Analysis of forensic DNA mixtures with artefacts

DNA is now routinely used in criminal investigations and court cases, although DNA samples taken at crime scenes are of varying quality and therefore present challenging problems for their interpretation. We present a statistical model for the quantitative peak information obtained from an electropherogram of a forensic DNA sample and illustrate its potential use for the analysis of criminal cases. In contrast with most previously used methods, we directly model the peak height information and incorporate important artefacts that are associated with the production of the electropherogram. Our model has a number of unknown parameters, and we show that these can be estimated by the method of maximum likelihood in the presence of multiple unknown individuals contributing to the sample, and their approximate standard errors calculated; the computations exploit a Bayesian network representation of the model. A case example from a UK trial, as reported in the literature, is used to illustrate the efficacy and use of the model, both in finding likelihood ratios to quantify the strength of evidence, and in the deconvolution of mixtures for finding likely profiles of the individuals contributing to the sample. Our model is readily extended to simultaneous analysis of more than one mixture as illustrated in a case example. We show that the combination of evidence from several samples may give an evidential strength which is close to that of a single-source trace and thus modelling of peak height information provides a potentially very efficient mixture analysis

Melt onset over Arctic sea ice controlled by atmospheric moisture transport

The timing of melt onset affects the surface energy uptake throughout the melt season. Yet the processes triggering melt and causing its large interannual variability are not well understood. Here we show that melt onset over Arctic sea ice is initiated by positive anomalies of water vapor, clouds, and air temperatures that increase the downwelling longwave radiation (LWD) to the surface. The earlier melt onset occurs; the stronger are these anomalies. Downwelling shortwave radiation (SWD) is smaller than usual at melt onset, indicating that melt is not triggered by SWD. When melt occurs early, an anomalously opaque atmosphere with positive LWD anomalies preconditions the surface for weeks preceding melt. In contrast, when melt begins late, clearer than usual conditions are evident prior to melt. Hence, atmospheric processes are imperative for melt onset. It is also found that spring LWD increased during recent decades, consistent with trends toward an earlier melt onset. ©2016. American Geophysical Union. All Rights Reserved

Climate feedback efficiency and synergy

The Author(s) 2013. This article is published with open access at Springerlink.com Abstract Earth’s climate sensitivity to radiative forcing induced by a doubling of the atmospheric CO2 is deter-mined by feedback mechanisms, including changes in atmospheric water vapor, clouds and surface albedo, that act to either amplify or dampen the response. The climate system is frequently interpreted in terms of a simple energy balance model, in which it is assumed that individual feedback mechanisms are additive and act independently. Here we test these assumptions by systematically control-ling, or locking, the radiative feedbacks in a state-of-the-art climate model. The method is shown to yield a near-perfect decomposition of change into partial temperature contri-butions pertaining to forcing and each of the feedbacks. In the studied model water vapor feedback stands for about half the temperature change, CO2-forcing about one third, while cloud and surface albedo feedback contributions are relatively small. We find a close correspondence between forcing, feedback and partial surface temperature response for the water vapor and surface albedo feedbacks, while the cloud feedback is inefficient in inducing surface tempera-ture change. Analysis suggests that cloud-induced warming in the upper tropical troposphere, consistent with rising convective cloud anvils in a warming climate enhances the negative lapse-rate feedback, thereby offsetting some of the warming that would otherwise be attributable to this positive cloud feedback. By subsequently combining feedback mechanisms we find a positive synergy acting between the water vapor feedback and the cloud feedback; that is, the combined cloud and water vapor feedback is greater than the sum of its parts. Negative synergies sur-round the surface albedo feedback, as associated cloud and water vapor changes dampen the anticipated climate change induced by retreating snow and ice. Our results highlight the importance of treating the coupling between clouds, water vapor and temperature in a deepening troposphere

Tetranectin Binds to the Kringle 1-4 Form of Angiostatin and Modifies Its Functional Activity

Tetranectin is a plasminogen kringle 4 domain-binding protein present in plasma and various tissue locations. Decreased plasma tetranectin or increased tetranectin in stroma of cancers correlates with cancer progression and adverse prognosis. A possible mechanism through which tetranectin could influence cancer progression is by altering activities of plasminogen or the plasminogen fragment, angiostatin. Tetranectin was found to bind to the kringle 1-4 form of angiostatin (AST(K1-4)). In addition, tetranectin inhibited binding of plasminogen or AST(K1-4) to extracellular matrix (ECM) deposited by endothelial cells. Finally, tetranectin partially counteracted the ability of AST(K1-4) to inhibit proliferation of endothelial cells. This latter effect of tetranectin was specific for AST(K1-4) since it did not counteract the antiproliferative activities of the kringle 1-3 form of angiostatin (AST(K1-3)) or endostatin. These findings suggest that tetranectin may modulate angiogenesis through interactions with AST

Poleward energy transport: is the standard definition physically relevant at all time scales?

Poleward energy transport in the atmosphere and oceans constitutes an important branch of the global energy budget, and its role in the climate system has been the subject of many studies. In the atmosphere, the transport is affected by “eddies” and large scale meridional cells, both with zero net mass transport across latitude circles, but also partly by processes associated with a net transport of mass across latitude circles. The latter must cease to operate in steady state, but they may be significant when time variability of the heat budget is considered. Indeed, examination of reanalysis data on short (daily to monthly) timescales shows that mass variations on these timescales result in surprisingly large fluctuations (in excess of 10^15 W = 1 PW) in the poleward heat transport. These fluctuations are referred to as “extensive”, for they primarily alter the mass integrated energy of the region considered, but not its averaged value. It is suggested that extensive fluctuations mask more meaningful climate signals present in the heat transport variability on monthly and interannual timescales, and a new formulation is proposed to isolate the latter. This new formulation is applied successfully to reanalysis data and climate model simulations

Body mass index trajectories from 2 to 18 years - exploring differences between European cohorts.

BACKGROUND: In recent decades, there has been an increase in the prevalence of childhood overweight in most high-income countries. Within northern Europe, prevalence tends to be higher in the UK compared with the Scandinavian countries. We aimed to study differences in body mass index (BMI) trajectories between large cohorts of children from UK and Scandinavian populations. METHODS: We compared BMI trajectories in participants from the English Avon Longitudinal Study of Parents and Children born in 1991-1993 (ALSPAC) (N = 6517), the Northern Finland Birth Cohorts born in 1966 (NFBC1966) (N = 3321) and 1986 (NFBC1986) (N = 4764), and the Danish Aarhus Birth Cohort born in 1990-1992 (ABC) (N = 1920). We used multilevel models to estimate BMI trajectories from 2 to 18 years. We explored whether cohort differences were explained by maternal BMI, height, education or smoking during pregnancy and whether differences were attributable to changes in the degree of skew in the BMI distribution. RESULTS: Differences in mean BMI between the cohorts were small but emerged early and persisted in most cases across childhood. Girls in ALSPAC had a higher BMI than all other cohorts throughout childhood, e.g. compared with the NFBC1986 BMI was 2.2-3.5% higher. For boys, the difference emerging over time (comparing the two NFBC's) exceeded the differences across populations (comparing NFBC1986, ABC and ALSPAC). BMI distribution demonstrated increasing right skew with age. CONCLUSION: Population-level differences between cohorts were small, tended to emerge very early, persisted across childhood, and demonstrated an increase in the right-hand tail of the BMI distribution

The impact of type 2 diabetes on long-term gastrointestinal sequelae after colorectal cancer surgery:national population-based study

BACKGROUND: Long-term gastrointestinal sequelae are common after colorectal cancer surgery, but the impact of type 2 diabetes (T2D) is unknown. METHODS: In a cross-sectional design, questionnaires regarding bowel function and quality of life (QoL) were sent to all Danish colorectal cancer survivors, who had undergone surgery between 2001 and 2014 and had more than 2 years follow-up without relapse. The prevalence of long-term gastrointestinal sequelae among colorectal cancer survivors with and without T2D were compared while stratifying for type of surgical resection and adjusting for age, sex, and time since surgery. RESULTS: A total of 8747 out of 14 488 colorectal cancer survivors answered the questionnaire (response rate 60 per cent), consisting of 3116 right-sided colonic, 2861 sigmoid, and 2770 rectal resections. Of these, 690 (7.9 per cent) had a diagnosis of T2D before surgery. Survivors with T2D following rectal resection had a 15 per cent (95 per cent c.i. 7.8 to 22) higher absolute risk of major low anterior resection syndrome, whereas survivors with T2D following right-sided and sigmoid resection had an 8 per cent higher risk of constipation (P < 0.001) but otherwise nearly the same long-term risk of bowel symptoms as those without T2D. For all types of colorectal cancer resections, T2D was associated with a 6–10 per cent higher risk of severe pain (P < 0.035) and a 4–8 per cent higher risk of impaired QoL. CONCLUSION: T2D at time of surgery was associated with a higher risk of long-term bowel dysfunction after rectal resection, but not after colon resection excluding a higher risk of constipation. T2D was associated with a slightly higher frequency of severe pain and inferior QoL after both rectal and colonic cancer resection

The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo.

UNLABELLED: Pharmacologically-induced activation of replication competent proviruses from latency in the presence of antiretroviral treatment (ART) has been proposed as a step towards curing HIV-1 infection. However, until now, approaches to reverse HIV-1 latency in humans have yielded mixed results. Here, we report a proof-of-concept phase Ib/IIa trial where 6 aviremic HIV-1 infected adults received intravenous 5 mg/m2 romidepsin (Celgene) once weekly for 3 weeks while maintaining ART. Lymphocyte histone H3 acetylation, a cellular measure of the pharmacodynamic response to romidepsin, increased rapidly (maximum fold range: 3.7-7.7 relative to baseline) within the first hours following each romidepsin administration. Concurrently, HIV-1 transcription quantified as copies of cell-associated un-spliced HIV-1 RNA increased significantly from baseline during treatment (range of fold-increase: 2.4-5.0; p = 0.03). Plasma HIV-1 RNA increased from &lt;20 copies/mL at baseline to readily quantifiable levels at multiple post-infusion time-points in 5 of 6 patients (range 46-103 copies/mL following the second infusion, p = 0.04). Importantly, romidepsin did not decrease the number of HIV-specific T cells or inhibit T cell cytokine production. Adverse events (all grade 1-2) were consistent with the known side effects of romidepsin. In conclusion, romidepsin safely induced HIV-1 transcription resulting in plasma HIV-1 RNA that was readily detected with standard commercial assays demonstrating that significant reversal of HIV-1 latency in vivo is possible without blunting T cell-mediated immune responses. These finding have major implications for future trials aiming to eradicate the HIV-1 reservoir. TRIAL REGISTRATION: clinicaltrials.gov NTC02092116

Intraperitoneal aerosolization of albumin-stabilized paclitaxel nanoparticles (Abraxane™) for peritoneal carcinomatosis - a phase I first-in-human study.

Nanoparticles hold considerable promise for aerosol-based intraperitoneal delivery in patients with carcinomatosis. Recently, results from preclinical and early clinical trials suggested that albumin-bound paclitaxel (ABP, Abraxane™) may result in superior efficacy in the treatment of peritoneal metastases (PM) compared to the standard solvent-based paclitaxel formulation (Taxol™). Here, we propose a phase I study of pressurized intraperitoneal aerosol chemotherapy (PIPAC) using ABP in patients with upper Gastrointestinal, breast, or ovarian cancer. Eligible patients with advanced, biopsy-proven PM from ovarian, breast, gastric, hepatobiliary, or pancreatic origin will undergo three PIPAC treatments using ABP with a 4-week interval. The dose of ABP will be escalated from 35 to 140 mg/m² using a Bayesian approach until the maximally tolerated dose is determined. The primary end point is dose-limiting toxicity. Secondary analyses include surgical morbidity, non-access rate, pharmacokinetic and pharmacodynamic analyses, quality of life, and exploratory circulating biomarker analyses. ABP holds considerable promise for intraperitoneal aerosol delivery. The aim of this study is to determine the dose level for future randomized phase II trials using ABP in PIPAC therapy. This trial is registered as EudraCT: 2017-001688-20 and Clinicaltrials.gov: NCT03304210

Surgical treatment of patients with infective endocarditis:changes in temporal use, patient characteristics, and mortality—a nationwide study

BACKGROUND: Valve surgery guidelines for infective endocarditis (IE) are unchanged over decades and nationwide data about the use of valve surgery do not exist. METHODS: We included patients with first-time IE (1999–2018) using Danish nationwide registries. Proportions of valve surgery were reported for calendar periods (1999–2003, 2004–2008, 2009–2013, 2014–2018). Comparing calendar periods in multivariable analyses, we computed likelihoods of valve surgery with logistic regression and rates of 30 day postoperative mortality with Cox regression. RESULTS: We included 8804 patients with first-time IE; 1981 (22.5%) underwent surgery during admission, decreasing by calendar periods (N = 360 [24.4%], N = 483 [24.0%], N = 553 [23.5%], N = 585 [19.7%], P = < 0.001 for trend). For patients undergoing valve surgery, median age increased from 59.7 to 66.9 years (P ≤ 0.001) and the proportion of males increased from 67.8% to 72.6% (P = 0.008) from 1999–2003 to 2014–2018. Compared with 1999–2003, associated likelihoods of valve surgery were: Odds ratio (OR) = 1.14 (95% CI: 0.96–1.35), OR = 1.20 (95% CI: 1.02–1.42), and OR = 1.10 (95% CI: 0.93–1.29) in 2004–2008, 2009–2013, and 2014–2018, respectively. 30 day postoperative mortalities were: 12.7%, 12.8%, 6.9%, and 9.7% by calendar periods. Compared with 1999–2003, associated mortality rates were: Hazard ratio (HR) = 0.96 (95% CI: 0.65–1.41), HR = 0.43 (95% CI: 0.28–0.67), and HR = 0.55 (95% CI 0.37–0.83) in 2004–2008, 2009–2013, and 2014–2018, respectively. CONCLUSIONS: On a nationwide scale, 22.5% of patients with IE underwent valve surgery. Patient characteristics changed considerably and use of valve surgery decreased over time. The adjusted likelihood of valve surgery was similar between calendar periods with a trend towards an increase while rates of 30 day postoperative mortality decreased. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12872-022-02761-z