Aortic pulse wave velocity measurement via heart sounds and impedance plethysmography

Full abstract in the manuscript

High-quality, high-throughput measurement of protein-DNA binding using HiTS-FLIP

In order to understand in more depth and on a genome wide scale the behavior of transcription factors (TFs), novel quantitative experiments with high-throughput are needed. Recently, HiTS-FLIP (High-Throughput Sequencing-Fluorescent Ligand Interaction Profiling) was invented by the Burge lab at the MIT (Nutiu et al. (2011)). Based on an Illumina GA-IIx machine for next-generation sequencing, HiTS-FLIP allows to measure the affinity of fluorescent labeled proteins to millions of DNA clusters at equilibrium in an unbiased and untargeted way examining the entire sequence space by Determination of dissociation constants (Kds) for all 12-mer DNA motifs. During my PhD I helped to improve the experimental design of this method to allow measuring the protein-DNA binding events at equilibrium omitting any washing step by utilizing the TIRF (Total Internal Reflection Fluorescence) based optics of the GA-IIx. In addition, I developed the first versions of XML based controlling software that automates the measurement procedure. Meeting the needs for processing the vast amount of data produced by each run, I developed a sophisticated, high performance software pipeline that locates DNA clusters, normalizes and extracts the fluorescent signals. Moreover, cluster contained k-mer motifs are ranked and their DNA binding affinities are quantified with high accuracy. My approach of applying phase-correlation to estimate the relative translative Offset between the observed tile images and the template images omits resequencing and thus allows to reuse the flow cell for several HiTS-FLIP experiments, which greatly reduces cost and time. Instead of using information from the sequencing images like Nutiu et al. (2011) for normalizing the cluster intensities which introduces a nucleotide specific bias, I estimate the cluster related normalization factors directly from the protein Images which captures the non-even illumination bias more accurately and leads to an improved correction for each tile image. My analysis of the ranking algorithm by Nutiu et al. (2011) has revealed that it is unable to rank all measured k-mers. Discarding all the clusters related to previously ranked k-mers has the side effect of eliminating any clusters on which k-mers could be ranked that share submotifs with previously ranked k-mers. This shortcoming affects even strong binding k-mers with only one mutation away from the top ranked k-mer. My findings show that omitting the cluster deletion step in the ranking process overcomes this limitation and allows to rank the full spectrum of all possible k-mers. In addition, the performance of the ranking algorithm is drastically reduced by my insight from a quadratic to a linear run time. The experimental improvements combined with the sophisticated processing of the data has led to a very high accuracy of the HiTS-FLIP dissociation constants (Kds) comparable to the Kds measured by the very sensitive HiP-FA assay (Jung et al. (2015)). However, experimentally HiTS-FLIP is a very challenging assay. In total, eight HiTS-FLIP experiments were performed but only one showed saturation, the others exhibited Protein aggregation occurring at the amplified DNA clusters. This biochemical issue could not be remedied. As example TF for studying the details of HiTS-FLIP, GCN4 was chosen which is a dimeric, basic leucine zipper TF and which acts as the master regulator of the amino acid starvation Response in Saccharomyces cerevisiae (Natarajan et al. (2001)). The fluorescent dye was mOrange. The HiTS-FLIP Kds for the TF GCN4 were validated by the HiP-FA assay and a Pearson correlation coefficient of R=0.99 and a relative error of delta=30.91% was achieved. Thus, a unique and comprehensive data set of utmost quantitative precision was obtained that allowed to study the complex binding behavior of GCN4 in a new way. My Downstream analyses reveal that the known 7-mer consensus motif of GCN4, which is TGACTCA, is modulated by its 2-mer neighboring flanking regions spanning an affinity range over two orders of magnitude from a Kd=1.56 nM to Kd=552.51 nM. These results suggest that the common 9-mer PWM (Position Weight Matrix) for GCN4 is insufficient to describe the binding behavior of GCN4. Rather, an additional left and right flanking nucleotide is required to extend the 9-mer to an 11-mer. My analyses regarding mutations and related delta delta G values suggest long-range interdependencies between nucleotides of the two dimeric half-sites of GCN4. Consequently, models assuming positional independence, such as a PWM, are insufficient to explain these interdependencies. Instead, the full spectrum of affinity values for all k-mers of appropriate size should be measured and applied in further analyses as proposed by Nutiu et al. (2011). Another discovery were new binding motifs of GCN4, which can only be detected with a method like HiTS-FLIP that examines the entire sequence space and allows for unbiased, de-novo motif discovery. All These new motifs contain GTGT as a submotif and the data collected suggests that GCN4 binds as monomer to these new motifs. Therefore, it might be even possible to detect different binding modes with HiTS-FLIP. My results emphasize the binding complexity of GCN4 and demonstrate the advantage of HiTS-FLIP for investigating the complexity of regulative processes

On the Cusp: A School District and Two Communities Respond to an Oil Pre-Boom

This case study is an investigation of the attitudes, perceptions, and reactions of school staff and community members in a rural pre-boom school district. In the early stage of an oil boom, real and perceived disruptions commonly occur in the schools and communities that are affected. The preparations and responses that residents make to the changes may determine the community’s future success, so understanding the impacts in the initial pre-boom growth stage is vital. Using qualitative methods of interviews, participant observations, and document analyses, this study researched 41 participants in a rural school district and two communities. The literature review and data investigation were framed partly around the Social Disruption Hypothesis, and the analysis suggests that the oil pre-boom stage impacts space, teaching and learning, and causes social disruptions. These three affected areas contribute to and are influenced by the uncertain future that accompanies boom cycles. Individual variables seem to determine community member responses to a boom, and these participants responded to change by supporting, resisting, or deserting their communities. The school district was challenged with transient students, changes to funding, teacher workload, and teacher paradigm shifts in the way they viewed their future instruction. Community support for the schools, as well as peer acceptance of new students, remained strong. Community contexts, including history, physical location, and types of growth, may partially explain differences in residents’ preparations and reactions. Recommendations for community planning, school teaching and administration, and university preparation of pre-service teachers are provided. Key Words: oil boom, pre-boom, boomtown, Social Disruption Hypothesis, community identity, community attachment, acceptance, student transience, community contex

Workstation Ergonomics Improves Posture and Reduces Musculoskeletal Pain in Video Interpreters

Abstract Sign language interpreting is commonly associated with musculoskeletal injuries secondary to repetitive strain. This mixed methods study sought to identify the musculoskeletal symptoms experienced specifically by video interpreters (VIs), to demonstrate that VIs gain ergonomic knowledge after participation in a 6-hour workshop, and to determine whether or not participation in the workshop is associated with improved posture and lessened complaints of musculoskeletal pain. One hundred and one video interpreters across the United States and Canada participated: 78 intervention participants who attended the workshop and 23 control participants who did not attend. Ergonomic knowledge was measured using a pre and post workshop quiz. Dynamic pre and post-workshop photos of participants’ posture were scored with a modified REEDCO Posture Score Sheet. Musculoskeletal symptoms at baseline and pre-workshop pain ratings using the Numeric Pain Rating Scale (NPRS) were collected via a survey. A four-week post-workshop NPRS of the identified body region was elicited via email. Results showed that participants identified the neck as the body region with the highest incidence of pain. Examination of subgroups within the sample revealed there was no correlation between baseline musculoskeletal pain levels and years of VRS employment. Those who self-reported a pre-existing condition had no decrease in musculoskeletal pain, whereas participants without pre-existing conditions demonstrated significant decrease. Participants who attended the workshop improved their ergonomic knowledge compared with controls, with the greatest workshop-related gains made by participants with the least initial level of knowledge. Furthermore, attendance at the workshop was associated with improved posture and decreased pain regardless of initial knowledge. These data suggest that attendance at the ergonomic workshop is effective in improving posture and pain management for VIs across a broad range of pre-workshop ergonomic knowledge

A frequent variant in the human bile salt export pump gene ABCB11 is associated with hepatitis C virus infection, but not liver stiffness in a German population

Background: The human ATP-binding cassette, subfamily B, member 11 (ABCB11) gene encodes the bile salt export pump, which is exclusively expressed at the canalicular membrane of hepatocytes. A frequent variant in the coding region, c.1331 T > C, leading to the amino acid exchange p.V444A, has been associated with altered serum bile salt levels in healthy individuals and predisposes homozygous carriers of the [C] allele for obstetric cholestasis. Recently, elevated bile salt levels were shown to be significantly associated with rates and risk of cirrhosis in patients with chronic hepatitis C virus (HCV) infection treated with pegylated interferon-alpha2 and ribavirin, suggesting a potential role for bile salt levels in HCV treatment outcomes and in the fibrogenic evolution of HCV-related liver disease. The aim of this study was to investigate a possible association of ABCB11 c.1331 T > C with hepatitis C virus (HCV) infection and fibrosis stages as assessed by non-invasive transient elastography in a German cohort of patients. Methods: ABCB11 c.1331 T > C genotype was determined by allelic discrimination assay in 649 HCV infected cases and 413 controls. Overall, 444 cases were staged for fibrotic progression by measurement of liver stiffness. Results: Homo- or heterozygous presence of the frequent [C] allele was associated with HCV positivity (OR = 1.41, CI = 1.02 - 1.95, p = 0.037). No association was detectable between the ABCB11 c.1331 T > C genotype and increased liver stiffness. Conclusions: Our data confirm that homozygous presence of the major [C] allele of ABCB11 c.1331 T > C is a genetic susceptibility factor for HCV infection, but not for liver fibrosis

Robust ordinal regression for value functions handling interacting criteria

International audienceWe present a new method called UTAGMS–INT for ranking a finite set of alternatives evaluated on multiple criteria. It belongs to the family of Robust Ordinal Regression (ROR) methods which build a set of preference models compatible with preference information elicited by the Decision Maker (DM). The preference model used by UTAGMS–INT is a general additive value function augmented by two types of components corresponding to ‘‘bonus’’ or ‘‘penalty’’ values for positively or negatively interacting pairs of criteria, respectively. When calculating value of a particular alternative, a bonus is added to the additive component of the value function if a given pair of criteria is in a positive synergy for performances of this alternative on the two criteria. Similarly, a penalty is subtracted from the additive component of the value function if a given pair of criteria is in a negative synergy for performances of the considered alternative on the two criteria. The preference information elicited by the DM is composed of pairwise comparisons of some reference alternatives, as well as of comparisons of some pairs of reference alternatives with respect to intensity of preference, either comprehensively or on a particular criterion. In UTAGMS–INT, ROR starts with identification of pairs of interacting criteria for given preference information by solving a mixed-integer linear program. Once the interacting pairs are validated by the DM, ROR continues calculations with the whole set of compatible value functions handling the interacting criteria, to get necessary and possible preference relations in the considered set of alternatives. A single representative value function can be calculated to attribute specific scores to alternatives. It also gives values to bonuses and penalties. UTAGMS–INT handles quite general interactions among criteria and provides an interesting alternative to the Choquet integral

Writing Disability in ADHD Children

The psychological examination aims at objectifying the key symptoms of hyperactivity, i.e. attention and executive function disorders (in short, activation-inhibition control). The files of 237 patients from our consultations, aged between 5 and 17 years old and examined between 2004 and 2016, are analyzed retrospectively. Of whom 40 cases show the typical ADHD syndrome, mixed presentation, according to DSM-5 criteria. These ADHD children and adolescents show not only a characteristic impulsivity on computerized attention tests, but also a deficit in the acquisition of writing, an early manifestation of their neurodevelopmental disorders. This association correctly classifies 82.4% of hyperactives and controls, a strong effect given the difficult diagnosis of ADHD syndrome