Human-induced changes to river loads of nutrients and sediments pose a significant threat to marine ecosystems. Ongoing land-use change can further increase these loads, and amplify the impacts of land-based threats on vulnerable marine ecosystems. Consequently, there is a need to assess these threats and prioritise actions to mitigate their impacts. A key question regarding prioritisation is whether actions in catchments to maintain coastal-marine water quality can be spatially congruent with actions for other management objectives, such as conserving terrestrial biodiversity. In selected catchments draining into the Gulf of California, Mexico, we employed Land Change Modeller to assess the vulnerability of areas with native vegetation to conversion into crops, pasture, and urban areas. We then used SedNet, a catchment modelling tool, to map the sources and estimate pollutant loads delivered to the Gulf by these catchments. Following these analyses, we used modelled river plumes to identify marine areas likely influenced by land-based pollutants. Finally, we prioritised areas for catchment management based on objectives for conservation of terrestrial biodiversity and objectives for water quality that recognised links between pollutant sources and affected marine areas. Our objectives for coastal-marine water quality were to reduce sediment and nutrient discharges from anthropic areas, and minimise future increases in coastal sedimentation and eutrophication. Our objectives for protection of terrestrial biodiversity covered species of vertebrates. We used Marxan, a conservation planning tool, to prioritise interventions and explore spatial differences in priorities for both objectives. Notable differences in the distributions of land values for terrestrial biodiversity and coastal-marine water quality indicated the likely need for trade-offs between catchment management objectives. However, there were priority areas that contributed to both sets of objectives. Our study demonstrates a practical approach to integrating models of catchments, land-use change, and river plumes with conservation planning software to inform prioritisation of catchment management. Human-induced changes in flows of nutrients and sediments are threatening marine ecosystems , 2, compAlterations to pollutant loads resulting from land-use change have been extensively studied in some regions, such as the Great Barrier Reef in Australia  and ChesMinimising the impacts of land-based threats to marine ecosystems is an important objective of catchment management, but it has to be balanced with other local management objectives, such as protection of terrestrial and freshwater biodiversity, and maintenance of ecosystem services , 26. ConMethods to target catchment management have advanced rapidly in the past decade , 36, 37,(Q1) How can we improve targeting of catchment management to reduce end-of-river loads of sediments and nutrients originating from anthropic land uses to maximise benefits to coastal-marine ecosystems?; (Q2) How can we identify areas of native vegetation requiring protection to prevent erosion and the delivery of further sediment to marine-coastal areas of conservation importance?; and (Q3) Is it possible to protect areas in catchments that contribute to both local  and downstream (marine) management objectives? To answer these questions, we studied the Gulf of California, Mexico, a marine biodiversity hotspot [Given the need to minimise land-based threats to marine ecosystems and to optimise the use of limited management resources, three key questions arise:  hotspot  threaten hotspot . A major hotspot , is the  hotspot , 24, in  hotspot .The overall goal of our study is to develop a method to integrate models of land-use change, pollutant loads from catchments, and river plumes for applications of land-sea conservation planning. The proposed method can help answer our research questions by identifying areas within catchments that need to be protected/managed to maintain or improve coastal-marine water quality (downstream objective) and to conserve terrestrial biodiversity . Actions within catchments apply to two types of areas: those with native vegetation that could be protected against clearing to minimise further increases in sediment loads and/or to conserve habitat of terrestrial species; and those with anthropic land uses that require management to reduce current loads of pollutants delivered to the sea, for example through the implementation of best-practice management in agriculture. The outputs of our method can also be used to assess the spatial congruence between priority management for water quality and areas that are important for conservation of terrestrial biodiversity, thus helping planners to identify potential co-benefits/trade-offs associated with different management alternatives. Previous studies have found variable congruence between priority areas to achieve downstream  and local management objectives  , 49, 50;Fig 1). Numbered statements here refer to numbered parts of S1 Fig for more detail on each part of Fig 1.Our study proposes a novel method to integrate several models and analyses for land-sea conservation planning. Here we summarise and describe the models used (and key outputs), as well as the integration of models to answer our research questions . NumbereFig 2). While the western coast of the Gulf of California remains comparatively undisturbed, many eastern coastal areas have been extensively cleared for agricultural and urban land uses [Our study focuses on selected catchments draining into the Gulf of California, Mexico  is needed to maximise the potential benefits of management actions . The resFig 2C). The native vegetation map was constructed based on the earliest land-use map available, i.e., 1976 [Fig 2D). Our map of native vegetation should be interpreted with care and used as a proxy in the absence of better information, but further refinements are desirable [We explored past changes in land use by comparing three national-scale  land-use/cover (hereafter ‘land use’) datasets: 1976, 1993, and 2000 , which we., 1976 , for whie., 1976 , ecoregie., 1976 , and Tere., 1976 . This maesirable , particuTo model transition potentials, we selected a number of potential explanatory variables  to model each of the transition potential sub-models. The selected variables have been identified by a number of studies as important in determining land-use suitability for human occupation and agriculture, or related to physical accessibility , 66, 67.Fig 3).The selected variables were used to calculate the probability of change for the modelled transitions within a 20-year period using a Multi-Layer Perceptron Neural Network . This isWe used SedNet  to modelprioritise catchment management: scenarios and objectives‘ section). We delineated sub-catchments with SedNet by using a drainage area threshold of 40 km2, which resulted in 1,655 sub-catchments , with a mean size of ~60 km2 (standard deviation: 39 km2); this ensured that most small coastal catchments were covered by the modelling domain. A detailed explanation of the parameterization of SedNet for this study, as well as a discussion on the advantages, difficulties, and limitations of our catchment model are documented by Álvarez-Romero et al. [Our main requirements for delineating sub-catchments related to catchment modelling  and prioo et al. .We used the catchment model to create three types of outputs: Output 1) total catchment loads for TSS and DIN based on ‘natural’ and ‘current’ land use conditions; Output 2) potential reduction in TSS and DIN supply after implementing best-practice management; and Output 3) maximum TSS supply if existing naturally vegetated areas are transformed into anthropic land uses .Fig 2C and 2D). Of the thirty-nine selected catchments draining into the marine management units, four catchments comprise ~88% of the total study area : Yaqui , Mayo , Mátape , and Cocoraque . When combined, these catchments contributed approximately 67% and 87% of the ‘current’ TSS and DIN region-wide loads, respectively [We calculated the total catchment loads (tonne/year) for TSS and DIN by adding the supply of their corresponding sub-catchments, which were modelled using the ‘natural’ and ‘current’ land use maps (ectively .Table 1). These values were set to represent realistic potential reductions in nutrient runoff based on reported reductions from literature [Table 1). We excluded urban areas from the TSS reduction scenario because, once these are established, they do not contribute significantly to erosion. Second, we calculated the difference between the ‘best-practice management’ and ‘current’ scenarios (described above) to represent a hypothetical maximum reduction .To create the scenarios of potential reduction in TSS and DIN supply from implementing best-practice management we followed two steps. First, we created maps representing the estimated supply from sub-catchments of DIN and TSS if 100% of the areas under cropland, pasture, and urban areas implemented best-practice management to reduce these two pollutants. To simulate reductions in DIN supply associated with best-practice management, we adjusted the event mean concentration–EMC  of DIN fterature , 79. Sinterature  for cropterature . We assuFinally, we modelled the maximum TSS supply assuming all areas with remnant native vegetation are transformed into anthropic land uses. We created these maps by applying a uniform C-factor  to all areas with any of the eight native vegetation classes. The resulting TSS supply maps were then adjusted using the results of the land-use change model (details below), effectively reducing the maximum TSS supply of a given area based on its probability of being converted from native vegetation to anthropic land uses.TSScrops_max, natural-to-pasture: TSSpasture_max, and natural-to-urban: TSSurban_max) with the maps depicting the probability of change from native vegetation to anthropic land uses  calculated using the land-use change model (see ‘land-use change model‘ section). Finally, we used the following function (TSSmax); this map  represents the proportional contribution of sub-catchments to the region-wide TSS load given expected land use changes:The outputs from the land-use change and catchment models were combined to create three maps representing the estimated proportional contribution of sub-catchments to the region-wide TSS load given the probability of change from native vegetation into each of the three anthropic land uses. We focused on TSS because we modelled only probability of change  to anthropic land uses and not the future distribution of land uses , which would be required to model increases in DIN loads. To do this, we began with the maps showing the estimated maximum TSS supply, assuming all areas with native vegetation are converted into cropland, pasture, or urban areas, and transformed them into maps depicting the proportional contribution (%) of each sub-catchment (only sub-catchments with native vegetation) to the region-wide (study area) TSS load. Then, we combined each of the transformed maps  and TSS supply  to incorporate the magnitude of these changes. To do this, we calculated a change factor (CF), representing the proportional change in TSS/DIN load from ‘natural’ to ‘current’ land use conditions, which was calculated at catchment level . We assigned a CF to each catchment (and sub-catchments within them) based on the observed proportional changes in loads of TSS and DIN from ‘natural’ to ‘current’ land use according to Table 2. Effectively, this reduced the importance  of sub-catchments that have experienced less change in the amount of exported sediments and nutrients; see ‘linking sub-catchments with marine units‘ section.Quantifying changes in pollutant loads  is necessary to set ecologically-relevant objectives for catchment management , 17. ThiFig 2B [MP) factor to associated catchments; see ‘linking sub-catchments with marine units‘ section. The MP factor represents the importance of sub-catchments for coastal-marine water quality based on the priority of marine management areas that are potentially affected by the catchment to which each sub-catchment belongs. Therefore, sub-catchments that are linked to marine units with high conservation priority  have a higher MP value. The MP was calculated using the following function based on expert opinion on the ecological importance and vulnerability of ecosystems and species within marine management units (This step was needed to prioritise catchments (for downstream benefits) based on the conservation priority of marine units that are likely influenced by their corresponding river plumes. We used the model of Halpern et al. , in combFig 2B , to assint units :MP=CI×VWhereCI: Conservation Index (0 to 1): ecological importance based on species richness, productivity, presence of threatened/protected species , endemic algae, wetlands, bays and coastal lagoons, and protected areas.VI: Vulnerability Index (0 to 1): higher values indicate areas where high fragility of coastal-marine ecosystems and human-pressures (other than catchment effects) co-occur.CI and VI) were allocated to marine management units following a consultative process with experts and stakeholders as part of a marine spatial planning process for the Gulf of California [Both indices . We identified the catchments influencing marine areas by overlaying mapped river plumes . Due to the lack of spatial information on the extent of river plumes originating from the smaller coastal catchments, we assumed that their influence would be restricted to marine management units into which they drain directly. Based on the link to and priority of marine management units , we adjusted the pollutant supply maps ; see ‘linking sub-catchments with marine units‘ section. The adjusted maps were then used to prioritise the protection or management of sub-catchments to achieve our marine objectives .We used a global model for land-based threats  as an apn et al. ) and marTSScrops-reduction, TSSpasture_reduction, DINcrops_reduction, DINurban_reduction, Fig 4) using the two factors described above: change factor  and marine priority :We used the following functions Eqs –6 to incTSSmax, Fig 5) using the proportional change  and marine priority  factors:As for the previous functions (regarding management of anthropic areas), we used the following function  to incorCF factor was incorporated to increase the importance of sub-catchments that have experienced larger changes in the amount of exported sediments and nutrients and are, at least potentially, having a higher impact on marine ecosystems. Likewise, the MP factor adjusts the importance of sub-catchments for coastal-marine water quality based on the priority of marine management areas that are potentially affected by the catchment to which each sub-catchment belongs. The scaled TSS/DIN maps were thus used to represent the relative contribution of sub-catchments to achieving water quality objectives (described below).In both sets of functions (above), the S1)–implementation of best-practice management in anthropic areas to improve coastal-marine water quality; Scenario 2 (S2)–protection of native vegetation to maintain coastal-marine water quality; and Scenario 3 (S3)–protection of native vegetation to conserve terrestrial biodiversity (Table 3). Scenarios 1 and 2 incorporate objectives to minimise land-based pollution to marine areas of conservation priority. We used the decision-support tool Marxan [Table 3.We defined three management scenarios to guide our prioritisation: Scenario 1 (l Marxan  to exploTable 3). We set four objectives (two for TSS: cropland and pasture and two for DIN: cropland and urban areas) based on potential reductions in end-of-river loads of TSS and DIN following the implementation of best-practice management (see ‘catchment model‘ section). In the absence of information to determine ecologically based objectives , we arbitrarily set our objectives as 30% of the scaled maximum potential reduction of TSS (for cropland and pasture) and DIN (for cropland and urban areas) following implementation of best-practice management. Our water quality objectives are comparable to recent target-setting exercises, which take into account technical and socioeconomic feasibility [The first set of water-quality objectives considered the implementation of best-practice management in sub-catchments with anthropic land uses  to reduce loads of DIN and TSS delivered to high-priority marine conservation areas . This objective aimed to avoid as much additional loss of water quality as possible, by prioritising the protection of sub-catchments with both the highest risk of transformation and the highest potential contribution to end-of-river TSS loads if transformed. As above, we arbitrarily set this objective as 30% of the scaled maximum TSS supply from sub-catchments with remnant native vegetation that could potentially contribute to the region-wide TSS load if converted into anthropic land uses.The second water-quality objective concerned maintenance of end-of-river water quality through the protection of sub-catchments with remnant native vegetation to prevent erosion and thus sedimentation impacts on coastal-marine ecosystems (Table 3), in this case vertebrate species . Variable objectives were set for different species, ranging from 5% to 100% of their potential distributions. We used the objectives that the Mexican Government determined for species based on their conservation and protection status following expert advice [The second objective regarding protection of native vegetation was to protect natural areas to conserve terrestrial biodiversity .We also created a map identifying the areas of coincidence in selection frequency  to identify areas where protection of native vegetation scenarios could lead to co-benefits for water quality and biodiversity conservation.For each scenario, our maps of land values at the resolution of planning units (sub-catchments) were the ‘summed solution’ (hereafter ‘selection frequency’) and ‘best solution’ from Marxan analyses. The selection frequency shows the number of times, out of 100 Marxan solutions, that each planning unit was selected. The best solution shows one possible configuration of sub-catchments that achieves the defined objectives at least cost, i.e., the most efficient solution of the 100 Marxan runs . We compS1 and S2) followed expected patterns. The selection frequency map for best-practice management (S1) was spatially sparse , which can be partially related to the patchy distribution of anthropic land uses , but also to the divergent distribution patterns of areas targeted for the reduction in TSS or DIN loads . In contrast, the selection frequency map for the protection water-quality objective (S2) was notably clumped within the two larger catchments , with higher selection frequencies corresponding with sub-catchments potentially contributing the most to the TSS load, Fig 5).The Marxan results for the water quality scenarios  and protection  scenarios. Differences between the selection frequency maps for achieving water-quality objectives through management (S1) and protection (S2) were particularly striking, showing a negative correlation . However, these were expected because selections for management objectives targeted sub-catchments containing anthropic land uses to improve water quality  whereas selections for protection targeted sub-catchments with remnant native vegetation, particularly those areas with potential for both high erosion and extensive clearing . Consequently, a comparison of the best-solution outputs from Marxan for the two water quality scenarios showed almost no overlap , indicating that sub-catchments with both high current supply of TSS and DIN  and sub-catchments with significant remnant native vegetation and high erosion potential  were rare. The configurations of the best-solution outputs for the management and protection scenarios also differed notably. For instance, the best solution for the management scenario (S1) contained 134 sub-catchments  and covered 8,600 km2 (8.4% of the study area). Conversely, the best solution for the protection scenario (S2) contained only 67 sub-catchments  and covered 5,880 km2 (5.8% of the study area).Our results showed important differences in the spatial distribution of local  and downstream  land values, for both the management (S3) were concentrated in the upper regions of the Yaqui and Mayo catchments . Overall, there was very low spatial similarity between the selection-frequency maps for protection to maintain water quality  and that for protecting vertebrate species , with a weak negative relationship overall . The number of units and total area of the best-solution output for terrestrial vertebrates was much larger  than in the best solutions for the other two scenarios. A visual comparison of the maps for protection for water quality and protection for vertebrates  revealed that few sub-catchments were part of the best solutions in both scenarios. Subtracting the selection frequency map of S3 from S2 highlighted these differences . However, we found some coincidence for a number of sub-catchments , indicating some potential to achieve both water quality and biodiversity objectives through the protection of these areas.Higher selection frequencies for terrestrial vertebrates (CF) to adjust the potential contribution of sub-catchments to reduce TSS/DIN loads allowed us to prioritise the management of catchments that are  having larger effects on marine ecosystems. Likewise, including the priority of marine management units further directed efforts to sub-catchments linked to marine areas of higher conservation priority. A limitation of this management scenario is the lack of information to set ecologically relevant objectives based on potential responses of ecosystems and species to current and improved water quality [The method proposed here can help catchment managers to identify sub-catchments with anthropic land uses where best-practice management can be implemented to achieve, with a budget, the maximum potential reduction in coastal sedimentation and nutrient enrichment. Using the proportional change in catchment TSS/DIN loads from natural to current land uses  andWhile our study does not yet reach full integration of land and sea conservation–which would involve simultaneous planning to achieve objectives for land and adjacent marine waters and their interactions –it repreA second important limitation of our study is that we used pre-existing marine conservation priorities instead of targeting marine and terrestrial conservation areas simultaneously. However, this approach was necessary to accommodate previously established marine priorities resulting from an extensive consultative marine planning process. The marine spatial plan for the Gulf of California currently guides actions for conservation and management of coastal-marine areas in the region . Fully iFinally, we recognise inherent limitations following the integration of multiple  models into prioritisation analyses. Quantifying and accounting for uncertainty in model outputs (which can be compounded across models) is needed to communicate the reliability of results to decision-makers, and could avoid suboptimal allocation of management actions . TherefoThe need to integrate land and marine conservation planning has been pointed out by several studies , 92, 97,S1 Fig(PDF)Click here for additional data file.S1 Text(PDF)Click here for additional data file.


Secondary antibody deficiency can occur as a result of haematological malignancies or certain medications, but not much is known about the clinical and immunological features of this group of patients as a whole. Here we describe a cohort of 167 patients with primary or secondary antibody deficiencies on immunoglobulin (Ig)-replacement treatment. The demographics, causes of immunodeficiency, diagnostic delay, clinical and laboratory features, and infection frequency were analysed retrospectively. Chemotherapy for B cell lymphoma and the use of Rituximab, corticosteroids or immunosuppressive medications were the most common causes of secondary antibody deficiency in this cohort. There was no difference in diagnostic delay or bronchiectasis between primary and secondary antibody deficiency patients, and both groups experienced disorders associated with immune dysregulation. Secondary antibody deficiency patients had similar baseline levels of serum IgG, but higher IgM and IgA, and a higher frequency of switched memory B cells than primary antibody deficiency patients. Serious and non-serious infections before and after Ig-replacement were also compared in both groups. Although secondary antibody deficiency patients had more serious infections before initiation of Ig-replacement, treatment resulted in a significant reduction of serious and non-serious infections in both primary and secondary antibody deficiency patients. Patients with secondary antibody deficiency experience similar delays in diagnosis as primary antibody deficiency patients and can also benefit from immunoglobulin-replacement treatment. Antibody deficiencies are defined by a loss of immunoglobulins or failure of immunoglobulin function, resulting in increased susceptibility to infection. In primary deficiencies inherited or sporadic genetic mutation(s), in some cases with unknown environmental cofactors, are suspected with no other known cause Although primary immunodeficiencies are rare, the advent of international registries has enabled more data to be pooled to further advance the understanding of clinical characteristics and treatment This study aimed to describe and compare features of primary and secondary antibody deficiency patients. We describe the characteristics of the cohort in terms of diagnosis, delay in diagnosis, bronchiectasis, possible causes of secondary immunodeficiency, concomitant disorders and immunological parameters. Serious and non-serious infection outcomes after Ig-replacement treatment are also compared in primary and secondary antibody deficiency patients.All data was collected after obtaining written informed consent and in accordance with approval by the City and East London Research Ethics Committee.BTK mutation and one had autosomal recessive agammaglobulinaemia. The other primary immunodeficiencies were defined by genetic testing and/or clinical symptoms according to standard criteria Adult subjects receiving Ig-replacement treatment in May 2013 seen in the immunodeficiency clinic at Barts Health NHS Trust were included in the study. Diagnoses were made by use of standard criteria where appropriate Categorisation into ‘Primary’ or ‘Secondary’ antibody deficiency groups was based largely on patients fulfilling positive diagnostic criteria  for the primary group. For diagnosis of secondary antibody deficiency, clinical judgement took into account the timing of potential causes of deficiency (e.g. chemotherapy) and the development of symptoms or abnormal immunoglobulin levels. The ‘probable’ primary and secondary groups included those in whom a primary or secondary deficiency was suspected based on clinical history, but where other causes could not be excluded or where definitive information about timing of symptoms was not available . Demographic and diagnostic data were obtained retrospectively by reviewing medical records.+CD27+IgM−IgD−) determined as a percentage of total B cells using standard methods Diagnostic delay was defined as the time between patient-reported symptom onset or first documented serious infection, and antibody deficiency diagnosis. Subjects for whom dates of symptoms or diagnosis were unclear were excluded from this analysis. Serum IgG, IgA and IgM levels were recorded and the frequency of switched memory B cells , the number of infections were normalised on a pro-rata basis. Infections that overlapped with diagnosis and initiation of Ig-replacement were only included in the pre-treatment count. Infection data was available for a minimum of 53/126 primary and 28/39 secondary subjects pre-treatment, and for 115/126 primary and 37/39 secondary subjects post-treatment. ‘Serious infections’ were defined as infections requiring hospitalisation and/or intravenous antibiotics. ‘Non-serious’ infections included any mild or moderate infection, with or without antibiotic treatment. The number and type of non-serious infections were largely patient-reported with microbiological confirmation when appropriate and serious infection data was collected from medical records. For all historical pre-treatment data, infection counts were taken from clinical notes.Data between primary and secondary groups were analysed by a two-tailed unpaired t-test with Welch's correction . A two-tailed paired t-test was used for analysis of infection frequency pre- and post-treatment. Where comparisons were made between diagnostic sub-groups the Kruskal-Wallis test was used. Data on the number of switched memory B cells and bronchiectasis was only available for a small number of patients and was analysed using the Mann-Whitney test. P values of <0.05 were considered significant; all data analysis was carried out using GraphPad Prism 5.0.A total of 167 patients receiving Ig-replacement were identified (98 women and 69 men) including 113 with primary immunodeficiencies, 13 with a probable primary deficiency, 26 with secondary immunodeficiencies, 13 with a probable secondary immunodeficiency and 2 that could not be definitively classified. The subjects with secondary or probable secondary deficiencies were older (median age 64.5 yrs and 58 yrs) than the primary groups (45 yrs and 52 yrs). The most common diagnosis in the primary group was CVID accounting for 69.9% of the group (of which 20.3% had inflammatory CVID), and 10.6% of the primary group had agammaglobulinemia. A diagnosis of hypogammaglobulinemia was more common in the secondary and probable secondary groups (80.8% and 69.2%) and a smaller proportion had a specific or subclass defect . The ‘deBased on the clinical history and/or timing of drug treatments relative to onset of symptoms, the most likely cause of secondary antibody deficiency in each subject was identified . The mosThe type of medications used before antibody deficiency diagnosis and the time between first use and diagnosis are shown for the secondary group  and for Delay in diagnosis of antibody deficiencies has been associated with greater infection-related morbidity Bronchiectasis is a complication of lung infections and has been shown to be associated with delay in diagnosis of antibody deficiency in some CVID cohorts Autoimmune disorders, suggesting immune dysregulation, were present in both primary and secondary immunodeficiency subjects (Table S2 in +CD27+IgM−IgD−) have been associated with inflammatory/granulomatous and splenomegaly CVID clinical phenotypes Mean serum immunoglobulin levels were calculated for the year preceding initiation of Ig-replacement (excluding specific or subclass deficiency subjects). There was no significant difference in the pre-treatment IgG level between primary and secondary groups (median 2.79 g/L vs. 3.30 g/L) . HoweverThe number of infections in subjects was compared before Ig-replacement (in the year preceding treatment) and after treatment (in the year 2012/2013). In this cohort, the primary group had been on Ig-replacement for a significantly longer time than the secondary group (median 3 yrs vs. 1 yr). The majority of subjects were on home therapy and a large proportion on sub-cutaneous administration . AlthougIn the year before Ig-replacement, the secondary group had a significantly higher frequency of serious infections requiring hospitalisation and/or IV antibiotics, and a greater proportion of subjects with more than one serious infection compared to the primary group . There wThe majority of secondary antibody deficiency patients received a trial of antibiotic prophylaxis as standard before Ig-replacement treatment We show that for our cohort, whatever the underlying cause of antibody deficiency, infection frequency is reduced by Ig-replacement. Secondary antibody deficiency patients respond at least as well, and possibly better, to antibody replacement, as evidenced by the similar reduction in serious infection frequency, greater reduction in non-serious infection frequency and lower immunoglobulin dose required by the secondary antibody deficiency group.Registry studies have identified a smaller proportion (<1%) of antibody deficiency subjects with a secondary cause In the secondary group, a delay of several years was noted between initial immunosuppressive therapy and the onset of infections. This delay was different for each drug type which may be due to the frequency, potency and regimens of the drugs used. Hypogammaglobulinaemia has previously been noted in RTX-treated patients after a delay of 1–2 years Since this study only includes those that are symptomatic and have been started on Ig-replacement, it is not clear what proportion of all those on such immunosuppressive drugs develop hypogammaglobulinaemia and how many become symptomatic. Estimates vary, with studies describing the incidence of hypogammaglobulinaemia as 14–35% following RTX treatment Despite the differences in causes of antibody deficiencies between the primary and secondary groups, they had a similar frequency of disorders related to immune dysregulation  and for chronic lung disease. This overlap has led to diagnostic uncertainty which we have reflected in our patients classified as ‘probable’; the similar characteristics of the ‘probable’ and ‘definite’ groups in terms of diagnosis type, immune parameters and infection outcomes (data not shown), lead us to believe that the classification is reliable.There was a surprisingly high incidence of bronchiectasis in our cohort (∼34%) compared to 11.2% in another study + B cells, including the pro-B-cell to mature GC phenotypes, plasma cells are unaffected, and follicular dendritic and T-helper cell numbers in tissue may also be reduced The primary antibody deficient patients, of whom the majority had CVID or XLA, had lower baseline levels of serum IgM and IgA and fewer switched memory B cells than the secondary patients before Ig-replacement therapy. Sub-groups of CVID patients have been identified based on the number of total, switched memory and transitional B cells In the year preceding Ig-replacement, the secondary group had a greater number of serious infections and several patients had more than one. Since there did not appear to be any diagnostic delay between the primary and secondary groups, secondary deficiency patients may be relatively asymptomatic until they develop a serious infection that warrants referral to an immunologist. The greater occurrence of serious infections may also be explained by the older age and co-morbidities, including drug and disease-associated immune defects of the secondary group. An alternative explanation is that only those secondary antibody deficient patients with severe enough symptoms to be on Ig-replacement were included, whereas Ig-replacement is initiated as first-line treatment for most confirmed primary antibody deficiency patients. The rate of decline of immunoglobulin levels in some secondary immunodeficiency patients may also have a bearing on the rate of emergence of infectious complications.After Ig-replacement, infections were significantly reduced in both groups thus the cause of antibody deficiency may not be important in itself. Ig-replacement has been previously shown to be effective in reducing infections in haematological malignancy patients with hypogammaglobulinaemia This study is the first to describe a cohort of unselected secondary antibody deficiency compared to primary antibody deficiency patients and to compare outcomes on Ig-replacement therapy. Secondary antibody deficiency manifesting as hypogammaglobulinaemia or specific/subclass deficiencies can occur with haematological malignancies or after cell depletion therapy, chemotherapy, immunosuppressive or corticosteroid medications. Despite having a greater number of serious infections in the year before Ig-replacement therapy, secondary antibody deficiency patients had significantly fewer non-serious infections than the primary group after therapy. Therefore, regardless of whether the cause of symptomatic antibody deficiency is primary or secondary, both groups benefit from Ig-replacement therapy.Figure S1Primary and secondary antibody deficiency diagnoses. The number of subjects with each diagnosis classified as having a primary, probable primary, secondary, probable secondary or unknown antibody deficiency is shown.(TIF)Click here for additional data file.Figure S2Diagnostic delay by primary and secondary antibody deficiency sub-groups. Diagnostic delay (time between symptom onset and antibody deficiency diagnosis) was analysed by diagnosis for the primary group (A) and by likely cause of deficiency for the secondary group (B). Data were analysed by the Kruskal-Wallis test, p values of <0.05 were considered significant; n.s. non-significant.(TIF)Click here for additional data file.Figure S3Bronchiectasis by primary and secondary antibody deficiency sub-groups. The percentage of each sub-group with or without bronchiectasis (determined by high-resolution CT scan) is shown by diagnosis for the primary group (A) and by likely cause of deficiency for the secondary group (B).(TIF)Click here for additional data file.Figure S4Prophylactic antibiotics and the occurrence of non-serious infections. The number of non-serious infections in those receiving antibiotic prophylaxis compared to those not on prophylactic antibiotics before (A) and after (B) Ig-replacement is shown. Data were analysed by a two-tailed unequal variance t-test; * p<0.05.(TIF)Click here for additional data file.Tables S1Contains the following files: Table S1. Immunosuppressive therapies used by individual patients before diagnosis. Table S2. Disorders in primary and secondary antibody deficiency patients. Table S3. Number and type of infections experienced by the primary and secondary group before and after Ig-replacement.(DOCX)Click here for additional data file.Dataset S1A file of the full dataset is provided.(XLS)Click here for additional data file.


The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights into the evolution of dosage compensation and thus into the causes of different compensation strategies. Using deep RNA sequencing, we investigate differential expression patterns along the young XY chromosomes of threespine sticklebacks. Our strata-specific analyses provide new insights into the spatial patterns during the early stages of the evolution of dosage compensation. In particular, our results indicate systematic upregulation of male gene expression in stratum II, which in turn causes female hypertranscription in the same stratum. These findings are consistent with theoretical predictions that selection during early stages of sex chromosome evolution is stronger for a compensating upregulation in males than for the countercompensation of female hyperexpression. In contrast, no elevated gene expression is detectable in stratum I. We argue that strata-specific differences in compensating male gene expression may evolve in response to differences in the prevailing mechanism of Y chromosome degeneration. The suppression of recombination between the X and Y chromosomes and the subsequent Y degeneration are thought of as key stages in the evolution of heteromorphic sex chromosomes . The losSilene latifolia provides limited evidence that dosage compensation can evolve quickly, that is, within 10 Myr, by increasing the expression of X-linked genes in response to the ongoing degeneration of the Y  . The sudden deletion of large blocks of the Y chromosome in stratum II and the lack of such a deletion in stratum I offer a prime opportunity to evaluate the effects of differential Y degeneration on dosage compensation. This study targets these spatial dynamics by investigating expression patterns in the young sex chromosome system of the threespine stickleback, culeatus . The XY ngitius)  at leastngitius) . This agdization  and the dization : A pseuddization   were caught in four Alaskan lakes during breeding season in June 2010 . RNA from whole brain tissue was extracted with a phenol-based phase separation  following the Trizol-protocol from SIGMA with minor modifications, that is, replacing chloroform with 1-Bromo-3-chloropropane and adding an extra ethanol wash for the RNA. For every lake population, we pooled an equivalent amount of RNA from five specimens per sex to produce representative male and female pools for each lake. This amounts to a total of eight samples . The sample libraries were created with Illumina TruSeq reagents and were sequenced using 100 base paired-end sequencing in two separate lanes  on an Illumina HiSeq 2000 platform at the Beijing Genomics Institute. A total of approximately 45 million reads per sample were trimmed for low quality bases using the program ConDeTri with default settings  where the reported flip in the orientation of the last two supercontings in chromosome XIX was corrected  we used the R package “DESeq2” 1.4.5 on untransformed read counts, which were generated with “HTSeq” . After a testing , genes wP = 0.05 level if the observed values lay outside the confidence intervals.Differential gene expression between sex chromosomal and autosomal genes: Expression differences between sex chromosomal and autosomal genes were assessed by pooling the four sample populations of both sexes . We calculated ratios of median expression levels for a) the entire sex chromosome, b) the PAR, c) stratum I, and d) stratum II to the median expression level of all autosomal genes, respectively  Sex-specific gene expression and (2) differential gene expression between autosomal and sex-linked genes. Due to the absence of a Y chromosome sequence, it is not possible to unambiguously identify all reads originating from the Y. Hence, the reads from each male sample in the subsequent differential expression analyses likely contain reads from both the X and Y chromosomes .Variant calling was performed with SAMtools 0.1.19 and BCFtools 0.1.19 . Genotypsupplementary material S1, Supplementary Material online). For further analyses, we only retained genes that 1) exhibited Y-specific SNPs neither in the RNA nor in the DNA data set (hemizygous genes) or 2) exhibited Y-specific SNPs in the exons in the DNA data set but not in the RNA (silenced genes). Male expression from these genes is most likely originating merely from the single male X copy, which enables us to approximate an Xmale:AA ratio by repeating the analysis of differential gene expression between sex chromosomal and autosomal genes with this set of genes (henceforth referred to as X-linked genes). In order to test whether any changes in expression levels in these genes were confined to males or were detectable in females, we likewise conducted the analysis with the same set of genes for females. Additionally, we evaluated the robustness of the results of the differential expression analysis by employing criteria of varying rigor for identifying genes with a Y-linked copy. These data are presented in supplementary material S2, Supplementary Material online.Loci that were heterozygous in all male samples but homozygous in all female samples in the sex chromosome were considered Y-specific, that is, these allelic variants in males constitute Y chromosomal variants. In order to estimate expression levels from the male X copy, we identified all genes carrying these Y-specific single nucleotide polymorphisms (SNPs) and removed them from the data set. We then crosschecked and refined our selection of genes without an expressed Y copy by performing variant calling on two male individuals for which we obtained whole-genome sequence data . Two differential expression analyses were performed based on normalized read counts: 1) Differential expression between the sexes and 2) differential expression between genes in the sex chromosome and genes in the autosomes for each sex, respectively. The analysis of the assembled transcriptome data identified 26,093 genes in the autosomes, 4,243 genes in unmapped scaffolds (covering 3.5 mega bases), and 1,464 genes in the sex chromosome . The PAR recombines in both sexes, and thus cis-regulated expression differences between the sexes are less likely to evolve in this region. Accordingly, we found only two male-biased genes, one female-biased gene (A), and one gene carrying a Y-specific SNP in the PAR . In total, 158 genes in stratum I exhibited female-biased expression levels. Their mean logarithmic fold change was −0.79 and their variance was much smaller than that of the male-biased genes . Almost one-third of the identified genes in stratum I maintained a transcribed Y-linked copy .The majority of differentially expressed genes between the sexes was confined to the two sex-linked strata . Stratumfig. 2C). The variance of the fold changes of the female-biased genes was again comparatively low (SD: 0.14) and the logarithmic mean fold change of these genes was −0.93. As a large part of stratum II is deleted from the Y (fig. 2F).Stratum II harbored only three genes with male-biased expression, whereas the majority of genes had female-biased expression  to the median autosomal expression level (AA) using FPKM-normalized count data. The analysis was conducted with four different data sets: All sex chromosomal versus autosomal genes, PAR versus autosomal genes, stratum I versus autosomal genes, and stratum II versus autosomal genes. To estimate confidence intervals, we generated 10,000 pooled bootstrap samples of each data set and recalculated the ratios of medians as well as the 95% confidence intervals for the distributions.P < 0.001; P values are provided in The observed ratio of median sex-linked and autosomal expression levels for the entire sex chromosome was 1.03 for females , table 2In stratum II the observed median XXfemale:AA ratio was 1.21 , indicatA–C), and between genes in the entire sex chromosome and genes in the autosomes  offer an alternative explanation for the preservation of these genes in the Y: Assuming that transcription rates are limited, males cannot compensate for the loss of a copy of an initially highly expressed gene by further upregulating their remaining X copy, for example, through modifier genes  and consequently are only maintained in the X chromosome. Moreover, the proportion of these X-linked genes among male-biased genes in this stratum (0.64) is higher than the proportion of X-linked genes among unbiased genes . This is in concordance with theoretical models based on dominance that predict an increase of putative male-beneficial mutations in hemizygous regions of the X (Drosophila (C and F). An alternative  explanation is that the upregulation of the male X in stratum II . However, examining the spatial distribution and magnitude of the estimated dS values provides no conclusive statistical evidence as to the relative ages of the two strata . One possible explanation is that recombination between the X and Y in both strata may have stopped in relatively close temporal proximity. Alternatively, crucial differences in dS values between the strata may have been erased by the large deletion in the Y, hampering reliable age estimation in this young sex chromosome system. In light of the differences in gene expression between the strata , the authors argue that a stable evolutionary solution was achieved with this intermediate stage of dosage compensation and a countercompensation of females is not necessary. In contrast, threespine sticklebacks have considerably younger sex chromosomes and the currently observed expression patterns may not constitute the endpoint of their evolutionary trajectory. It is thus conceivable that in the future females will be forced to countercompensate for the progressing male X upregulation following further Y deterioration  reduces transcription of both X copies using a dosage compensation complex  A successive gene-by-gene degeneration in stratum I, that may allow for a likewise successive gene-by-gene mechanism of dosage compensation, and 2) a deletion of large segments in the wake of chromosome inversions in stratum II . The resSupplementary materials S1–S3 are available at Genome Biology and Evolution online .


Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family  Viruses with single-stranded (ss)DNA genomes constitute a large class of economically, medically and ecologically important pathogens that infect hosts in all three domains of life231567891213Bidnaviridae do not conform to this general pattern. The family Bidnaviridae includes small isometric viruses that infect the silkworm Bombyx moriBombyx mori bidensovirus (BmBDV). Based on the linear structure of the genome, BmBDV was initially placed in the family Parvoviridae, but upon closer examination it was reclassified into an independent virus familyEukaryotic ssDNA viruses typically have small icosahedral capsids and for genome replication rely on the rolling circle-like mechanism initiated by a distinct virus-encoded endonuclease1Parvoviridae.The single-strandedness of the bidnavirus genomes as well as the dimensions and morphology of the virions seem to point to their possible relatedness to parvoviruses. Another feature shared between these two groups of viruses is the superfamily 3 helicase S3H. In parv1918Parvoviridae is divided into two subfamilies: members of the Parvovirinae infect vertebrate hosts, whereas members of the Densovirinae replicate in arthropodsParvoviridae representatives infecting different hosts revealed the conservation of all three diagnostic motifs typical of S3H proteinsDensovirinae subfamily, suggesting that BmBDV either evolved from an ancestor belonging to this viral group or horizontally acquired the S3H gene from a densovirus.Based on the genomic features as well as the host range of corresponding viruses, the family The virions of parvoviruses for which high resolution structural information is available, consist of homologous CPs that adopt the jelly-roll fold262728Fig. 2aThe major constituent protein of the BmBDV virions is encoded by VD1 ORF318B. mori-encoded lipase associated with the virionsAt the N-terminus of the CP (preceding the glycine-rich and the jelly-roll domains), most parvoviruses contain a conserved phospholipase A2 domain which is important for virus entry33Bidnaviridae. A BlastP search against the non-redundant (nr) NCBI protein database seeded with the sequence of PolB of BmBDV returned as the best hit a PolB from the endoparasitoid wasp Glyptapanteles flavicoxis . Analysis of the genomic context of the G.flavicoxis PolB gene showed that it is an integral part of the previously described large transposable element36G.flavicoxis. To further investigate the provenance of the bidnavirus PolB, we constructed a maximum likelihood tree . We hypothesized that the key event that led to the secession of the bidnaviruses from parvoviruses was the acquisition of the PolB gene. Consequently, identification of the likely donor of the PolB gene is central for understanding the origin of the ood tree , which iood tree . This trViruses that replicate their genomes via the protein-primed mechanism typically encode terminal proteins which are covalently attached to the genome termini and serve as primers for DNA replicationSpinareovirinae) were retrieved . However, after several iterations, proteins of reoviruses from other genera were retrieved as well, including the extensively studied rice dwarf virus . The homologous regions of reoviral and bidnaviral proteins were aligned and a phylogenetic tree was constructed using the maximum likelihood method  is located on the second genomic segment, VD2. The VD2 ORF1 encodes the 133 kDa minor capsid protein (1160 amino acids) that shows sequence similarity to proteins of some reoviruses1214143d method . In thisCryptophlebia leucotreta granulovirus Junonia coenia densovirus is essential for viral DNA replicationA non-structural protein encoded by VD2 ORF2, denoted NS3, has been reported to share sequence similarity with NS3 proteins from several densovirusesCryptophlebia leucotreta granulovirus, other viruses with dsDNA genomes from the family Baculoviridae (genera Alphabaculovirus and Betabaculovirus) and the unassigned genus Nudivirus were also found to encode NS3-like proteins (Betabaculovirus). Consistently, in BlastP analysis, the best match was to the protein gp025  from Choristoneura occidentalis granulovirus, whereas the best-matching homolog among densoviruses  was retrieved with a substantially lower significance (E = 5e-05). Unexpectedly, densoviruses themselves did not form a monophyletic clade (Periplaneta fuliginosa densovirus clustered with the Oryctes rhinoceros virus (genus Nudivirus) as a sister clade to the alphabaculoviruses. This tree topology is best consistent with multiple cases of horizontal gene transfer among arthropod-infecting viruses with ssDNA and dsDNA genomes. In particular, BmBDV most likely acquired its NS3 gene from a granulovirus rather than from a densovirus.We performed a search for BmBDV NS3 homologs using PSI-Blast and found that this protein is distributed much wider than currently consideredproteins . The funproteins . Insteadic clade : PeriplaSequence alignment of the NS3-like proteins from diverse viruses revealed a conserved Zn-finger motif . ProteinParvoviridae. Although it is not currently possible to pinpoint the exact ancestral parvovirus, it appears reasonable to suggest that the split postdates the separation of vertebrate and arthropod-infecting parvoviruses. The key event in the emergence of the Bidnaviridae family apparently was the loss of the characteristic RCRE domain of parvoviral NS1 proteins, which could have been concomitant or subsequent to the acquisition of the PolB gene from an arthropod-associated polintoviruses  and S78547 (segment VD2). Homologues of the bidensoviral proteins were searched for using PSI-BLASThttp://toolkit.tuebingen.mpg.de/blastclust. Multiple sequences alignments were built using Promals3Dhttp://imed.med.ucm.es/Tools/sias.html. The secondary structure was predicted using PSI-PredThe genome sequences of M.K. collected the data; M.K. and E.V.K. analyzed the data and wrote the manuscript. Both authors read and approved the final version.Figure S1


Summary: In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution simultaneously fuses and deconvolves the images in 3D, but processing takes a multiple of the acquisition time and constitutes the bottleneck in the imaging pipeline. Here, we show that MV deconvolution in 3D can finally be achieved in real-time by processing cross-sectional planes individually on the massively parallel architecture of a graphics processing unit (GPU). Our approximation is valid in the typical case where the rotation axis lies in the imaging plane.Availability and implementation: Source code and binaries are available on github (https://github.com/bene51/), native code under the repository ‘gpu_deconvolution’, Java wrappers implementing Fiji plugins under ‘SPIM_Reconstruction_Cuda’.Contact:bschmid@mpi-cbg.de or huisken@mpi-cbg.deSupplementary information:Supplementary data are available at Bioinformatics online. MV imaging is particularly useful in light-sheet microscopy where consecutive views are acquired in short succession, allowing reconstruction of entire developing organisms without artifacts (Supplementary Note S1). Previous attempts therefore required splitting the data into blocks of appropriate size. Each block then either had to be transferred to and from the GPU in each RL iteration (The RL deconvolution iterations consist only of convolutions and pixel-wise arithmetic operations and could therefore be significantly accelerated using dedicated hardware such as a graphics processing unit (GPU). The large memory requirements of MV deconvolution, however, exceed the limited resources of modern GPUs even for moderate data sizes (Supplementary Note S2). Compared with 3D MV deconvolution, with and without GPU support, we thereby reduced processing times by a factor of up to 25 and 75, respectively (Supplementary Table S1), while producing comparable results.The primary goal of MV fusion is the improvement of the poor axial resolution in a single 3D dataset using the superior lateral resolution of an additional, overlapping dataset, and not necessarily to improve resolution beyond the intrinsic lateral resolution. We therefore approximated the full 3D point spread function (PSF) with a 2D PSF, neglecting one lateral component , and processed each plane orthogonal to the rotation axis independently a. MemorySupplementary Fig. S1).We compared the results of our implementation to the methods commonly used in the light-sheet community, such as established 3D deconvolution d–i. BothAlthough registration of the different views is still required, it can be performed in pre-processing before starting a time-lapse experiment, due to the repeatability of high-quality microscope stages. Multi-view deconvolution can then be performed in real time directly as the data is transferred from the camera.Supplementary Material).We provide our software as a C library that can be directly linked to camera acquisition software for real-time processing, and as plugins for Fiji , we confirmed the applicability of our approximation even if the rotation axis is slightly tilted . Its validity is independent of the amount of noise , but depends on the lateral extents of the PSF. Keeping its axial standard deviation fixed at eight pixels, a typical value measured on our microscopes, we found that up to a lateral standard deviation of 2–3 pixels, results from plane-wise and 3D deconvolution are undistinguishable . The measured lateral standard deviation of the PSF was typically between 1.5 and 1.8 pixels on our microscopes.Our plane-wise deconvolution approximates 3D deconvolution by neglecting the contribution of the PSF along the rotation axis. It is therefore suited for systems with a single rotation axis lying within the imaging plane. Using artificial data (The photo-efficiency of light-sheet microscopy enables long time-lapse imaging of living samples to study fundamental questions in developmental biology. However, its huge data rates also open new challenges for data processing. A key problem in light-sheet microscopy has been the fusion of data recorded from multiple angles. In this article, we presented a new method that performs MV deconvolution plane-wise, which reduces memory requirements compared with existing methods and thus permits an entirely GPU-based implementation. The achieved acceleration makes MV deconvolution for the first time applicable in real-time without the need for data cropping or resampling.


Posttraumatic stress disorder (PTSD) is reportedly associated with lower rates of physical activity participation despite the known benefits of regular physical activity for improving both mental and physical health. However, no studies have evaluated the validity or feasibility of assessing physical activity within this population resulting in uncertainty around the reported lower rates of physical activity participation. This study aimed to evaluate the feasibility and concurrent validity of the International Physical Activity Questionnaire-Short Form (IPAQ-SF) and the Actigraph accelerometer  among inpatients with PTSD.Fifty-nine adult hospital inpatients with a Diagnostic Statistical Manual Mental Disorder-IV-TR diagnosis of primary PTSD  participated in the study. Participants were asked to wear an Actigraph accelerometer for seven consecutive days then complete the IPAQ-SF. The Spearman rho correlation coefficient compared the amount of moderate to vigorous physical activity (MVPA) measured with the Actigraph and the total physical activity reported in the IPAQ-SF.Lower than expected compliance with wearing accelerometers  (n = 20) was found suggesting that the use of accelerometers within this population may not be feasible. Complete IPAQ-SF data were available for 45 participants (76%) indicating that this tool also has its limitations in this population. The Spearman rho was 0.46 (p = 0.01) for the 29 participants with four or more valid days of accelerometer data (as per literature standards) and available IPAQ-SF.The IPAQ-SF and the Actigraph accelerometer have limitations in people with PTSD but in those able to provide data, show correlations of a magnitude comparable to those observed in the general population. The development and testing of mental health specific tools may enhance measurement of physical activity in this population. Post-traumatic stress disorder (PTSD) has been recently reconceptualised in the most recent edition of the Diagnostic and Statistical Manual of Mental Disorders (5th edition) within a new dedicated chapter on trauma and stress related disorders. Previously identified as an anxiety disorder, PTSD is categorised by symptoms of hyper-arousal, re-experiencing and avoidance. Lifetime prevalence rates of PTSD within the general population are estimated to be between 5-10% , 3.Similar to other mental health conditions, people with PTSD have higher rates of metabolic disturbances and poor physical health compared to the general population with higher rates of coronary heart disease, diabetes and substance abuse . People Regular physical activity, or structured exercise, has been shown to have anti-depressant and anxiolytic qualities , 8, althAs physical activity programs become routinely incorporated into PTSD treatment facilities, it is vital that clinicians have reliable and valid measures of physical activity that are also feasible to collect. Common methods of physical activity assessment include self-report questionnaires and objective monitors such as accelerometers. The International Physical Activity Questionnaire- Short Form (IPAQ-SF) is a frequently used four question, self-report measure of physical activity participation during the previous seven-day period . A 2011 The aim of this study was to a) evaluate the feasibility of the International Physical Activity Questionnaire-Short Form (IPAQ-SF) and the Actigraph accelerometer among inpatients with posttraumatic stress disorder (PTSD) and b) determine the concurrent validity of these two instruments.Fifty-nine adult participants were recruited from the inpatient trauma program at St John of God Health Care, Richmond Hospital  between May 2011 and April 2012. All participants met DSM-IV diagnostic criteria for PTSD, were ambulatory and cognitively able to provide consent. Potential participants were excluded if they were pregnant or medically restricted from participating in physical activity due to significant physical injury or illness. Ethical approval was obtained for this study from St John of God Health Care’s Ethical Committee (REF: 412) and The University of Sydney Human Research Ethics Committee (Protocol No 14091). Written informed consent was obtained from all participants.Demographic information including age, sex and general medical and psychiatric history was collected by means of a questionnaire. The Health of Our Nation Outcome Scale (HoNOS)  was usedThe Actigraph GT3X accelerometer  is a small electronic device the size of a small beeper worn by individuals to record levels of physical activity and sedentary behaviour. Participants were provided with an Actigraph GT3X accelerometer as well as written wearing instructions, and were asked to wear the accelerometer on the right hip for all waking hours during a 7-day period, except during water-based activities. Participants were instructed to wear the accelerometer if napping during daytime hours. The Actigraph output includes movement counts/ minute for the vertical, anterior-posterior, and mediolateral axes. The epoch was set at 1-second intervals. Accelerometer cut-points were defined as sedentary (<100 counts/minute), light activity (100–1951 counts/minute), moderate activity (1952–5724 counts/minute) and vigorous activity (>5725 counts/minute) . In ordeFollowing the 7-day period, participants completed the IPAQ-SF. The IPAQ-SF assesses four domains of physical activity over the previous week, including vigorous activity , moderate activity , walking and time spent sitting. Data from the IPAQ-SF were scored as per the IPAQ-SF scoring manual . As recoParticipants were included in the statistical analyses if they recorded at least three valid days of accelerometer data. Analyses were conducted with both at least three, and at least four valid days. A valid day was defined as at least 10 hours of wear time, and periods of 60-minutes or more of consecutive zeros were considered as non-wear time. All analyses were performed with SPSS statistical software. The concurrent validity of the IPAQ-SF against the accelerometer was determined using Spearman rho correlation coefficients, calculated for both minutes per day of moderate to vigorous physical activity, and total sitting (IPAQ-SF) and sedentary time (accelerometer) per weekday. Bland-Altman plots with 95% limits of agreement were calculated as the measures of agreement between the instruments. The median HoNOS score (21) was used as the dichotomisation point to stratify participants according to illness severity, and t-tests were used to determine the impact of illness severity on accelerometer-recorded physical activity.2 (m)/ weight (kg)) was 30.2 (SD = 4.6), with 9% of participants being normal weight, 48% overweight, and 44% obese (class I or II obesity) [Anthropomorphic, demographic and diagnostic participant data are included in Table obesity)   recorded zero, one or two valid days of accelerometer data, whilst only eight (14%) recorded the full seven valid days. A further ten participants (17%) recorded three valid days, five (15%) recorded four valid days, nine (15%) recorded five valid days and 17 29%) recorded six valid days. Literature standard is to only include participants with at least four valid days of data, but given the poor compliance we performed sensitivity analyses for both 3+ and 4+ valid days, which showed similar results  IPAQ-SFs were incomplete due to sudden or early discharge and eight of 59 (14%) reported values that were considered erroneously high  and were excluded from the analysis as advised in the IPAQ-SF scoring manual. Illness severity was not found to significantly impact compliance with either the accelerometer or the IPAQ-SF.As shown in Table For participants with a greater illness severity as defined by a HoNOS score of ≥21, the Spearman correlation for physical activity between the accelerometer and the IPAQ-SF was 0.46  and 0.59 .For those with a lesser illness severity the correlation was 0.46 (95%CI = −0.05 to 0.78)  and 0.48  Table .Table 3The Spearman correlation between sitting time based on the IPAQ-SF and accelerometer for those with a greater illness severity was −0.001  and 0.33 . For participants with a lesser illness severity the correlation was 0.28  and 0.34 (95% CI = −0.17 to 0.71), ≥four valid days; n = 17).The Bland-Altman plot for moderate-vigorous physical activity Figure  indicateThis study found poorer than expected compliance with both measures of physical activity but found that, among those who provided data for both tools, the IPAQ-SF and Actigraph have similar correlations compared to the general population .The high number of participants excluded from the final analysis due to invalid accelerometer data or erroneous IPAQ-SF questionnaire responses is an important finding. Contributing factors to poor accelerometer compliance may include a lack of motivation and fatigue, the location of the objective monitoring device , and external and internal motivators for wearing the monitors. Future studies utilising accelerometer measurements within inpatient PTSD populations may benefit from a multi-disciplinary approach to increasing compliance by utilising health professionals in contact with patients on a regular basis, such as nursing staff, psychologists and occupational therapists.Of the 52 completed IPAQ-SF questionnaires, eight were excluded from the analysis due to erroneously high values. Future research with psychiatric inpatients may also benefit from using an interview to administer the IPAQ-SF to improve the accuracy of physical activity reporting. Nursing and allied health staff in regular contact with inpatients would be appropriately placed to administer such an interview. Given that 74% of participants in this study were from a police or defence background, it is possible that participants may have reported physical activity based on their pre-trauma levels of participation, in which physical activity and regular exercise would have been required for occupational purposes. Over reporting has previously been acknowledged as a key limitation of self-reported measures of physical activity .Among those who provided data for both tools, the correlation between the IPAQ-SF and Actigraph was reasonably high (0.46) indicating acceptable concurrent validity for estimating the physical activity of inpatients with PTSD based on findings from similar studies in other populations . This deIllness severity was not strongly associated with physical activity levels, or compliance with either the accelerometer or IPAQ-SF. Illness severity however did impact upon the strength of the relationship between time spent in sedentary behaviour and sitting time as per the IPAQ-SF. This has implications for practice, and highlights a need for greater physical activity interventions within psychiatric facilities, especially for those with a greater illness severity.The high rate of excluded data is a significant limitation of this study, and serves to highlight the pragmatic limitations associated with assessing physical activity in PTSD. The relatively small number of female participants is another potential limitation, as differences in feasibility and compliance to either measure may exist between sexes that were unable to be assessed within this study. The IPAQ-SF asks participants about physical activity participation in bouts of at least ten-minutes only. This was not accounted for in the analysis of the accelerometer data, which we acknowledge as a potential limitation of this study.Both the IPAQ-SF and accelerometers have limitations when used with inpatients with PTSD, including over-reporting and poor compliance to wearing objective monitors. The quick administration time and moderate correlation with an objective measure of physical activity are strengths of the IPAQ-SF, however further research is needed to identify optimal approaches to measurement of physical activity in people with mental health problems . The dev


Plasmodium vivax infections and also the only drug against the mature sexual stages of Plasmodium falciparum which are responsible for onward transmission to mosquitoes. Nevertheless, uncertainty associated with this drug’s safety results in under-use due to difficulties with diagnosing glucose-6-phosphate dehydrogenase deficiency (G6PDd) in point-of-care settings. This common genetic disorder makes patients susceptible to potentially severe, and occasionally even fatal, primaquine-induced haemolysis.Primaquine is an essential drug for malaria control and elimination by being the only drug active against the liver-reservoir of Policy shifts towards malaria elimination in recent years have led to a surge of clinical trials and reviews of historical data to promote safe primaquine use. This talk will examine evidence of the drug’s use and outcomes in geographic regions with distinct epidemiological characteristics. For each setting, the parasite epidemiology, the population’s G6PDd characteristics, and the current primaquine policies will be discussed. The quality and completeness of the parasitological, G6PDd and clinical evidence-bases that inform primaquine policy is examined; the importance of context-specific evaluations of primaquine use is emphasized.


Lung transplantation has evolved into a life-saving therapy for select patients with end-stage lung diseases. However, long-term survival remains limited because of bronchiolitis obliterans syndrome (BOS). Soluble HLA-G, a mediator of adaptive immunity that modulates regulatory T cells and certain classes of effector T cells, may be a useful marker of survival free of BOS. We conducted a retrospective, single-center, pilot review of 38 lung transplant recipients who underwent collection of serum and bronchoalveolar lavage fluid 3, 6 and 12 months after transplantation, and compared soluble HLA-G concentrations in each to the presence of type A rejection and lymphocytic bronchiolitis in the first 12 months and to the presence of BOS at 24 months after transplantation. Lung soluble HLA-G concentrations were directly related to the presence of type A rejection but not to lymphocytic bronchiolitis. Our data demonstrate that soluble HLA-G concentrations in bronchoalveolar lavage but not in serum correlates with the number of acute rejection episodes in the first 12 months after lung transplantation, and thus may be a reactive marker of rejection. Lung transplantation (LT) remains the best hope for selected patients with end-stage lung diseases. Chronic allograft rejection, clinically manifested as bronchiolitis obliterans syndrome (BOS), remains a major limitation to long-term survival: BOS occurs in 40–60% of lung transplant recipients within 4 years and is the leading cause of death after the first year, despite advances in the use of immunosuppressive therapy HLA-G is a major histocompatibility complex class I antigen encoded by a gene on chromosome 6p21 HLA-G has been demonstrated in heart transplant allografts: patients with higher HLA-G expression had fewer acute rejection episodes (AREs) and less evidence for chronic rejection We have previously demonstrated that low numbers of FoxP3+ Treg cells are associated with accelerated rejection and the development of BOS in LT Approval was obtained from the University of Chicago Institutional Review Board (IRB) for this study, and was continuously updated as required during the study. Informed written consent done on forms approved by the IRB was obtained from all patients included in this analysis prior to their participation.Adult subjects receiving a single or bilateral sequential lung transplant from June, 2006 to September, 2011 at the University of Chicago Hospitals were evaluated. Clinical data, blood samples, and BAL fluid collected by bronchoscopy in the first 12 months after transplantation, and clinical status and pathology samples to determine the presence or absence of acute rejection episodes and BOS in the first 48 months after transplantation, were evaluated. As the point of the study was to evaluate a potential marker for the development of BOS, patients had to survive for 12 months or longer after transplantation to be included in this study.Baseline immunosuppression for all patients included tacrolimus (target trough level: 10 ng/mL), azathioprine (2 mg/kg/day), and prednisone (tapered to 5 mg/day by 3 months post-transplantation). Daclizumab induction therapy was administered to all patients per the manufacturer's instructions. Immunosuppression was changed because of declining pulmonary function per the discretion of the attending transplant physician.g and 4°C for 10 min, after which the supernatant was removed, passed through a 1.2-µm filter, and frozen at −80°C until used. Cell pellets were also frozen at −80°C until analyzed. For transbronchial biopsies, samples were collected by standard technique from the recipient lung and processed for evaluation of rejection.We have previously described these methods Blood was collected on the same day as bronchoscopy in heparin-containing tubes and immediately placed on ice. Plasma was separated by centrifugation and stored in aliquots at −80°C until use.Acute rejection was determined by histological analysis of transbronchial biopsies obtained during each surveillance bronchoscopy and clinical bronchoscopies. Acute rejection was graded in accordance with International Society of Heart and Lung Transplantation (ISHLT) guidelines sHLA-G was measured in plasma and in BAL fluid using ELISA . The capture antibody, MEM-G/9, recognizes both shed G1 and soluble G5. The limit of sensitivity is ∼1 U/ml. Concentrations in BAL fluid were not normalized for BAL fluid protein content or other markers.Clinical data are expressed as the mean ± standard deviation or as the median with interquartile ranges. When HLA-G concentrations were below the limit of detection the value was recorded as ‘0’. Results were compared using the non-parametric Kruskal-Wallis test. The Spearman correlation was used to determine associations between HLA-G concentrations and grade A or B rejection. The associations between HLA-G, RA or LB and mortality or BOS-free survival were analyzed using Kaplan–Meier analysis and Cox regression model. The log-rank test was used to compare differences of groups. The survival time was measured from the beginning of lung transplant to the date of death or to the end of the study  and BOS-free survival was calculated from lung transplant date to the first of observation of BOS or death or the end of study, whichever was earlier. A p value less than 0.05 was considered significant. The data was analyzed using the statistic software Stata/SE 13.0 and IBM SPSS Statistics 20.We performed 53 lung transplants in the time period of this study in which patients survived for 1 year or longer; of these 38 subjects were eligible for inclusion . SubjectBoth RA and LB were noted in a majority of subjects prior to the onset of BOS . There wA total of 71 plasma and 85 BAL samples were collected in the first year after transplantation in 38 subjects. Plasma sHLA-G concentrations could be measured in every subject at every encounter, whereas 10 BAL samples had an sHLA-G concentration below the limit of sensitivity. Substantial variance was noted in both plasma and BAL maximum concentrations in the first year .There was no relation between either maximum plasma HLA-G concentration recorded in the first year, or in mean plasma HLA-G concentration of all first year samples, and overall survival or BOS-free survival. Likewise, there was no relation between either maximum BAL HLA-G concentration recorded in the first year, or in mean BAL HLA-G concentration of all first year samples, and overall survival. Contrary to our expectations, an increased maximum BAL HLA-G concentration was associated with a higher grade of RA prior to a clinical diagnosis of BOS  . In contBoth blood and lung infection, as demonstrated by positive cultures in blood or BAL fluid respectively, were noted in a majority of subjects prior to the onset of BOS . There wBronchiolitis obliterans syndrome remains the major limitation to long-term survival after lung transplantation despite advances in immunosuppressive therapy, infection control, and management of other complications. The poor prognosis associated with BOS reflects in part an inadequate understanding to date of disease processes which in turn leads either to under-treatment with immunosuppressive medications, and thus BOS progression, or to over-treatment or inappropriate treatment, and thus the increased number of infections and complications seen in this patient population. Our study demonstrates that the local (BAL) presence of HLA-G in the first year after transplantation in the lung correlates with the number of grade A rejection, and that circulating plasma HLA-G in the first year after transplantation correlates inversely with LB. Our study suggests that HLA-G may be a biological marker of rejection in a lung allograft. Such a marker, if confirmed in larger studies, would be useful to segregate those patients with a higher risk of rejection and BOS who require more intense immunosuppressive therapy from those in whom such therapy would entail increased risk without commensurate benefit.Concentrations of sHLA-G were usually, but not always, detected in BAL fluid collected from LT recipients, and some variance was seen in BAL concentrations. We hypothesized that increased HLA-G levels in the lung would be associated with a lower rejection score as has been seen in patients following other solid-organ transplant There was variance also in circulating serum HLA-G concentrations in the first year after transplantation, and these were inversely associated with LB, but not RA, status. Serum HLA-G concentrations in subjects with a score of 1 in LB status was not different than that seen in recipients with a score of 0, while subjects with a score ≥2 had lower HLA-G concentrations. This suggests that mild lymphocytic bronchiolitis demonstrated on transbronchial biopsies may not be associated with changes in immune status sufficient to in turn decrease serum levels. The downward trend in serum HLA-G concentrations in patients with significant RA noted on transbronchial biopsy is not statistically significant but will need to be examined in the context of a larger study. Serum markers clearly are easier to obtain and, along with other serum markers, provide context for the overall status of the immune system. Correlations with circulating regulatory and effector T cell trafficking to the lung allograft will be needed to understand the potential role of serum sHLA-G in LT recipients.In one recent single-center, retrospective study of 64 LT recipients within 1 year of transplant, HLA-G protein expression was seen in both bronchial and alveolar epithelial cells most frequently in stable patients but less so in patients with frequent AREs or in patients with BOS HLA-G in the allograft may stimulate the presence and/or survival of lung Treg lymphocytes that then may modulate tolerance; this will need to be confirmed in future studies. In particular, our data do not make clear whether the change in allograft HLA-G expression is reactive, due to some rejection episode or stimulus from cells that ordinarily mediate rejection, or is innate and dependent more on a subject's  genotype. HLA-G also inhibits both NK cell- and CD8+ T cell-mediated cytolysis HLA-G induces expansion of CD4+FoxP3+ Treg cells Our study was too small to detect whether either plasma or local lung (BAL) HLA-G concentrations were associated with survival or BOS-free survival. Similarly, given the few time points that were collected for each subject and the missing samples, we were unable to assess changes in sHLA-G concentrations in BAL and serum reliably over time. Both limitations are typical of single-center studies and suggests that a multi-center trial with a significantly larger number of study subjects will be required to answer this question. Nevertheless our study does suggest that HLA-G is protective against LB; we predict that over a longer period of time and in larger studies that this will translate into improved BOS-free survival.An additional issue is whether sHLA-G concentrations in BAL fluid reflect the local concentrations of sHLA-G at the tissue level. Previous studies in heart and lung transplant recipients have evaluated sHLA-G presence in endomyocardial and transbronchial biopsies, respectively HLA-G genotype of both the donor graft and recipient has been examined in small studies of other solid organ transplants. While alleles encoding polymorphisms in the coding region apparently have little effect in renal transplantation HLA-G may help predict renal HLA-G and its expression in lung allografts and in recipients will be needed to answer this question.Our study also was too small to examine the potential relation of genotype on lung allograft function and the development of BOS. The influence of As may often happen in clinical studies with the collection of biological specimens, data were not available at each pre-specified time point because of the clinical condition  of the patient or logistics of specimen collection. However, the data remain useful despite these missing samples. In addition, we cannot exclude that different patient phenotypes or the variety of clinical events such as infection may bias our results. The putative use of lung sHLA-G as a biomarker for early allograft rejection clearly will require further study and confirmation in larger cohorts from different transplant centers.In summary, we demonstrate the presence of sHLA-G in both the lung and serum of LT recipients. There is an association of high BAL sHLA-G presence and the development of grade A rejection within 2 years. While the mechanisms by which lung sHLA-G presence increases are not clear, this adaptive immunity mediator may be a marker of rejection in lung transplantation.


In three former studies headache sufferers (in particular migraineurs) had more perivascular spaces (PVS) on MRI than headache-free.To evaluate the association between headache and PVS in a relatively large and population-based imaging study with a blinded design.The study was part of a large longitudinal epidemiological study ). The 1006 participants were 50-65 years at inclusion, had participated in all previous HUNT studies , and had been randomly selected to a population-based imaging study of the head . The number of dilated PVS in the basal ganglia (BG) and hemispheric white matter (HWM) was compared in headache sufferers  and headache-free. Both cross-sectional and longitudinal analyses were performed.The cross-sectional analysis showed that migraineurs without aura in HUNT 3 had fewer PVS than headache-free  in BG. In the longitudinal analysis those with migraine in only HUNT 2 were found to have fewer PVS than headache-free  in HWM. There was no relation between PVS and any other headache types.In contrast to the findings of previous studies the present study showed no increase in number of dilated PVS among headache sufferers. Fewer PVS in migraineurs without aura may be an incidental finding.No conflict of interest.


In a quiescent cell, centrioles can migrate to the apical surface of the cell and nucleate hair-like projections called cilia and flagella. The stages of ciliogenesis require a large number of proteins and complexes to be trafficked through to the cilium and are carefully coordinated by the centrosome and centrosome-associated proteins. Here, we studied centrosome proteins named outer dense fiber-2 like (ODF2L) to establish their role in ciliogenesis We identified the ODF2L as a satellite protein in proliferating cells by using immunofluorescent-labeling and expression of this protein is changed when the ciliation is induced. When ciliation induced, ODF2L seems to localise into the centrioles or completely diminish the expression in hTERT-RPE-1 cells. When lysate of the quiescent cells was analysed for the ODF2L expression revealed the complete removal of the protein. When ODF2L was over expressed, hTERT-RPE-1, were unable to ciliate even after initiation of ciliation by serum depravation. Furthermore, knocking down of ODF2L with SiRNA in hTERT-RPE-1 cells resulted in four times more cilia cultured in serum supplemented media. In zebrafish depleting the transcript by using anti-sensing morpholinos resulted in the phenotype of varied development and curved back with ectopic otoliths which resembles other ciliary function compromised phenotypes observed when the known ciliary components were depleted. Furthermore, whole mount immunoflorescent studies of morphants revealed shortened cilia in the pronephros.ODF2L may negatively regulate ciliation by changing the expression and its localisation within mammalian cells however in zebrafish exact function is yet to be discovered.


High water cut and low velocity vertical upward oil-water two-phase flow is a typical complex system with the features of multiscale, unstable and non-homogenous. We first measure local flow information by using distributed conductance sensor and then develop a multivariate multiscale complex network (MMCN) to reveal the dispersed oil-in-water local flow behavior. Specifically, we infer complex networks at different scales from multi-channel measurements for three typical vertical oil-in-water flow patterns. Then we characterize the generated multiscale complex networks in terms of network clustering measure. The results suggest that the clustering coefficient entropy from the MMCN not only allows indicating the oil-in-water flow pattern transition but also enables to probe the dynamical flow behavior governing the transitions of vertical oil-water two-phase flow. Vertical upward oil-water two-phase flow is widely encountered in petroleum industry. An oil well is vertically drilled through the ground at first, and then it goes on following an inclined angle before it finally enters into the oil reservoir. The oil and water usually coexist during the above oil-well production, and these two immiscible fluids can distribute themselves in many temporal-spatial configurations, known as flow patterns, which greatly depend on the fluid properties, volume fraction and flow rates. Note that the flow behavior underlying multiphase flow is much more complicated than that of single-phase flow, due to the influence of phase interfacial interactions and local relative movements. Characterizing the dynamic behavior governing the transitions among vertical upward oil-water flow patterns has become a challenging subject of significant importance, especially for the physical modeling and flow parameters measurement.The investigations on complicated flow behaviors underlying two-phase flow patterns have drawn a great deal of attention from various research areas. The nonlinear time series analysis methods1In recent years, the research into complex networks has undergone a remarkable development9101112131415171819202122232426283233Multivariate multiscale analyses provided us with an important perspective for characterizing complex systems35We carry out the oil-water two-phase flow experiment in a vertical upward small diameter plexiglass pipe (20 mm-inner-diameter) at Tianjin University. The experiential mediums are tap water and No. 3 industry white oil. As shown in v is defined asOur method enables to map a multivariate time series into a multiscale complex network, which allows us to investigate the inherent properties of multivariate time series from the perspective of complex network analysis and multiscale analysis. Then we use network clustering measure to characterize the inherent structure of the MMCN. The clustering coefficientTv is the total number of closed triangles containing node v and kv is the degree of node v. A large clustering coefficient indicates a specific network configuration associated with the cliquish feature of a node. According to the information entropy, we develop a novel clustering coefficient entropy, denoted as EC, which is calculated by:where N is the total number of nodes in the network. For the MMCN analysis, we calculate the EC under different scales and then plot EC with changing scale factors to uncover the multiscale features of the MMCN. Aiming to reveal the dynamic flow behavior in the evolution of oil-in-water flow patterns, we derive the MMCN from experimental measurements for different flow conditions. The results are shown in Kw denotes the fixed water cut and Um represents the total velocity of the oil-water mixture. We can see that, the distributions of EC at different scales for three oil-in-water flow patterns present distinct features. Vertical oil-in-water slug flows occur at low oil-water mixture flow rate, where there exist many oil slugs whose diameters nearly equal to the pipe diameter. The local flow behavior for this flow pattern presents the features of the slow movements, intermittent oscillation and non-homogenous distribution. In particular, some small numbers of oil droplets simultaneously follow the cap-shaped oil slugs. Correspondingly, as shown in where Characterizing complicated patterns arising from vertical upward oil-water two-phase flow is a contemporary problem of significant importance. We measure the local flow information from three vertical oil-in-water flow patterns and then develop a multivariate multiscale complex network to investigate the dynamic behavior in the transitions among different oil-in-water flow patterns from multi-channel measurements. The basic idea of the MMCN is to define temporal scales in terms of the coarse-grain process and then reconstruct the phase-space from coarse-grained multivariate time series for each scale to construct a multiscale complex network. Our results indicate that the clustering coefficient entropy at different scales allows faithfully revealing the dynamical flow behavior associated with different mixture flow rate and water cut in the evolution of different flow patterns. Bridging the MMCN analysis and oil-water two-phase flow provides deep insights into the understanding of the fluid mechanism governing the formation and transition among different vertical oil-in-water flow patterns.p sub-time series of equal length LFor a multivariate time series containing e represents the scale factor. Next we derive complex networks from each where where (a) We generate A can be obtained following the rule that two nodes are connected if the distance between them is smaller than the threshold: Aij = 1 indicates node i and j are connected, while Aij = 0 means node i and j are disconnected. The topological structure of the network can be described by the adjacency matrix A. (d) Finally, we can get the MMCN by performing steps (a–c) on each coarse-grained multivariate time series. It should be pointed out that, according to Ref. Tr(S) to determine the threshold for constructing the MMCN, where S is the covariance matrix of multivariate time series.(c) We can derive a complex network by representing each phase space vector as a node and determining the connections in terms of their distances. By determining a threshold, a network adjacency matrix How to cite this article: Gao, Z.-K. et al. Multivariate multiscale complex network analysis of vertical upward oil-water two-phase flow in a small diameter pipe. Sci. Rep. 6, 20052; doi: 10.1038/srep20052 (2016).