Using Prior Information from the Medical Literature in GWAS of Oral Cancer Identifies Novel Susceptibility Variant on Chromosome 4-the AdAPT Method

Background: Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS. Methods: We developed a method that searches through PubMed abstracts for pre-assigned keywords and key concepts, and uses this information to assign prior probabilities of association for each single nucleotide polymorphism (SNP) with the phenotype of interest - the Adjusting Association Priors with Text (AdAPT) method. Association results from a GWAS can subsequently be ranked in the context of these priors using the Bayes False Discovery Probability (BFDP) framework. We initially tested AdAPT by comparing rankings of known susceptibility alleles in a previous lung cancer GWAS, and subsequently applied it in a two-phase GWAS of oral cancer. Results: Known lung cancer susceptibility SNPs were consistently ranked higher by AdAPT BFDPs than by p-values. In the oral cancer GWAS, we sought to replicate the top five SNPs as ranked by AdAPT BFDPs, of which rs991316, located in the ADH gene region of 4q23, displayed a statistically significant association with oral cancer risk in the replication phase (per-rare-allele log additive p-value [p(trend)] = 2.5 x 10(-3)). The combined OR for having one additional rare allele was 0.83 (95% CI: 0.76-0.90), and this association was independent of previously identified susceptibility SNPs that are associated with overall UADT cancer in this gene region. We also investigated if rs991316 was associated with other cancers of the upper aerodigestive tract (UADT), but no additional association signal was found. Conclusion: This study highlights the potential utility of systematically incorporating prior knowledge from the medical literature in genome-wide analyses using the AdAPT methodology. AdAPT is available online (url: http://services.gate.ac.uk/lld/gwas/service/config).

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

A Unitary Approach to Information and Estimation Theory in Digital Communication Systems

This thesis presents the outcomes of a Ph.D. course in telecommunications engineering. It is focused on the optimization of the physical layer of digital communication systems and it provides innovations for both multi- and single-carrier systems. For the former type we have first addressed the problem of the capacity in presence of several nuisances. Moreover, we have extended the concept of Single Frequency Network to the satellite scenario, and then we have introduced a novel concept in subcarrier data mapping, resulting in a very low PAPR of the OFDM signal. For single carrier systems we have proposed a method to optimize constellation design in presence of a strong distortion, such as the non linear distortion provided by satellites' on board high power amplifier, then we developed a method to calculate the bit/symbol error rate related to a given constellation, achieving an improved accuracy with respect to the traditional Union Bound with no additional complexity. Finally we have designed a low complexity SNR estimator, which saves one-half of multiplication with respect to the ML estimator, and it has similar estimation accuracy.

Social learning and action understanding in human observers: contributions of sensori-motor constraints and prior information

The aim of this thesis was to investigate the respective contribution of prior information and sensorimotor constraints to action understanding, and to estimate their consequences on the evolution of human social learning. Even though a huge amount of literature is dedicated to the study of action understanding and its role in social learning, these issues are still largely debated. Here, I critically describe two main perspectives. The first perspective interprets faithful social learning as an outcome of a fine-grained representation of others’ actions and intentions that requires sophisticated socio-cognitive skills. In contrast, the second perspective highlights the role of simpler decision heuristics, the recruitment of which is determined by individual and ecological constraints. The present thesis aims to show, through four experimental works, that these two contributions are not mutually exclusive. A first study investigates the role of the inferior frontal cortex (IFC), the anterior intraparietal area (AIP) and the primary somatosensory cortex (S1) in the recognition of other people’s actions, using a transcranial magnetic stimulation adaptation paradigm (TMSA). The second work studies whether, and how, higher-order and lower-order prior information (acquired from the probabilistic sampling of past events vs. derived from an estimation of biomechanical constraints of observed actions) interacts during the prediction of other people’s intentions. Using a single-pulse TMS procedure, the third study investigates whether the interaction between these two classes of priors modulates the motor system activity. The fourth study tests the extent to which behavioral and ecological constraints influence the emergence of faithful social learning strategies at a population level. The collected data contribute to elucidate how higher-order and lower-order prior expectations interact during action prediction, and clarify the neural mechanisms underlying such interaction. Finally, these works provide/open promising perspectives for a better understanding of social learning, with possible extensions to animal models.

Visual-somatosensory interactions in mental representations of the body and the face

The body is represented in the brain at levels that incorporate multisensory information. This thesis focused on interactions between vision and cutaneous sensations (i.e., touch and pain). Experiment 1 revealed that there are partially dissociable pathways for visual enhancement of touch (VET) depending upon whether one sees one’s own body or the body of another person. This indicates that VET, a seeming low-level effect on spatial tactile acuity, is actually sensitive to body identity. Experiments 2-4 explored the effect of viewing one’s own body on pain perception. They demonstrated that viewing the body biases pain intensity judgments irrespective of actual stimulus intensity, and, more importantly, reduces the discriminative capacities of the nociceptive pathway encoding noxious stimulus intensity. The latter effect only occurs if the pain-inducing event itself is not visible, suggesting that viewing the body alone and viewing a stimulus event on the body have distinct effects on cutaneous sensations. Experiment 5 replicated an enhancement of visual remapping of touch (VRT) when viewing fearful human faces being touched, and further demonstrated that VRT does not occur for observed touch on non-human faces, even fearful ones. This suggests that the facial expressions of non-human animals may not be simulated within the somatosensory system of the human observer in the same way that the facial expressions of other humans are. Finally, Experiment 6 examined the enfacement illusion, in which synchronous visuo-tactile inputs cause another’s face to be assimilated into the mental self-face representation. The strength of enfacement was not affected by the other’s facial expression, supporting an asymmetric relationship between processing of facial identity and facial expressions. Together, these studies indicate that multisensory representations of the body in the brain link low-level perceptual processes with the perception of emotional cues and body/face identity, and interact in complex ways depending upon contextual factors.

Alternate or additional findings to stone disease on unenhanced computerized tomography for acute flank pain can impact management

PURPOSE: We evaluated the incidence and clinical relevance of alternate or additional findings on unenhanced CT in patients with acute flank pain and suspected urinary calculi. MATERIALS AND METHODS: A consecutive series of 1,500 patients underwent unenhanced CT due to acute flank pain. The absence or presence of urinary tract calculi and their localization were recorded. Alternate or additional CT findings were classified according to whether they required immediate or deferred treatment, or were of little or no clinical importance. RESULTS: Of the 1,500 patients 1,035 (69%) had urinary tract calculi, including 309 (30%) with nephrolithiasis, 377 (36%) with ureterolithiasis and 349 (34%) with the 2 conditions. Urolithiasis alone was found in 331 of these patients (32%) and additional pathological conditions were noted in 704 (68%). Of all patients 1,064 (71%) had other or additional CT findings. Of all patients 207 (14%) had nonstone related CT findings requiring immediate or deferred treatment, 464 (31%) had pathological conditions of little clinical importance and 393 (26%) had pathological conditions of no clinical relevance. CT was normal in 105 of all patients (7%). CONCLUSIONS: Unenhanced CT in patients with acute flank pain allows the accurate diagnosis of urinary stone disease and it can also provide further important information leading to emergency or deferred treatment in a substantial number of patients.

A Fully Bayesian Approach for Combining Multilevel Failure Information in Fault Tree Quantification and Corresponding Optimal Resource Allocation

This paper presents a fully Bayesian approach that simultaneously combines basic event and statistically independent higher event-level failure data in fault tree quantification. Such higher-level data could correspond to train, sub-system or system failure events. The full Bayesian approach also allows the highest-level data that are usually available for existing facilities to be automatically propagated to lower levels. A simple example illustrates the proposed approach. The optimal allocation of resources for collecting additional data from a choice of different level events is also presented. The optimization is achieved using a genetic algorithm.

An interfering Go/No-go task does not affect accuracy in a Concealed Information Test

Following the idea that response inhibition processes play a central role in concealing information, the present study investigated the influence of a Go/No-go task as an interfering mental activity, performed parallel to the Concealed Information Test (CIT), on the detectability of concealed information. 40 undergraduate students participated in a mock-crime experiment and simultaneously performed a CIT and a Go/No-go task. Electrodermal activity (EDA), respiration line length (RLL), heart rate (HR) and finger pulse waveform length (FPWL) were registered. Reaction times were recorded as behavioral measures in the Go/No-go task as well as in the CIT. As a within-subject control condition, the CIT was also applied without an additional task. The parallel task did not influence the mean differences of the physiological measures of the mock-crime-related probe and the irrelevant items. This finding might possibly be due to the fact that the applied parallel task induced a tonic rather than a phasic mental activity, which did not influence differential responding to CIT items. No physiological evidence for an interaction between the parallel task and sub-processes of deception (e.g. inhibition) was found. Subjects' performance in the Go/No-go parallel task did not contribute to the detection of concealed information. Generalizability needs further investigations of different variations of the parallel task.

[Role of coronary artery bypass grafting in the treatment of coronary artery disease - a well-balanced information of the patients and objective decision making are welcome]

Most recently discussion about the optimal treatment for different subsets of patients suffering from coronary artery disease has re-emerged, mainly because of the uncertainty caused by doctors and patients regarding the phenomenon of unpredictable early and late stent thrombosis. Surgical revascularization using multiple arterial bypass grafts has repeatedly proven its superiority compared to percutaneous intervention techniques, especially in patients suffering from left main stem disease and coronary 3-vessels disease. Several prospective randomized multicenter studies comparing early and mid-term results following PCI and CABG have been really restrictive, with respect to patient enrollment, with less than 5% of all patients treated during the same time period been enrolled. Coronary artery bypass grafting allows the most complete revascularization in one session, because all target coronary vessels larger than 1 mm can be bypassed in their distal segments. Once the patient has been turn-off for surgery, surgeons have to consider the most complete arterial revascularization in order to decrease the long-term necessity for re-revascularization; for instance patency rate of the left internal thoracic artery grafted to the distal part left anterior descending artery may be as high as 90-95% after 10 to 15 years. Early mortality following isolated CABG operation has been as low as 0.6 to 1% in the most recent period (reports from the University Hospital Berne and the University Hospital of Zurich); beside these excellent results, the CABG option seems to be less expensive than PCI with time, since the necessity for additional PCI is rather high following initial PCI, and the price of stent devices is still very high, particularly in Switzerland. Patients, insurance and experts in health care should be better and more honestly informed concerning the risk and costs of PCI and CABG procedures as well as about the much higher rate of subsequent interventions following PCI. Team approach for all patients in whom both options could be offered seems mandatory to avoid unbalanced information of the patients. Looking at the recent developments in transcatheter valve treatments, the revival of cardiological-cardiosurgical conferences seems to a good option to optimize the cooperation between the two medical specialties: cardiology and cardiac surgery.

RFID Transponders : Link between information and material flows. How reliable are identification procedures?

Along with the growing complexity of logistic chains the demand for transparency of informations has increased. The use of intelligent RFID-Technology offers the possibility to optimize and control all capacities in use, since it enables the identification and tracking of goods alongside the entire supply chain. Every single product can be located at any given time and a multitude of current and historical data can be transferred. The interaction of the flow of material and the flow of information between the various process steps can be optimized by using RFID-Technology since it guarantees that all required data is available at the right time and at the right place. The local accessibility and convertibility of data allows a flexible, decentralised control of logistic systems. As additional advantages of RFID-Components can be considered that they are individually writable and that their identification can be achieved over considerable distances even if there is no intervisibility between tag and reader. The use of RFID-Transponder opens up new potentials regarding process security, reduction of logistic costs or availability of products. These advantages depend on reliability of the identification processes. The undisputed potentials that are made accessible by the use of RFID-Elements can only be beneficial when the informations that are decentralised and attached to goods and loading equipment can be reliably retrieved at the required points. The communication between tag and reader can be influenced by different materials such as metal, that can disturbed or complicate the radio contact. The communications reliability is subject of various tests and experiments that analyse the effects of different filling materials as well as different alignments of tags on the loading equipment.

Influence of Information and Instructions on Human Behavior in Tunnel Accidents: A Virtual Reality Study

Human behavior is a major factor modulating the consequences of road tunnel accidents. We investigated the effect of information and instruction on drivers' behavior as well as the usability of virtual environments to simulate such emergency situations. Tunnel safety knowledge of the general population was assessed using an online questionnaire, and tunnel safety behavior was investigated in a virtual reality experiment. Forty-four participants completed three drives through a virtual road tunnel and were confronted with a traffic jam, no event, and an accident blocking the road. Participants were randomly assigned to a control group (no intervention), an informed group who read a brochure containing safety information prior to the tunnel drives, or an informed and instructed group who read the same brochure and received additional instructions during the emergency situation. Informed participants showed better and quicker safety behavior than the control group. Self-reports of anxiety were assessed three times during each drive. Anxiety was elevated during and after the emergency situation. The findings demonstrate problematic safety behavior in the control group and that knowledge of safety information fosters adequate behavior in tunnel emergencies. Enhanced anxiety ratings during the emergency situation indicate external validity of the virtual environment.

Non-ignorable loss to follow-up: correcting mortality estimates based on additional outcome ascertainment

Loss to follow-up (LTFU) is a common problem in many epidemiological studies. In antiretroviral treatment (ART) programs for patients with human immunodeficiency virus (HIV), mortality estimates can be biased if the LTFU mechanism is non-ignorable, that is, mortality differs between lost and retained patients. In this setting, routine procedures for handling missing data may lead to biased estimates. To appropriately deal with non-ignorable LTFU, explicit modeling of the missing data mechanism is needed. This can be based on additional outcome ascertainment for a sample of patients LTFU, for example, through linkage to national registries or through survey-based methods. In this paper, we demonstrate how this additional information can be used to construct estimators based on inverse probability weights (IPW) or multiple imputation. We use simulations to contrast the performance of the proposed estimators with methods widely used in HIV cohort research for dealing with missing data. The practical implications of our approach are illustrated using South African ART data, which are partially linkable to South African national vital registration data. Our results demonstrate that while IPWs and proper imputation procedures can be easily constructed from additional outcome ascertainment to obtain valid overall estimates, neglecting non-ignorable LTFU can result in substantial bias. We believe the proposed estimators are readily applicable to a growing number of studies where LTFU is appreciable, but additional outcome data are available through linkage or surveys of patients LTFU. Copyright © 2013 John Wiley & Sons, Ltd.

The additional facet of immunoscore: immunoprofiling as a possible predictive tool for cancer treatment

Recent investigations of the tumor microenvironment have shown that many tumors are infiltrated by inflammatory and lymphocytic cells. Increasing evidence suggests that the number, type and location of these tumor-infiltrating lymphocytes in primary tumors has prognostic value, and this has led to the development of an 'immunoscore. As well as providing useful prognostic information, the immunoscore concept also has the potential to help predict response to treatment, thereby improving decision- making with regard to choice of therapy. This predictive aspect of the tumor microenvironment forms the basis for the concept of immunoprofiling, which can be described as 'using an individual's immune system signature (or profile) to predict that patient's response to therapy' The immunoprofile of an individual can be genetically determined or tumor-induced (and therefore dynamic). Ipilimumab is the first in a series of immunomodulating antibodies and has been shown to be associated with improved overall survival in patients with advanced melanoma. Other immunotherapies in development include anti-programmed death 1 protein (nivolumab), anti-PD-ligand 1, anti-CD137 (urelumab), and anti-OX40. Biomarkers that can be used as predictive factors for these treatments have not yet been clinically validated. However, there is already evidence that the tumor microenvironment can have a predictive role, with clinical activity of ipilimumab related to high baseline expression of the immune-related genes FoxP3 and indoleamine 2,3-dioxygenase and an increase in tumor-infiltrating lymphocytes. These biomarkers could represent the first potential proposal for an immunoprofiling panel in patients for whom anti-CTLA-4 therapy is being considered, although prospective data are required. In conclusion, the evaluation of systemic and local immunological biomarkers could offer useful prognostic information and facilitate clinical decision making. The challenge will be to identify the individual immunoprofile of each patient and the consequent choice of optimal therapy or combination of therapies to be used.

Repeatedly experiencing information overload in a product customization: a case of sequential overchoice

The present study demonstrates how consumers can suffer from sequential overchoice. Customizing a tailor-made suit from combined-attribute choices (e.g., deciding on color and fabric in combination) leads to less satisfaction and less additional consumption than customizing it from single-attribute choices (e.g., deciding on color, then on fabric). The effect is mediated by information overload and moderated by consideration set size.

Spatial cognition, body representation and affective processes: the role of vestibular information beyond ocular reflexes and control of posture

A growing number of studies in humans demonstrate the involvement of vestibular information in tasks that are seemingly remote from well-known functions such as space constancy or postural control. In this review article we point out three emerging streams of research highlighting the importance of vestibular input: (1) Spatial Cognition: Modulation of vestibular signals can induce specific changes in spatial cognitive tasks like mental imagery and the processing of numbers. This has been shown in studies manipulating body orientation (changing the input from the otoliths), body rotation (changing the input from the semicircular canals), in clinical findings with vestibular patients, and in studies carried out in microgravity. There is also an effect in the reverse direction; top-down processes can affect perception of vestibular stimuli. (2) Body Representation: Numerous studies demonstrate that vestibular stimulation changes the representation of body parts, and sensitivity to tactile input or pain. Thus, the vestibular system plays an integral role in multisensory coordination of body representation. (3) Affective Processes and Disorders: Studies in psychiatric patients and patients with a vestibular disorder report a high comorbidity of vestibular dysfunctions and psychiatric symptoms. Recent studies investigated the beneficial effect of vestibular stimulation on psychiatric disorders, and how vestibular input can change mood and affect. These three emerging streams of research in vestibular science are—at least in part—associated with different neuronal core mechanisms. Spatial transformations draw on parietal areas, body representation is associated with somatosensory areas, and affective processes involve insular and cingulate cortices, all of which receive vestibular input. Even though a wide range of different vestibular cortical projection areas has been ascertained, their functionality still is scarcely understood.