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Background Exome and genome sequencing is becoming the method of choice for rare disease diagnostics. One of the key challenges remaining is distinguishing the disease causing variants from the benign background variation. After analysis and annotation of the sequencing data there are typically thousands of candidate variants requiring further investigation. One of the most effective and least biased ways to reduce this number is to assess the rarity of a variant in any population. Currently, there are a number of reliable sources of information for major population frequencies when considering single nucleotide variants (SNVs) and small insertion and deletions (INDELs), with gnomAD as the most prominent public resource available. However, local variation or frequencies in sub-populations may be underrepresented in these public resources. In contrast, for structural variation (SV), the background frequency in the general population is more or less unknown mostly due to challenges in calling SVs in a consistent way. Keeping track of local variation is one way to overcome these problems and significantly reduce the number of potential disease causing variants retained for manual inspection, both for SNVs and SVs. Results Here, we present loqusdb, a tool to solve the challenge of keeping track of any type of variant observations from genome sequencing data. Loqusdb was designed to handle a large flow of samples and unlike other solutions, samples can be added continuously to the database without rebuilding it, facilitating improvements and additions. We assessed the added value of a local observations database using 98 samples annotated with information from a background of 888 unrelated individuals. Conclusions We show both how powerful SV analysis can be when filtering for population frequencies and how the number of apparently rare SNVs/INDELs can be reduced by adding local population information even after annotating the data with other large frequency databases, such as gnomAD. In conclusion, we show that a local frequency database is an attractive, and a necessary addition to the publicly available databases that facilitate the analysis of exome and genome data in a clinical setting.

Objective To perform a comprehensive characterization of a cohort of patients with congenital mirror movements (CMMs) in Sweden. Methods Clinical examination with the Woods and Teuber scale for mirror movements (MMs), neuroimaging, navigated transcranial magnetic stimulation (nTMS), and massive parallel sequencing (MPS) were applied. Results The cohort is ethnically diverse and includes a total of 7 patients distributed in 2 families and 2 sporadic cases. The degree of MMs was variable in this cohort. MPS revealed 2 novel heterozygous frameshift variants in DCC netrin 1 receptor (DCC). Two siblings harboring the pathogenic variant in c.1466_1476del display a complex syndrome featuring MMs and in 1 case receptive-expressive language disorder, chorea, epilepsy, and agenesis of the corpus callosum. The second DCC variant, c.1729delG, was associated with a typical benign CMM phenotype. No variants in DCC, NTN1, RAD51, or DNAL4 were found for the 2 sporadic CMM cases. However, one of these sporadic cases had concomitant high-risk myelodysplastic syndrome and a homozygous variant in ERCC excision repair like 2 (ERCC6L2). Reorganized corticospinal projection patterns to upper extremities were demonstrated with nTMS. Conclusions The presence of chorea expands the clinical spectrum of syndromes associated with variants in DCC. Biallelic pathogenic variants in ERCC6L2 cause bone marrow failure, but a potential association with CMM remains to be studied in larger cohorts.

The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase separation. When modelings thermodynamic phase changes, it is well-known that finite-size scaling analysis can be a valuable tool. However, to our knowledge, this approach has not been applied before to the computationally challenging problem of modeling sequence-dependent biomolecular phase separation. Here, we implement finite-size scaling methods to investigate the phase behavior of two 10-bead sequences in a continuous hydrophobic/polar protein model. Combined with reversible explicit-chain Monte Carlo simulations of these sequences, finite-size scaling analysis turns out to be both feasible and rewarding, despite relying on theoretical results for asymptotically large systems. While both sequences form dense clusters at low temperature, this analysis shows that only one of them undergoes liquid-liquid phase separation. Furthermore, the transition temperature at which droplet formation sets in, is observed to converge slowly with system size, so that even for our largest systems the transition is shifted by about 8%. Using finite-size scaling analysis, this shift can be estimated and corrected for., Comment: 18 pages, 8 figures, to appear in Physical Review E

Objective Peroxisome proliferator-activated receptors (PPARs) are key transcription factors that regulate adipose development and function, and the conversion of white into brown-like adipocytes. Here we investigated whether PPARα and PPARγ activation synergize to induce the browning of white fat. Methods A selection of PPAR activators was tested for their ability to induce the browning of both mouse and human white adipocytes in vitro, and in vivo in lean and obese mice. Results All dual PPARα/γ activators tested robustly increased uncoupling protein 1 (Ucp1) expression in both mouse and human adipocytes in vitro, with tesaglitazar leading to the largest Ucp1 induction. Importantly, dual PPARα/γ activator tesaglitazar strongly induced browning of white fat in vivo in both lean and obese male mice at thermoneutrality, greatly exceeding the increase in Ucp1 observed with the selective PPARγ activator rosiglitazone. While selective PPARγ activation was sufficient for the conversion of white into brown-like adipocytes in vitro, dual PPARα/γ activation was superior to selective PPARγ activation at inducing white fat browning in vivo. Mechanistically, the superiority of dual PPARα/γ activators is mediated at least in part via a PPARα-driven increase in fibroblast growth factor 21 (FGF21). Combined treatment with rosiglitazone and FGF21 resulted in a synergistic increase in Ucp1 mRNA levels both in vitro and in vivo. Tesaglitazar-induced browning was associated with increased energy expenditure, enhanced insulin sensitivity, reduced liver steatosis, and an overall improved metabolic profile compared to rosiglitazone and vehicle control groups. Conclusions PPARγ and PPARα synergize to induce robust browning of white fat in vivo, via PPARγ activation in adipose, and PPARα-mediated increase in FGF21., Graphical abstract Dual PPARα/γ activation is superior to selective PPARγ activation at inducing browning of white fat in vivo: via PPARγ action in the adipose and a PPARα-mediated action in the liver resulting in increased circulating fibroblast growth factor 21 (FGF21).Image 1, Highlights • Dual PPARα/γ activators robustly induce browning of white fat in vitro and in vivo. • PPARγ action alone is sufficient to convert white into brown-like adipocytes in vitro. • Dual PPARα/γ activators are superior to PPARγ activators for browning of white fat in vivo. • PPARγ action in adipose and PPARα-mediated increase in FGF21 synergize to induce browning of white fat in vivo.

Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While nonallelic homologous recombination is thought to play a major role, recent data suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short‐read whole‐genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital polymerase chain reaction and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by a copy‐number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the resolved inversions, the mutational signatures are consistent with nonhomologous end‐joining (8/13, 62%) or microhomology‐mediated break‐induced replication (5/13, 38%). Our study indicates that short‐read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication‐based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy‐number variation potentially contributing to the overall phenotypic presentation of those patients., This study indicates that short‐read whole‐genome sequencing can detect a substantial fraction of cytogenetically visible chromosomal inversions. In addition, replication‐based mechanisms are responsible for approximately 38% of those events, leading to a significant proportion of inversions that are actually accompanied by additional copy‐number variation potentially contributing to the overall phenotypic presentation of those patients.

Novel sequences (NSs), not present in the human reference genome, are abundant and remain largely unexplored. Here, we utilize de novo assembly to study NS in 1,000 Swedish individuals first sequenced as part of the SweGen project revealing a total of 46 Mb in 61,044 distinct contigs of sequences not present in GRCh38. The contigs were aligned to recently published catalogs of Icelandic and Pan-African NSs, as well as the chimpanzee genome, revealing a great diversity of shared sequences. Analyzing the positioning of NS across the chimpanzee genome, we find that 2,807 NS align confidently within 143 chimpanzee orthologs of human genes. Aligning the whole genome sequencing data to the chimpanzee genome, we discover ancestral NS common throughout the Swedish population. The NSs were searched for repeats and repeat elements: revealing a majority of repetitive sequence (56%), and enrichment of simple repeats (28%) and satellites (15%). Lastly, we align the unmappable reads of a subset of the thousand genomes data to our collection of NS, as well as the previously published Pan-African NS: revealing that both the Swedish and Pan-African NS are widespread, and that the Swedish NSs are largely a subset of the Pan-African NS. Overall, these results highlight the importance of creating a more diverse reference genome and illustrate that significant amounts of the NS may be of ancestral origin.

Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.

Purpose - In an age where e-commerce can provide a huge variety of different products online, customers still face the issue of the last mile challenge. The purpose of this paper is to find out if last mile delivery of products is efficient and explore the possible improvement for this service. Design/methodology/approach - This paper employs a qualitative and a quantitative approach. Qualitative data in the form of an analysis of options of delivery methods of 51 firms, and a qualitative approach in the form of 196 survey respondents. The supply side of services offered by companies are then compared to the demand side expectations of customers. Findings - This research shows that home delivery is the preferred method of last mile delivery. A significant gap was disclosed between the available options for delivery on e-commerce websites and consumer preferences of last mile delivery. Time of delivery and accuracy are the greatest barriers in the delivery chain. The research also shows that there is a lack of home delivery services provided in the market. Moreover, the study shows that the solution may be authorize others to pick up the packages, for example a community delivery service. Research limitations/implications - The research is limited by the usage of non-probability sampling and an equal distribution of respondents of all ages. Also, this research is limited to the biggest three e-commerce industries in Sweden for delivery method offerings. Originality/value - This paper provides a valuable update to online retailers of the last mile challenge and customer satisfaction of the current range of delivery services on the market. The research identifies a clear gap between customers’ demands in the last mile and the firms’ offerings. Companies filling this gap will be able to gain a competitive advantage. Findings in Sweden are of value to other countries as Sweden is considered one of the leading countries in the development of e-commerce.

Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products. One such gene pair is the “native” PgiC1 and “foreign” PgiC2 in the perennial grass Festuca ovina. Both PgiC1 and PgiC2 encode cytosolic phosphoglucose isomerase, a dimeric enzyme whose proper binding is functionally essential. Here, we use biophysical simulations to explore the inter-monomer binding of the two homodimers and the heterodimer that can be produced by PgiC1 and PgiC2 in F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results suggest that the inter-monomer binding is tighter in the PgiC2 than the PgiC1 homodimer, which could explain the more frequent occurrence of the foreign PgiC2 homodimer in dry habitats. We further find that the PgiC1 and PgiC2 monomers are compatible with heterodimer formation; the computed binding tightness is comparable to that of the PgiC1 homodimer. Enhanced homodimer stability and capability of heterodimer formation with PgiC1 are properties of PgiC2 that may contribute to the retaining of the otherwise redundant PgiC2 gene.

Communities around the world are increasingly exposed to larger and more intense wildfires. A common method that officials use to protect community members from harm is evacuation. Data on how people behave during wildfires is critical when planning for evacuation and deciding when and how to evacuate entire communities during an event. Using a similar method to the 2016 Chimney Tops 2 Fire study, an online survey was conducted with households impacted by the 2019 Kincade fire in Sonoma County, California. The survey measured pre-event and event-based factors to 1) predict household perceptions and evacuation decisions and 2) compare results across fire events. Regression analysis identified the factors that influenced risk perception at the time of evacuation decision, i.e., pre-fire perceptions of safety, household makeup (of adults, pets, and livestock), income, education and threat assessment. Logistic regression analyses found that risk perception, length of residence, household makeup, income, education, evacuation order, fire cues, pre-fire perceptions of the safety, and homeownership influenced evacuation decisions. These results differ widely from the 2016 fire due to differences in fire conditions and experiences across populations. Results from this work bring the field closer to a generalized theory of human behavior during wildfire evacuation and improve community-wide evacuation planning and real-time decision-making.

Field-theory simulation by the complex Langevin method offers an alternative to conventional sampling techniques for exploring the forces driving biomolecular liquid-liquid phase separation. Such simulations have recently been used to study several polyampholyte systems. Here, we formulate a field theory corresponding to the hydrophobic/polar HP lattice protein model, with finite same-site repulsion and nearest-neighbor attraction between HH bead pairs. By direct comparison with particle-based Monte Carlo simulations, we show that complex Langevin sampling of the field theory reproduces the thermodynamic properties of the HP model only if the same-site repulsion is not too strong. Unfortunately, the repulsion has to be taken weaker than what is needed to prevent condensed droplets from assuming an artificially compact shape. Analysis of a minimal and analytically solvable toy model hints that the sampling problems caused by repulsive interaction may stem from a loss of ergodicity.

Skeletal dysplasias are a diverse group of rare Mendelian disorders with clinical and genetic heterogeneity. Here, we used targeted copy number variant (CNV) screening and identified intragenic exonic duplications, formed through Alu-Alu fusion events, in two individuals with skeletal dysplasia and negative exome sequencing results. First, we detected a homozygous tandem duplication of exon 9 and 10 in IFT81 in a boy with Jeune syndrome, or short-rib thoracic dysplasia (SRTD) (MIM# 208500). Western blot analysis did not detect any wild-type IFT81 protein in fibroblasts from the patient with the IFT81 duplication, but only a shorter isoform of IFT81 that was also present in the normal control samples. Complementary zebrafish studies suggested that loss of full-length IFT81 protein but expression of a shorter form of IFT81 protein affects the phenotype while being compatible with life. Second, a de novo tandem duplication of exons 2 to 5 in MATN3 was identified in a girl with multiple epiphyseal dysplasia (MED) type 5 (MIM# 607078). Our data highlights the importance of detection and careful characterization of intragenic duplication CNVs, presenting them as a novel and very rare genetic mechanism in IFT81-related Jeune syndrome and MATN3-related MED.

The seemingly unstoppable rise of populism has caught observers by surprise. Donald Trump’s US election victory, the Brexit referendum in Britain, and President Erdogan’s emboldened power in Turkey...

Despite the total evacuation time of occupants in a multi-storey building not being affected by pedestrian merging on stairs, the calculation of evacuation times in each individual floor depends on the pedestrian merging ratio. In fact, different merging ratios may cause an evacuation to take place from the top to the bottom or vice versa. A simplified simulation model for the calculation of evacuation time at each floor is presented here. This model allows the investigation of the impact of two main variables affecting the evacuation time at each floor, namely 1) different initial numbers of pedestrians at each floor (i.e. occupant load), and 2) different merging ratios at each floor. This means that the model allows the calculation of the evacuation time at each floor considering a building with different occupancy types at different floors (e.g. office, residential, commercial, etc.) and different merging ratios which may be caused by a different configuration of the landing door at each floor. The model is presented in this paper using a case study of a hypothetical building. A detailed discussion on the model assumptions, advantages and limitations is also provided.

OBJECTIVEOne-third of cases of focal epilepsy are drug refractory, and surgery might provide a cure. Seizure-free outcome after surgery depends on the correct identification and resection of the epileptogenic zone. In patients with no visible abnormality on MRI, or in cases in which presurgical evaluation yields discordant data, invasive stereoelectroencephalography (SEEG) recordings might be necessary. SEEG is a procedure in which multiple electrodes are placed stereotactically in key targets within the brain to record interictal and ictal electrophysiological activity. Correlating this activity with seizure semiology enables identification of the seizure-onset zone and key structures within the ictal network. The main risk related to electrode placement is hemorrhage, which occurs in 1% of patients who undergo the procedure. Planning safe electrode placement for SEEG requires meticulous adherence to the following: 1) maximize the distance from cerebral vasculature, 2) avoid crossing sulcal pial boundaries (sulci), 3) maximize gray matter sampling, 4) minimize electrode length, 5) drill at an angle orthogonal to the skull, and 6) avoid critical neurological structures. The authors provide a validation of surgical strategizing and planning with EpiNav, a multimodal platform that enables automated computer-assisted planning (CAP) for electrode placement with user-defined regions of interest.METHODSThirteen consecutive patients who underwent implantation of a total 116 electrodes over a 15-month period were studied retrospectively. Models of the cortex, gray matter, and sulci were generated from patient-specific whole-brain parcellation, and vascular segmentation was performed on the basis of preoperative MR venography. Then, the multidisciplinary implantation strategy and precise trajectory planning were reconstructed using CAP and compared with the implemented manually determined plans. Paired results for safety metric comparisons were available for 104 electrodes. External validity of the suitability and safety of electrode entry points, trajectories, and target-point feasibility was sought from 5 independent, blinded experts from outside institutions.RESULTSCAP-generated electrode trajectories resulted in a statistically significant improvement in electrode length, drilling angle, gray matter–sampling ratio, minimum distance from segmented vasculature, and risk (p < 0.05). The blinded external raters had various opinions of trajectory feasibility that were not statistically significant, and they considered a mean of 69.4% of manually determined trajectories and 62.2% of CAP-generated trajectories feasible; 19.4% of the CAP-generated electrode-placement plans were deemed feasible when the manually determined plans were not, whereas 26.5% of the manually determined electrode-placement plans were rated feasible when CAP-determined plans were not (no significant difference).CONCLUSIONSCAP generates clinically feasible electrode-placement plans and results in statistically improved safety metrics. CAP is a useful tool for automating the placement of electrodes for SEEG; however, it requires the operating surgeon to review the results before implantation, because only 62% of electrode-placement plans were rated feasible, compared with 69% of the manually determined placement plans, mainly because of proximity of the electrodes to unsegmented vasculature. Improved vascular segmentation and sulcal modeling could lead to further improvements in the feasibility of CAP-generated trajectories.

In order to increase the knowledge on human behaviour in smoke, an evacuation experiment was performed in a road tunnel in Stockholm in July 2014. Sixty-six participants, who were instructed to individually evacuate the tunnel, took part. Participants' walking speeds were measured in a smoke-filled section, as well as in a smoke-free section, of the tunnel. The walking speeds in non-irritant smoke were measured for extinction coefficients in the range of 0.5–1.1 m-1, which corresponds to approximately 2–4 m of visibility (for light reflecting signs). In addition, way-finding and exit choice in smoke were also investigated. Particularly, different emergency exit portal designs were evaluated in the smoke-filled section of the tunnel. The novel data-set on walking speed in smoke is presented, including coupled data on obstructed (movement in smoke) and unobstructed (smoke-free movement) walking speed. Results show that there is a weak relationship between an individual's ability to walk in smoke and the unobstructed walking speed, but more research is needed in this area. In addition, the results relating to way-finding and exit choice demonstrated that the emergency exit portal design in the experiments was appropriate for the intended use. However, in order to increase the performance of the design, the portal may be complemented with information signs on the wall opposite to the exit, namely way-finding signs including distances to the closest emergency exits on both tunnel walls, and a loudspeaker installation that can inform evacuees about the location of available exits.

Large infrastructure projects often involve important decision about evacuation safety measures, e.g., emergency exit portals, alarm systems, etc, that need to be taken in spite of limited information and knowledge about the topic. This has been shown to sometimes lead to design mistakes, but these mistakes can potentially be avoided if research is linked to the project at an early stage. This paper discusses how research can be connected to large infrastructure tunnel projects, and illustrates the process using the Stockholm Bypass Project as an example. In addition, the results of a research project, which was linked to the Stockholm Bypass Project, are presented and relevant additional publications are given.

Single-vehicle run-off-road crashes are a major traffic safety concern, as they are associated with a high proportion of fatal outcomes. In addressing run-off-road crashes, the development and evaluation of advanced driver assistance systems requires crash test scenarios that are representative of the variability found in real-world crashes. Current approaches subdivide crash data into predefined conflict situations. However, this approach does not take into account inherent patterns in the crash data variables, and may miss common mechanisms or factors. We apply hierarchical agglomerative cluster analysis of crash data variables to define similarities in a set of test scenarios that are representative of run-off-road crashes in the German In-Depth Accident Study (GIDAS) database. Out of 13 clusters, nine test scenarios are derived, corresponding to crashes characterised by: drivers drifting off the road in daytime and night-time, high speed departures, high-angle departures on narrow roads, highways, snowy roads, loss-of-control on wet roadways, sharp curves, and high speeds on roads with severe road surface conditions. In addition, each cluster was analysed with respect to crash variables related to the crash cause and reason for the unintended lane departure. The study shows that cluster analysis of representative data provides a statistically based method to identify relevant properties for run-off-road test scenarios. This was done to support development of vehicle-based run-off-road countermeasures and driver behaviour models used in virtual testing.

Nutrient removal has been one of the key issues since the harvesting of logging residues started in Sweden. This study examined the actual removal of nutrients by measuring the amounts of biomass r...

Denmark and Sweden have an annual cultivation of straw-producing crops on about 16,000 and 11,000 km2 respectively. However, the actual use of straw for energy differs considerably: 1.35 Tg y−1 in Denmark and 0.11 Tg y−1 in Sweden. The main objective of this study was to investigate why the use of straw for energy is much larger in Denmark than in Sweden. Differences and commonalities in the conditions for the production and use of straw were reviewed. It was shown that both countries have used a large number of governmental support programmes, as well as monetary instruments (e.g. CO2-taxes), to promote the use of bioenergy in general. In contrast to Denmark, however, there have been no specific governmental incentives in Sweden directed at increasing the use of straw for energy. One reason may be the vast and relatively low-cost resources of forest biomass in relation to the available resources of straw. The price of competing fuels such as wood chips and wood pellets has generally been 5–15% higher in Denmark than in Sweden. More in depth regional analyses for eastern Denmark and Scania in south Sweden showed that straw production costs are somewhat lower in eastern Denmark as a result of shorter transport distances, earlier ripening of straw-producing crops and better weather conditions during harvest. At present, expert knowledge and the existence of a mature industry favour the large-scale production and use of straw in Denmark.

// Jessada Thutkawkorapin 1 , Hovsep Mahdessian 1 , Tom Barber 2 , Simone Picelli 1 , Susanna von Holst 1 , Johanna Lundin 1 , Laura Valle 3 , Vinaykumar Kontham 1 , Tao Liu 1 , Daniel Nilsson 1 , Xiang Jiao 1 and Annika Lindblom 1 1 Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm SE-17176, Sweden 2 The Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA 3 Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, Barcelona 08908, Spain Correspondence to: Annika Lindblom, email: annika.lindblom@ki.se Keywords: familial colorectal cancer; risk haplotype; cancer predisposition; association study; next generation sequencing Received: November 26, 2017 Accepted: January 23, 2018 Published: January 29, 2018 ABSTRACT Highly penetrant cancer syndromes account for less than 5% of all cases with familial colorectal cancer (CRC), and other genetic contribution explains the majority of the genetic contribution to CRC. A CRC susceptibility locus on chromosome 9q has been suggested. In this study, families where risk of CRC was linked to the region, were used to search for predisposing mutations in all genes in the region. No disease-causing mutation was found. Next, haplotype association studies were performed in the region, comparing Swedish CRC cases (2664) and controls (4782). Two overlapping haplotypes were suggested. One 10-SNP haplotype was indicated in familial CRC (OR 1.4, p = 0.00005) and one 25-SNP haplotype was indicated in sporadic CRC (OR 2.2, p = 0.0000012). The allele frequencies of the 10-SNP and the 25-SNP haplotypes were 13.7% and 2.5% respectively and both included one RNA, RP11-332M4.1 and RP11-l80l4.2 , in the non-overlapping regions. The sporadic 25-SNP haplotype could not be studied further, but the familial 10-SNP haplotype was analyzed in 61 additional CRC families, and 6 of them were informative for all markers and had the risk haplotype. Targeted sequencing of the 10-SNP region in the linked families identified one variant in RP11-332M4.1 , suggestive to confer the increased CRC risk on this haplotype. Our results support the presence of two loci at 9q22.32, each with one RNA as the putative cause of increased CRC risk. These RNAs could exert their effect through the same, or different, genes/pathways, possibly through the regulation of neighboring genes, such as PTCH1, FANCC, DKFZP434H0512, ERCC6L2 or the processed transcript LINC00046 .

Maintenance of the composition of inner ear fluid and regulation of electrolytes and acid-base homeostasis in the collecting duct system of the kidney require an overlapping set of membrane transport proteins regulated by the forkhead transcription factor FOXI1. In two unrelated consanguineous families, we identified three patients with novel homozygous missense mutations in FOXI1 (p.L146F and p.R213P) predicted to affect the highly conserved DNA binding domain. Patients presented with early-onset sensorineural deafness and distal renal tubular acidosis. In cultured cells, the mutations reduced the DNA binding affinity of FOXI1, which hence, failed to adequately activate genes crucial for normal inner ear function and acid-base regulation in the kidney. A substantial proportion of patients with a clinical diagnosis of inherited distal renal tubular acidosis has no identified causative mutations in currently known disease genes. Our data suggest that recessive mutations in FOXI1 can explain the disease in a subset of these patients.

Computer simulation can provide valuable insight into the forces driving biomolecular liquid-liquid phase separation. However, the simulated systems have a limited size, which makes it important to minimize and control finite-size effects. Here, using a phenomenological free-energy ansatz, we investigate how the single-phase densities observed in a canonical system under coexistence conditions depend on the system size and the total density. We compare the theoretical expectations with results from Monte Carlo simulations based on a simple hydrophobic/polar protein model. We consider both cubic systems with spherical droplets and elongated systems with slab-like droplets. The results presented suggest that the slab simulation method greatly facilitates the estimation of the coexistence densities in the large-system limit.

Demand for wood pellets as a renewable alternative to fossil fuels has increased in the past decade. However, production and use of wood pellets involves several operations (biomass extraction, chipping, transport, drying, milling, pelleting, combustion) with negative impacts on e.g. the climate. In this study, the energy efficiency and climate impact of production and use of non-torrefied and torrefied wood pellets were analysed and compared. The wood pellets, produced from logging residues extracted from a boreal coniferous forest stand (Norway spruce (Picea abies (L.) H. Karst)) in northern Sweden, were assumed to be exported and finally used in a power plant. Time-dependent life cycle assessment, expressing the climate impact as global temperature change over time, was used to include annual greenhouse gas fluxes of both fossil and biogenic origin. The results showed that carbon stock changes due to extraction of logging residues contributed most of the warming effect on global temperature. Due to greater demand for raw material, a higher warming impact per gigajoule fuel was obtained for torrefied wood pellets than for non-torrefied wood pellets. However, torrefied wood pellets demonstrated a lower climate impact (per GJ electricity) when advantages such as higher electrical energy efficiency and higher co-firing rate were included. A general conclusion from this study is that replacing coal with non-torrefied or torrefied wood pellets made from logging residues can mitigate climate change. The energy output of these systems was about sevenfold the primary energy input.

Background The development of modern, biocompatible peritoneal dialysis (PD) fluids has not entirely eliminated the local pro-inflammatory effects of PD fluid administration. The present study was performed in order to establish the importance of known signaling pathways connected to mechano-, osmo- and chemo-sensors of the transient receptor potential (TRP) family for the acute inflammatory response to PD. Methods Rats were exposed to a single 4-hour dwell of lactate-buffered, 2.5% glucose, filter-sterilized PD fluid through an implanted PD catheter. In some groups, the PD dwell was preceded by intravenous administration of blockers of TRPV1 (BCTC), TRPA1 (HC030031), or neurokinin 1 (NK1) (Spantide II) receptors. Cytokine messenger ribonucleic acid (mRNA) expressions were quantified in tissue biopsies (real-time polymerase chain reaction [qPCR]), and cytokine concentrations were quantified in dialysate samples by enzyme-linked immunosorbent assay (ELISA). Tissue expressions of TRPV1, TRPA1, and NK1 were evaluated immuno-histochemically. Results The PD dwell induced peritoneal synthesis of Il1b, Tnf, and Il6 and a secretion of interleukin-6 (IL-6) into the dialysate. The catheter implantation already induced the transcription of Il1b and Tnf but did not significantly affect Il6 transcription. The Il6 response to the PD dwell could be virtually eliminated by blocking TRPA1 but was not affected by TRPV1 blockade. Blocking the substance P receptor, NK1, produced an insignificant trend towards Il6 inhibition. TRPA1 and NK1 showed a stronger immuno-reactivity than TRPV1 on cells of the peritoneal tissue. Conclusion The results show that IL-6 synthesis and secretion were connected to acute PD fluid exposure, and this response was triggered by TRPA1 receptors, possibly located to non-neuronal cells.

Short rotation coppice willow (SRCW) is a high-yielding energy crop that can be used to produce solid, liquid or gaseous biofuels. The crop is harvested during the winter, when the leaves have dropped. For economic reasons, however, most fuel processing plants require continuous year-round delivery of raw material. Thus, SRCW should be harvested as stems or in larger pieces in order to be storable, and not chipped directly at harvest for immediate use in large-scale heating plants, which is common practice at present. The aim of the project within which this study was conducted is to find cost-effective whole-stem harvesting and handling systems for year-round deliveries of natural-dried SRCW. A discrete event simulation model for such systems was developed in this study, taking weather, soil trafficability, geographical conditions, natural drying of the material and storage losses into account. The model was applied to a fictitious processing plant in Uppsala, Sweden. Machine performance and costs for a system with one stem harvester and up to three in-field shuttles, together with one chipper truck for chipping and transport, were investigated. The simulations showed that field trafficability had a crucial impact on total quantity harvested. The total cost was € 40 t −1 dry matter. Yield of SRCW and harvest productivity were important factors regarding costs. The model can be used to design cost-effective harvesting and handling systems for year-round deliveries of SRCW.

Pedestrian merging flows on stairs are defined as the confluence of a flow of pedestrians from a stair and pedestrians from each floor of a multi-storey building. This paper introduces a novel simplified mathematical model for the calculation of evacuation times on stairs which takes into account the impact of merging flows. The model allows calculating the impact of merging ratio (people accessing the stair landing from the floor and from the stair) on pedestrian flows and evacuation times at each floor in congested situations. The assumptions and implementation of the model are presented. A hypothetical model case study of a 10-floor building evacuation is investigated, where the results of the new model are compared with the results of an evacuation simulation model using SimTread. Advantages and limitations of the new model in relation to the existing methods adopted for the simulation of merging flows on stairs are discussed.

Singleton-Merten syndrome (MIM 182250) is an autosomal dominant inherited disorder characterized by early onset periodontitis, root resorption, osteopenia, osteoporosis, and aortic valve or thoracic aorta calcification. The disorder can have significant intrafamilial phenotypic variability. Here, we present a mother and daughter with Singleton-Merten syndrome harboring a previously described pathogenic missense mutation, c.2465G>A p.(Arg822Gln), in IFIH1 (interferon induced with helicase C domain 1), encoding MDA5 (Melanoma Differentiation-Associated protein 5). These data confirm the pathogenicity of IFIH1 c.2465G>A p.(Arg822Gln) for Singleton-Merten syndrome and affirm the striking phenotypic heterogeneity of this disorder. In addition, we expand the Singleton-Merten phenotype by adding severe systemic lupus erythematosus (SLE) to the clinical picture. Investigations of known SLE genes as well as a single nucleotide polymorphism suggested to be involved in development of SLE were normal.

Pseudohypoparathyroidism type Ib (PHP1B) is characterized primarily by resistance to parathyroid hormone (PTH) and thus hypocalcemia and hyperphosphatemia, in most cases without evidence for Albright hereditary osteodystrophy (AHO). PHP1B is associated with epigenetic changes at one or several differentially-methylated regions (DMRs) within GNAS, which encodes the α-subunit of the stimulatory G protein (Gsα) and splice variants thereof. Heterozygous, maternally inherited STX16 or GNAS deletions leading to isolated loss-of-methylation (LOM) at exon A/B alone or at all maternal DMRs are the cause of autosomal dominant PHP1B (AD-PHP1B). In this study, we analyzed three affected individuals, the female proband and her two sons. All three revealed isolated LOM at GNAS exon A/B, whereas the proband's healthy maternal grandmother and uncle showed normal methylation at this locus. Haplotype analysis was consistent with linkage to the STX16/GNAS region, yet no deletion could be identified. Whole-genome sequencing of one of the patients revealed a large heterozygous inversion (1,882,433 bp). The centromeric breakpoint of the inversion is located 7,225 bp downstream of GNAS exon XL, but its DMR showed no methylation abnormality, raising the possibility that the inversion disrupts a regulatory element required only for establishing or maintaining exon A/B methylation. Because our three patients presented phenotypes consistent with PHP1B, and not with PHP1A, the Gsα promoter is probably unaffected by the inversion. Our findings expand the spectrum of genetic mutations that lead to LOM at exon A/B alone and thus biallelic expression of the transcript derived from this alternative first GNAS exon. © 2017 American Society for Bone and Mineral Research.

Magnetic resonance diffusion tensor imaging (MR-DTI) is used increasingly to detect diffuse axonal injury (DAI) after traumatic brain injury (TBI).To investigate changes in the diffusion tensor imaging parameters of the corpus callosum 6 and 12 months after TBI, to optimize the timing of follow-up DTI investigations. A secondary goal was to study the relationship between DTI parameters and outcome.Longitudinal prospective study.MR-DTI was performed in 15 patients with suspected DAI, 6 and 12 months post-injury. Sixteen controls were also examined. Fractional anisotropy (FA) and diffusivity (trace) in the corpus callosum were analysed. The outcome measures were the extended Glasgow Outcome Scale and the Barrow Neurological Institute Screen for Higher Cerebral Functions, assessed at 6 and 12 months.FA decreased and trace increased at 6 and 12 months compared to controls. Trace continued to increase even further between 6 and 12 months, while FA remained unchanged. Patients with the worst outcomes had lower FA and higher trace compared to patients with better outcomes.DTI parameters have not reached a stable level at 6 months after DAI, but continue to change, probably reflecting an incessant microstructural alteration of the white matter.

Sweden aims to increase the proportion of renewable energy sources, ultimately to be able to phase out fossil fuels. To achieve this, new energy sources need to be explored. In this multi-disciplin ...

As Editors of Religion, State & Society we never fail to be fascinated and inspired by our contributors’ abilities to discern and illuminate multifaceted and unexpected configurations in the human ...

Background DNA damage accumulates over the course of cancer development. The often-substantial amount of somatic mutations in cancer poses a challenge to traditional methods to characterize tumors based on driver mutations. However, advances in machine learning technology can take advantage of this substantial amount of data. Results We developed a command line interface python package, pyCancerSig, to perform sample profiling by integrating single nucleotide variation (SNV), structural variation (SV) and microsatellite instability (MSI) profiles into a unified profile. It also provides a command to decipher underlying cancer processes, employing an unsupervised learning technique, Non-negative Matrix Factorization, and a command to visualize the results. The package accepts common standard file formats (vcf, bam). The program was evaluated using a cohort of breast- and colorectal cancer from The Cancer Genome Atlas project (TCGA). The result showed that by integrating multiple mutations modes, the tool can correctly identify cases with known clear mutational signatures and can strengthen signatures in cases with unclear signal from an SNV-only profile. The software package is available at https://github.com/jessada/pyCancerSig. Conclusions pyCancerSig has demonstrated its capability in identifying known and unknown cancer processes, and at the same time, illuminates the association within and between the mutation modes.

Increasing brown adipose tissue abundance or activity or converting white into brown adipocytes holds promise for the treatment of type 2 diabetes and obesity. Several PPARγ agonists, including rosiglitazone, have been shown to robustly induce browning of white adipose tissue (WAT) in vitro but their effects in vivo are less pronounced, while PPARα agonists show modest browning effects both in vitro or in vivo. In the present study, we investigated whether PPARα and PPARγ dual agonism would have synergistic effects in inducing browning of WAT. We found that all tested dual PPARα/γ agonists robustly increased uncoupling protein 1 (Ucp1) expression in both mouse and human preadipocytes, with tesaglitazar giving the largest Ucp1 induction. Notably, tesaglitazar also strongly induced browning of WAT in vivo in both lean and obese mice at thermoneutrality, largely exceeding the increase in Ucp1 observed with rosiglitazone. Mechanistically, we found that selective PPARγ agonism was sufficient for the conversion of white into brown-like adipocytes in vitro, but dual PPARα/γ agonism was superior to selective PPARγ agonism at inducing white fat browning in vivo, at least in part via a PPARα-mediated increase in fibroblast growth factor 21 (FGF-21). In human preadipocytes in vitro, combined treatment with rosiglitazone and FGF-21 resulted in a robust and synergistic increase in UCP1 mRNA levels, superior to rosiglitazone- or FGF-21-monotreatments. Tesaglitazar-induced browning in obese mice was associated with increased energy expenditure, enhanced insulin sensitivity, reduced liver steatosis, and an overall improved metabolic profile compared to rosiglitazone and vehicle control groups. In conclusion, we found that dual PPARα/γ agonism robustly promotes browning of white fat in vivo, via synergistic action of FGF-21 and PPARγ agonism. Our findings identify a novel opportunity to develop compounds with robust browning of WAT, via dual modulation of PPARα and PPARγ. Disclosure T. Kroon: Employee; Self; AstraZeneca. M.J. Harms: Employee; Self; AstraZeneca. D. Nilsson: None. A. Lindblom: Employee; Self; AstraZeneca. P. Gennemark: Employee; Self; AstraZeneca. G. O'Mahony: Employee; Self; AstraZeneca. V. Osinski: None. C.A. McNamara: None. J. Boucher: Employee; Self; AstraZeneca.

Background Since 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. Methods We 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. Results First, 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 850 kb (min 500 bp, max 155 Mb). 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 (> 10 kb) 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. Conclusion The 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.

Background The bladder exstrophy‐epispadias complex (BEEC) is a congenital malformation of the bladder and urethra. The underlying causes of this malformation are still largely unknown; however, aside from environment, genetics is thought to play an essential role. The recurrent 22q11.2 microduplication is the most persistently detected genetic aberration found in BEEC cases. Methods We performed array comparative genomic hybridization (array‐CGH) analysis of 76 Swedish BEEC patients. Statistical analysis was performed on current dataset pooled with previously published data on the 22q11.2 microduplication in BEEC patients. We performed massive parallel sequencing (MPS) of the 22q11.2 region in 20 BEEC patients without the 22q11.2 microduplication followed by functional studies. Results We identified three additional cases with the 22q11.2 microduplication. Pooling data from this study with previously published reports showed a statistically significant enrichment of the 22q11.2 microduplication in BEEC patients (2.61% in cases vs. 0.08% in controls; OR = 32.6; p = 8.7 × 10−4). MPS of the 22q11.2 region in 20 BEEC patients without the 22q11.2 microduplication identified a novel variant in LZTR1 (p.Ser698Phe) in one patient. Functional evaluation of the LZTR1 p.Ser698Phe variant in live NIH 3T3 cells showed that the concentration and cytoplasmic mobility differ between the Lztr1wt and Lztr1mut, indicating a potential functional effect of the LZTR1mut. Conclusion Our study further emphasizes the involvement of the 22q11.2 region in BEEC development and highlights LZTR1 as a candidate gene underlying the urogenital malformation.

Different virtual reality (VR) experimental tools and equipment are available for evacuation research, ranging from highly immersive systems such as cave automatic virtual environments (CAVEs) to head-mounted displays (HMDs). In particular, mobile-powered HMDs are an extremely cost-efficient solution, for which the research potential for evacuation studies needs to be assessed. This study compares the results of tunnel evacuation experiments aimed at investigating the design of flashing lights on emergency exit portals using two different VR methods (CAVE vs. mobile-powered HMD). The experiments were performed by repeating the same case study in a CAVE laboratory and a low-cost mobile-powered HMD. The CAVE experiment involved 96 participants, whereas the HMD experiment involved 55 participants. An affordance-based questionnaire was used to interview participants immersed in a VR road tunnel emergency evacuation scenario and rank different emergency portal designs. Questionnaire results show consistency between the two experimental methods for the variables investigated, thus leading to be in favor of the use of low-cost mobile-powered HMD tools in evacuation scenarios with a relatively limited level of complexity. (Less)

In surgery for brain tumors, the main challenge is to resect the tumor completely without causing injury to surrounding structures. Intraoperative MRI can provide updated information on remaining tumor and the relationship to critical brain structures. We report our initial experiences from an intraoperative 3 T MRI suite from a surgical, radiological and anesthesiological perspective. The technique has been useful in treating pediatric brain tumor patients, pituitary tumors, low-grade gliomas and epilepsy surgery patients. Image quality has been comparable to conventional diagnostic MRI and there have been no adverse events from the technique. Team-based training and simulation are key factors to manage this complex technical environment and make intraoperative MRI into a routine procedure.

Foxc2 is one of the earliest podocyte markers during glomerular development. To circumvent embryonic lethal effects of global deletion of Foxc2, and to specifically investigate the role of Foxc2 in podocytes, we generated mice with a podocyte‐specific Foxc2 deletion. Mice carrying the homozygous deletion developed early proteinuria which progressed rapidly into end stage kidney failure and death around postnatal day 10. Conditional loss of Foxc2 in podocytes caused typical characteristics of podocyte injury, such as podocyte foot process effacement and podocyte microvillus transformation, probably caused by disruption of the slit diaphragm. These effects were accompanied by a redistribution of several proteins known to be necessary for correct podocyte structure. One target gene that showed reduced glomerular expression was Nrp1, the gene encoding neuropilin 1, a protein that has been linked to diabetic nephropathy and proteinuria. We could show that NRP1 was regulated by Foxc2 in vitro, but podocyte‐specific ablation of Nrp1 in mice did not generate any phenotype in terms of proteinuria, suggesting that the gene might have more important roles in endothelial cells than in podocytes. Taken together, this study highlights a critical role for Foxc2 as an important gene for podocyte function.