Modelling dependencies in genetic-marker data and its application to haplotype analysis

The objective of this thesis is to develop new methods to reconstruct haplotypes from phaseunknown genotypes. The need for new methodologies is motivated by the increasing avail¬ ability of high-resolution marker data for many species. Such markers typically exhibit correlations, a phenomenon known as Linkage Disequilibrium (LD). It is believed that re¬ constructed haplotypes for markers in high LD can be valuable for a variety of application areas in population genetics, including reconstructing population history and identifying genetic disease variantsTraditionally, haplotype reconstruction methods can be categorized according to whether they operate on a single pedigree or a collection of unrelated individuals. The thesis begins with a critical assessment of the limitations of existing methods, and then presents a uni¬ fied statistical framework that can accommodate pedigree data, unrelated individuals and tightly linked markers. The framework makes use of graphical models, where inference entails representing the relevant joint probability distribution as a graph and then using associated algorithms to facilitate computation. The graphical model formalism provides invaluable tools to facilitate model specification, visualization, and inference.Once the unified framework is developed, a broad range of simulation studies are conducted using previously published haplotype data. Important contributions include demonstrating the different ways in which the haplotype frequency distribution can impact the accuracy of both the phase assignments and haplotype frequency estimates; evaluating the effectiveness of using family data to improve accuracy for different frequency profiles; and, assessing the dangers of treating related individuals as unrelated in an association study

Numerical simulations with a first order BSSN formulation of Einstein's field equations

We present a new fully first order strongly hyperbolic representation of the BSSN formulation of Einstein's equations with optional constraint damping terms. We describe the characteristic fields of the system, discuss its hyperbolicity properties, and present two numerical implementations and simulations: one using finite differences, adaptive mesh refinement and in particular binary black holes, and another one using the discontinuous Galerkin method in spherical symmetry. The results of this paper constitute a first step in an effort to combine the robustness of BSSN evolutions with very high accuracy numerical techniques, such as spectral collocation multi-domain or discontinuous Galerkin methods.Comment: To appear in Physical Review

Human-induced fire regime shifts during 19th century industrialization: A robust fire regime reconstruction using northern Polish lake sediments

Fire regime shifts are driven by climate and natural vegetation changes, but can be strongly affected by human land management. Yet, it is poorly known how humans have influenced fire regimes prior to active wildfire suppression. Among the last 250 years, the human contribution to the global increase in fire occurrence during the mid-19th century is especially unclear, as data sources are limited. Here, we test the extent to which forest management has driven fire regime shifts in a temperate forest landscape. We combine multiple fire proxies (macroscopic charcoal and fire-related biomarkers) derived from highly resolved lake sediments (i.e., 3–5 years per sample), and apply a new statistical approach to classify source area- and temperature-specific fire regimes (biomass burnt, fire episodes). We compare these records with independent climate and vegetation reconstructions. We find two prominent fire regime shifts during the 19th and 20th centuries, driven by an adaptive socio-ecological cycle in human forest management. Although individual fire episodes were triggered mainly by arson (as described in historical documents) during dry summers, the biomass burnt increased unintentionally during the mid-19th century due to the plantation of flammable, fast-growing pine tree monocultures needed for industrialization. State forest management reacted with active fire management and suppression during the 20th century. However, pine cover has been increasing since the 1990s and climate projections predict increasingly dry conditions, suggesting a renewed need for adaptations to reduce the increasing fire risk. © 2019 Dietze et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Event-related alpha suppression in response to facial motion

This article has been made available through the Brunel Open Access Publishing Fund.While biological motion refers to both face and body movements, little is known about the visual perception of facial motion. We therefore examined alpha wave suppression as a reduction in power is thought to reflect visual activity, in addition to attentional reorienting and memory processes. Nineteen neurologically healthy adults were tested on their ability to discriminate between successive facial motion captures. These animations exhibited both rigid and non-rigid facial motion, as well as speech expressions. The structural and surface appearance of these facial animations did not differ, thus participants decisions were based solely on differences in facial movements. Upright, orientation-inverted and luminance-inverted facial stimuli were compared. At occipital and parieto-occipital regions, upright facial motion evoked a transient increase in alpha which was then followed by a significant reduction. This finding is discussed in terms of neural efficiency, gating mechanisms and neural synchronization. Moreover, there was no difference in the amount of alpha suppression evoked by each facial stimulus at occipital regions, suggesting early visual processing remains unaffected by manipulation paradigms. However, upright facial motion evoked greater suppression at parieto-occipital sites, and did so in the shortest latency. Increased activity within this region may reflect higher attentional reorienting to natural facial motion but also involvement of areas associated with the visual control of body effectors. © 2014 Girges et al

Outcomes Associated With Intracranial Aneurysm Treatments Reported as Safe, Effective, or Durable:A Systematic Review and Meta-Analysis

Importance: Testing new medical devices or procedures in terms of safety, effectiveness, and durability should follow the strictest methodological rigor before implementation. Objectives: To review and analyze studies investigating devices and procedures used in intracranial aneurysm (IA) treatment for methods and completeness of reporting and to compare the results of studies with positive, uncertain, and negative conclusions. Data Sources: Embase, MEDLINE, Web of Science, and The Cochrane Central Register of Clinical Trials were searched for studies on IA treatment published between January 1, 1995, and the October 1, 2022. Grey literature was retrieved from Google Scholar. Study Selection: All studies making any kind of claims of safety, effectiveness, or durability in the field of IA treatment were included. Data Extraction and Synthesis: Using a predefined data dictionary and analysis plan, variables ranging from patient and aneurysm characteristics to the results of treatment were extracted, as were details pertaining to study methods and completeness of reporting. Extraction was performed by 10 independent reviewers. A blinded academic neuro-linguist without involvement in IA research evaluated the conclusion of each study as either positive, uncertain, or negative. The study followed Preferring Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Main Outcomes and Measures: The incidence of domain-specific outcomes between studies with positive, uncertain, or negative conclusions regarding safety, effectiveness, or durability were compared. The number of studies that provided a definition of safety, effectiveness, or durability and the incidence of incomplete reporting of domain-specific outcomes were evaluated.Results: Overall, 12 954 studies were screened, and 1356 studies were included, comprising a total of 410 993 treated patients. There was no difference in the proportion of patients with poor outcome or in-hospital mortality between studies claiming a technique was safe, uncertain, or not safe. Similarly, there was no difference in the proportion of IAs completely occluded at last follow-up between studies claiming a technique was effective, uncertain, or noneffective. Less than 2% of studies provided any definition of safety, effectiveness, or durability, and only 1 of the 1356 studies provided a threshold under which the technique would be considered unsafe. Incomplete reporting was found in 546 reports (40%).Conclusions and Relevance: In this systematic review and meta-analysis of IA treatment literature, studies claiming safety, effectiveness, or durability of IA treatment had methodological flaws and incomplete reporting of relevant outcomes supporting these claims.</p

Graft-versus-host disease in recipients of male unrelated donor compared with parous female sibling donor transplants

Optimal donor selection is critical for successful allogeneic hematopoietic cell transplantation (HCT). Donor sex and parity are well-established risk factors for graft-versus-host disease (GVHD), with male donors typically associated with lower rates of GVHD. Well-matched unrelated donors (URDs) have also been associated with increased risks of GVHD as compared with matched sibling donors. These observations raise the question of whether male URDs would lead to more (or less) favorable transplant outcomes as compared with parous female sibling donors. We used the Center for International Blood and Marrow Transplant Research registry to complete a retrospective cohort study in adults with acute myeloid leukemia, acute lymphoblastic leukemia, or myelodysplastic syndrome, who underwent T-cell replete HCT from these 2 donor types (parous female sibling or male URD) between 2000 and 2012. Primary outcomes included grade 2 to 4 acute GVHD (aGVHD), chronic GVHD (cGVHD), and overall survival. Secondary outcomes included disease-free survival, transplant-related mortality, and relapse. In 2813 recipients, patients receiving male URD transplants (n = 1921) had 1.6 times higher risk of grade 2 to 4 aGVHD (P \u3c .0001). For cGVHD, recipient sex was a significant factor, so donor/recipient pairs were evaluated. Female recipients of male URD grafts had a higher risk of cGVHD than those receiving parous female sibling grafts (relative risk [RR] = 1.43, P \u3c .0001), whereas male recipients had similar rates of cGVHD regardless of donor type (RR = 1.09, P = .23). Donor type did not significantly affect any other end point. We conclude that when available, parous female siblings are preferred over male URDs

Using Touchscreen Electronic Medical Record Systems to Support and Monitor National Scale-Up of Antiretroviral Therapy in Malawi

Gerry Douglas and colleagues describe the rationale and their experience with scaling up electronic health records in six antiretroviral treatment sites in Malawi

Improved survival after acute graft-

A cute graft- versus -host disease remains a major threat to a successful outcome after allogeneic hematopoietic cell transplantation. While improvements in treatment and supportive care have occurred, it is unknown whether these advances have resulted in improved outcome specifically among those diagnosed with acute graft- versus -host disease. We examined outcome following diagnosis of grade II-IV acute graft- versus -host disease according to time period, and explored effects according to original graft- versus -host disease prophylaxis regimen and maximum overall grade of acute graft- versus -host disease. Between 1999 and 2012, 2,905 patients with acute myeloid leukemia (56%), acute lymphoblastic leukemia (30%) or myelodysplastic syndromes (14%) received a sibling (24%) or unrelated donor (76%) blood (66%) or marrow (34%) transplant and developed grade II-IV acute graft- versus -host disease (n=497 for 1999-2001, n=962 for 2002-2005, n=1,446 for 2006-2010). The median (range) follow-up was 144 (4-174), 97 (4-147) and 60 (8-99) months for 1999-2001, 2002-2005, and 2006-2010, respectively. Among the cohort with grade II-IV acute graft- versus -host disease, there was a decrease in the proportion of grade III-IV disease over time with 56%, 47%, and 37% for 1999-2001, 2002-2005, and 2006-2012, respectively ( P <0.001). Considering the total study population, univariate analysis demonstrated significant improvements in overall survival and treatment-related mortality over time, and deaths from organ failure and infection declined. On multivariate analysis, significant improvements in overall survival ( P =0.003) and treatment-related mortality ( P =0.008) were only noted among those originally treated with tacrolimus-based graft- versus -host disease prophylaxis, and these effects were most apparent among those with overall grade II acute graft- versus -host disease. In conclusion, survival has improved over time for tacrolimus-treated transplant recipients with acute graft- versus -host disease