
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Journal article (peer-reviewed)abstract
- Newborn infants have pulmonary disorders with abnormal gas distribution, e. g. respiratory distress syndrome. Pulmonary radiography is the clinical routine for diagnosis. Our aim was to investigate a novel non-invasive optical technique for rapid non-radiographic bedside detection of oxygen gas in the lungs of full-term newborn infants.
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| 8. |
- Larsson, Jim, et al.
(author)
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A 3-D printed phantom for optical techniques in medicine
- 2017
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In: CLEO: Applications and Technology, CLEO_AT 2017. - 9781943580279 ; Part F43-CLEO_AT 2017
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Conference paper (peer-reviewed)abstract
- Development of optical techniques in medical applications can be difficult due to limited access to realistic phantoms. Here a 3-D printed model based on CT-images of the thorax of an infant is developed and tested.
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| 9. |
- Larsson, Jim, et al.
(author)
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Development of a 3-dimensional tissue lung phantom of a preterm infant for optical measurements of oxygen—Laser-detector position considerations
- 2018
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In: Journal of Biophotonics. - : Wiley. - 1864-063X. ; 11:3
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Journal article (peer-reviewed)abstract
- There is a need to further improve the clinical care of our most vulnerable patients—preterm infants. Novel diagnostic and treatment tools facilitate such advances. Here, we evaluate a potential percutaneous optical monitoring tool to assess the oxygen and water vapor content in the lungs of preterm babies. The aim is to prepare for further clinical studies by gaining a detailed understanding of how the measured light intensity and gas absorption signal behave for different possible geometries of light delivery and receiver. Such an experimental evaluation is conducted for the first time utilizing a specially developed 3-dimensional-printed optical phantom based on a geometry model obtained from computer tomography images of the thorax (chest) of a 1700-g premature infant. The measurements yield reliable signals for source–detector distances up to about 50 mm, with stronger gas absorption signals at long separations and positions related to the lower part of the lung, consistent with a larger relative volume of this. The limitations of this study include the omission of scattering tissue within the lungs and that similar optical properties are used for the wavelengths employed for the 2 gases, yielding no indication on the optimal wavelength pair to use.
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| 10. |
- Larsson, Jim, et al.
(author)
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Development of a compact multipass oxygen sensor used for gas diffusion studies in opaque media
- 2015
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In: Applied Optics. - 2155-3165. ; 54:33, s. 9772-9778
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Journal article (peer-reviewed)abstract
- A highly scattering porous ceramic sample is employed as a miniature random-scattering multipass gas cell for monitoring of oxygen content in opaque media, that is, wood materials in the present work. Gas in scattering media absorption spectroscopy is used by employing a 760 nm near-infrared laser diode to probe the absorption of molecular oxygen enclosed in the pores of the ceramic material working as the multipass gas cell, with a porosity of 75%. A path length enhancement of approximately 26 times and a signal-to-noise ratio of about 60 were obtained for the ceramic sample used in this work. The gas sensor was then used in a case study of the gas diffusion in wood materials, namely, oak, spruce, and mahogany samples. Differences depending on whether gas diffusion was studied longitudinal or radial to the tree annual rings are demonstrated, with very little gas diffusing in the radial direction. We can also observe that the gas diffusion for the densest material-oak-had the fastest diffusion time, and mahogany, which had the lowest density, showed the slowest diffusion time. (C) 2015 Optical Society of America
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| 11. |
- Lennartsson, Patrik R., et al.
(author)
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Pigment Production by the Edible Filamentous Fungus Neurospora Intermedia
- 2018
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In: Fermentation. - Göteborg : MDPI AG. - 2311-5637. ; 4:11, s. 1-15
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Journal article (peer-reviewed)abstract
- The production of pigments by edible filamentous fungi is gaining attention as a result of the increased interest in natural sources with added functionality in the food, feed, cosmetic, pharmaceutical and textile industries. The filamentous fungus Neurospora intermedia, used for production of the Indonesian food “oncom”, is one potential source of pigments. The objective of the study was to evaluate the fungus’ pigment production. The joint effect from different factors (carbon and nitrogen source, ZnCl2, MgCl2 and MnCl2) on pigment production by N. intermedia is reported for the first time. The scale-up to 4.5 L bubble column bioreactors was also performed to investigate the effect of pH and aeration. Pigment production of the fungus was successfully manipulated by varying several factors. The results showed that the formation of pigments was strongly influenced by light, carbon, pH, the co-factor Zn2+ and first- to fourth-order interactions between factors. The highest pigmentation (1.19 ± 0.08 mg carotenoids/g dry weight biomass) was achieved in a bubble column reactor. This study provides important insights into pigmentation of this biotechnologically important fungus and lays a foundation for future utilizations of N. intermedia for pigment production.
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| 12. |
- Liao, Peilang, et al.
(author)
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Computer simulation analysis of source-detector position for percutaneously measured O2-gas signal in a three-dimensional preterm infant lung
- 2018
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In: Journal of Biophotonics. - : Wiley. - 1864-063X. ; 11:11
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Journal article (peer-reviewed)abstract
- Further improvements in the clinical care of our most vulnerable patients-preterm infants-are needed. Novel diagnostic and surveillance tools facilitate such advances. The GASMAS technique has shown potential to become a tool to, noninvasively, monitor gas in the lungs of preterm infants, by placing a laser source and a detector on the chest wall skin. It is believed that this technology will become a valuable clinical diagnostic tool for monitoring the lung function of these patients. Today, the technology is, for this application, in an early stage and further investigations are needed. In the present study, a three-dimensional computer model of the thorax of an infant is constructed, from a set of CT images. Light transport simulations are performed to provide information about the position dependence of the laser- and detector probe on the thorax of the infant. The result of the simulations, based on the study method and the specified model used in this work, indicates that measurement geometries in front and on the side of the lung are favorable in order to obtain a good gas absorption signal.
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| 13. |
- Lindstrand, Anna, et al.
(author)
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From cytogenetics to cytogenomics : whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability
- 2019
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In: Genome Medicine. - : BMC. - 1756-994X. ; 11:1
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Journal article (peer-reviewed)abstract
- BackgroundSince different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test.MethodsWe analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n=68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n=156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure.ResultsFirst, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850kb (min 500bp, max 155Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (>10kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data.Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively.ConclusionThe overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.
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| 14. |
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| 15. |
- Lundin, Patrik, et al.
(author)
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Sensitivity enhancement and fringe reduction in tunable diode laser spectroscopy using hemispherical diffusers
- 2017
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In: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 88:5
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Journal article (peer-reviewed)abstract
- The use of diffuse, highly reflective optical components, in particular, a hemispherical BaSO4 diffuser, at the point of light injection into non-transparent or turbid media was evaluated as a means to increase the measurement sensitivity of spectroscopic absorption measurements. By performing the light injection from, e.g., an optical fiber through a component designed to make the light diffuse and to reflect (and thereby re-inject) light scattered from the sample, the total amount of light delivered into the sample is increased. Further, the occurrence of possible interference fringes is strongly reduced.
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| 16. |
- Nair, Ramkumar B., et al.
(author)
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Optimizing dilute phosphoric acid pretreatment of wheat straw in the laboratory and in a demonstration plant for ethanol and edible fungal biomass production using Neurospora intermedia.
- 2016
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In: Journal of chemical technology and biotechnology (1986). - : Wiley. - 0268-2575 .- 1097-4660.
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Journal article (peer-reviewed)abstract
- BACKGROUND : A method is described that uses dil. phosphoric acid for wheat straw pretreatment and subsequent ethanol and fungal biomass prodn. with the edible fungus Neurospora intermedia. Dil. phosphoric acid pretreatment of wheat straw was optimized at a lab. scale, and the results were validated in a biorefinery demonstration plant for the first time. The various conditions for the dil. acid pretreatment include such factors as phosphoric acid concns. (0.5-3.0% w/v), temp. (150-210 °C), and reaction time (5-20 min). RESULTS : The optimal pretreatment conditions were detd. as an acid concn. of 1.75% (w/v) at a temp. of 190 °C for 15 min, based on the max. enzymic digestibility with the min. inhibitor release. The efficiency of enzymic polysaccharide hydrolysis was 36% for untreated straw and 86% for straw pretreated with dil. phosphoric acid. Scale up of the pretreatment at a biorefinery demonstration plant improved the process, with the subsequent efficiency of polysaccharide hydrolysis being 95% of the theor. max. Ethanol fermn. of enzymically hydrolyzed wheat straw using N. intermedia showed an improvement in the ethanol yield from 29% (with untreated straw) to 94% (with dil. phosphoric acid pretreated straw) of the theor. max. CONCLUSION : This study opens up an alternative strategy for the efficient use of wheat straw for the prodn. of ethanol and edible fungal biomass in existing wheat-to-ethanol plants.
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| 17. |
- Nair, Ramkumar, et al.
(author)
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Dilute phosphoric acid pretreatment of wheat bran for enzymatic hydrolysis and subsequent ethanol production by edible fungi Neurospora intermedia.
- 2015
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In: Industrial crops and products (Print). - : Elsevier BV. - 0926-6690 .- 1872-633X. ; 69, s. 314-323
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Journal article (peer-reviewed)abstract
- The use of an underutilized and abundant lignocellulosic feedstock residue, wheat bran, was studied for ethanol prodn. using dil. phosphoric acid pretreatment followed by fermn. using edible fungi Neurospora intermedia. Wheat bran was subjected to dil. acid pretreatment at varying acid concns. (0.5-3.0% w/v), temp. (150-210 °C), and reaction time (5-20 min). The interaction of multiple factors showed the optimum pretreatment conditions at acid concn. of 1.75% (w/v), at 190 °C for 10 min. The max. total polysaccharide yield of 0.27 ± 0.01 g/g dry biomass loading, corresponding to 66% of the theor. max. was obsd. Subsequent fermn. with N. intermedia showed 85% of the theor. max. ethanol yield from the untreated bran glucose. The effect of the dil. acid pretreatment on the functional groups of the wheat bran cellulose was detd. with 78% redn. in the cellulose crystallinity index. The validation of the dil. phosphoric acid pretreatment in a demo plant is also reported for the first time. Enzymic hydrolysis of pretreated slurry from the demo plant showed 85% total theor. yield of polysaccharides. Compared to the untreated bran biomass, an increase of 51% was obsd. in the ethanol yield following pretreatment, with a total ethanol yield of 95% theor. max. Higher yield of ethanol is also attributed to the xylose fermenting capability of the fungi. [on SciFinder(R)]
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| 18. |
- Osadolor, Osagie Alex, 1987-, et al.
(author)
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Membrane stress analysis of collapsible tanks andbioreactors
- 2016
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In: Biochemical engineering journal. - : Elsevier BV. - 1369-703X .- 1873-295X.
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Journal article (peer-reviewed)abstract
- Collapsible tanks, vessels or bioreactors are finding increasing usage in small/medium scaleprocesses because they offer flexibility and lower cost. However, if they are to be used atlarge scale, they need to be shown capable of handling the physical stress exerted on them.Because of their nonconventional shape and non-uniform pressure distribution, thin shellanalysis cannot be used in calculating their stress. Defining curvature in terms of pressureaddressed these challenges. Using curvature and numerical analysis, the membrane stress incollapsible tanks designed as bioreactors of volumes between 100-1000 m3 were calculated.When the liquid/gas height and static pressure are known, an equation for calculating tensionper length was developed. An equation that could calculate the liquid height from thebioreactor’s volume, dimensions and working capacity was generated. The equation gavevalues of liquid height with a maximum deviation of 3% from that calculated by curvatureanalysis. The stress values from the liquid height and tension equations had a maximumdeviation of 6% from those calculated by curvature analysis. The calculated tensile stress in a1000 m3 collapsible tank was 14.2 MPa. From these calculations, materials that optimize bothcost and safety can be selected when designing collapsible tanks.
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| 19. |
- Svanberg, Emilie Krite, et al.
(author)
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Non-invasive monitoring of oxygen in the lungs of newborn infants using diode laser spectroscopy
- 2016
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In: Cancer Imaging and Therapy, CANCER 2016. - 9781943580101 ; Part F13-CANCER 2016
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Conference paper (peer-reviewed)abstract
- The main purpose of this study was to investigate a novel non-invasive optical technique for rapid bedside detection of oxygen gas in the lungs of full-term newborn infants. The results suggest that the technique will be clinically useful as a diagnostic and monitoring tool for infants with lung disorders.
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| 20. |
- West, Christina E., et al.
(author)
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Gut microbiome and innate immune response patterns in IgE-associated eczema
- 2015
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In: Clinical and Experimental Allergy. - : Wiley. - 0954-7894 .- 1365-2222. ; 45:9, s. 1419-1429
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Journal article (peer-reviewed)abstract
- Background Gut microbiome patterns have been associated with predisposition to eczema potentially through modulation of innate immune signaling. Objective We examined gut microbiome development in the first year of life in relation to innate immune responses and onset of IgE-associated eczema over the first 2.5 years in predisposed children due to maternal atopy [www.anzctr.org.au, trial ID ACTRN12606000280505]. Methods Microbial composition and diversity were analyzed with barcoded 16S rRNA 454 pyrosequencing in stool samples in pregnancy and at ages 1 week, 1 month and 12 months in infants (n=10) who developed IgE-associated eczema and infants who remained free of any allergic symptoms at 2.5 years of age (n=10). Microbiome data at 1 week and 1 month were analyzed in relation to previously assessed immune responses to TLR 2 and 4 ligands at 6 months of age. Results The relative abundance of Gram-positive Ruminococcaceae was lower at 1 week of age in infants developing IgE-associated eczema, compared with controls (p=0.0047). At that age, the relative abundance of Ruminococcus was inversely associated with TLR2 induced IL-6 (-0.567, p=0.042) and TNF-α (-0.597, p=0.032); there was also an inverse association between the abundance of Proteobacteria (comprising Gram-negative taxa) and TLR4 induced TNF-α (rs= -0.629, p=0.024). This relationship persisted at 1 month, with inverse associations between the relative abundance of Enterobacteriaceae (within the Protebacteria phylum) and TLR4 induced TNF-α (rs=-0.697, p=0.038) and Enterobacteriaceae and IL-6 (rs=-0.709, p=0.035). Mothers whose infants developed IgE-associated eczema had lower α-diversity of Bacteroidetes (p=0.04) although this was not seen later in their infants. At 1 year, α-diversity of Actinobacteria was lower in infants with IgE-associated eczema compared with controls (p=0.002). Conclusion and clinical relevance Our findings suggest that reduced relative abundance of potentially immunomodulatory gut bacteria is associated with exaggerated inflammatory cytokine responses to TLR ligands and subsequent development of IgE-associated eczema. This article is protected by copyright. All rights reserved.
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