Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty

This study explores how researchers' analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers' expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each team's workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers' results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.

Formal Classification of Medical Concept Descriptions: Graph-Oriented Operators

A crucial component of a medical concept representation system is the classifier. It requires features that are not sufficiently supported by current logic based formalisms like description logics and conceptual graphs. Those features are, for instance, the representation of partitive and spatial relations and their impact on sUbsumption. This paper introduces graph oriented classification operators for a concept representation language with normal forms. Emphasis is on the separation of generic and partitive relations and on the mutual interdependence of sUbsumption and part-whole. For that purpose operators are given for formal subsumption, formal part-whole, subsumptive part-whole and part-sensitive subsumption. These operators are based on the formal structure of concept descriptions and on explicitly introduced generic and partitive relationships between their constituents.

Biomaterials in Orthopedic Surgery: Effects of a Nickel-Reduced Stainless Steel on in Vitro Proliferation and Activation of Human Osteoblasts

A new austenitic stainless steel compound, P558, has been widely recognized to have good mechanical properties, excellent potential for corrosion resistance and negligible nickel ion release, making it a promising substitute for more expensive metallic prostheses with limited machinable features. The effect of P558 was studied in vitro and human osteoblast- like cells (MG63) were cultured directly on P558, Ti6Al4V alloy (Ti), and polystyrene (Control) for 72 hours. Osteoblast functions were evaluated by assaying cell proliferation and synthetic activity after 1.25(OH)2D3 stimulation. Results demonstrated that growth of MG63 on P558 was not negatively affected when compared to the Ti and Control groups and showed no alteration in the production of ALP, NO and PICP. Moreover, IL-6 was lower, whereas OC and TGFbeta1 were significantly higher. SEM images revealed that cells proliferated and differentiated on P558 without any alteration in their morphology. The current findings have demonstrated that P558 promotes osteoblast proliferation, activation and differentiation without negative effects and, thus, its good biocompatibility when used for orthopedic application.

Investigation of the exclusive 3He(e,e' pn)1H reaction

Cross sections for the 3He(e,e' pn)1H reaction were measured for the first time at energy transfers of 220 and 270 MeV for several momentum transfers ranging from 300 to 450 MeV/c. Cross sections are presented as a function of the momentum of the recoil proton and the momentum transfer. Continuum Faddeev calculations using the Argonne V18 and Bonn-B nucleon-nucleon potentials overestimate the measured cross sections by a factor 5 at low recoil proton momentum with the discrepancy becoming smaller at higher recoil proton momentum.

A new protein-protein docking scoring function based on interface residue properties

MOTIVATION

Protein-protein complexes are known to play key roles in many cellular processes. However, they are often not accessible to experimental study because of their low stability and difficulty to produce the proteins and assemble them in native conformation. Thus, docking algorithms have been developed to provide an in silico approach of the problem. A protein-protein docking procedure traditionally consists of two successive tasks: a search algorithm generates a large number of candidate solutions, and then a scoring function is used to rank them.

RESULTS

To address the second step, we developed a scoring function based on a Voronoï tessellation of the protein three-dimensional structure. We showed that the Voronoï representation may be used to describe in a simplified but useful manner, the geometric and physico-chemical complementarities of two molecular surfaces. We measured a set of parameters on native protein-protein complexes and on decoys, and used them as attributes in several statistical learning procedures: a logistic function, Support Vector Machines (SVM), and a genetic algorithm. For the later, we used ROGER, a genetic algorithm designed to optimize the area under the receiver operating characteristics curve. To further test the scores derived with ROGER, we ranked models generated by two different docking algorithms on targets of a blind prediction experiment, improving in almost all cases the rank of native-like solutions.

AVAILABILITY

http://genomics.eu.org/spip/-Bioinformatics-tools-

Soft tissue response to a new austenitic stainless steel with a negligible nickel content

This study evaluates the soft tissue response to a new austenitic stainless steel with a low nickel content (P558) in comparison with a conventional stainless steel (SSt)and a titanium alloy (Ti6Al4V). Previous findings showed its in vitro biocompatibility by culturing P558 with healthy and osteoporotic osteoblasts and its in vivo effectiveness as bone implant material. Regarding its use as a material in osteosynthesis,P558 biocompatibility when implanted in soft tissues, as subcutis and muscle, was assessed. Disks and rods of these metals were implanted in rat subcutis and in rabbit muscle, respectively. Four and twelve weeks post surgery implants with surrounding tissue were retrieved for histologic and histomorphometric analysis: fibrous capsule thickness and new vessel formation were measured. Around all implanted materials, light microscopy highlighted a reactive and fibrous capsule formation coupled with ongoing neoangiogenesis both in rats and in rabbits. Histomorphometric measurements revealed a stronger inflammatory response,in terms of capsule thickness,surrounding SSt implants (9.8% Ni content) both in rat subcutis and in rabbit muscle independently of shape and site of implantation. A progressive decrease in capsule thickness around P558 (<0.02% Ni content) and Ti6Al4V, respectively, was seen. Regarding new vessel density, the data showed a different response dependent on the site of implantation. However,in the light of the previous and present studies, P558 is a good material, instead of titanium alloys, in orthopedic research.

A new austenitic stainless steel with negligible nickel content: an in vitro and in vivo comparative investigation

New nickel (Ni)-reduced stainless-steel metals have recently been developed to avoid sensitivity to Ni. In the present study, an austenitic Ni-reduced SSt named P558 (P558, Böhler, Milan, Italy) was studied in vitro on primary osteoblasts and in vivo after bone implantation in the sheep tibia, and was compared to ISO 5832-9 SSt (SSt) and Ti6Al4V. Cells were cultured directly on P558 and Ti6Al4V. Cells cultured on polystyrene were used as controls. Osteoblast proliferation, viability and synthetic activity were evaluated at 72 h by assaying WST1, alkaline phosphatase activity (ALP), nitric oxide, pro-collagen I (PICP), osteocalcin (OC), transforming growth factor-beta1 (TGFbeta-1) and interleukin-6 (IL-6) after 1.25(OH)2D3 stimulation. Under general anaesthesia, four sheep were submitted for bilateral tibial implantation of P558, SSt and Ti6Al4V rods. In vitro results demonstrated that the effect of P558 on osteoblast viability, PICP, TGF beta-1, tumor necrosis factor-alpha production did not significantly differ from that exerted by Ti6Al4V and controls. Furthermore, P558 enhanced osteoblast differentiation, as confirmed by ALP and OC levels, and reduced IL-6 production. At 26 weeks, the bone-to-implant contact was higher in P558 than in SSt (28%, p<0.005) and Ti6Al4V (4%, p<0.05), and was higher in Ti6Al4V than in SSt (22%, p<0.005). The tested materials did not affect bone microhardness in pre-existing host bone as evidenced by the measurements taken at 1000 microm from the bone-biomaterial interface (F=1.89, ns). At the bone-biomaterial interface the lowest HV value was found for SSt, whereas no differences in HV were observed between materials (F=1.55, ns). The current findings demonstrate P558 biocompatibility both in vitro and in vivo, and osteointegration processes are shown to be significantly improved by P558 as compared to the other materials tested.

A new austenitic stainless steel with a negligible amount of nickel: Anin vitro study in view of its clinical application in osteoporotic bone

A biomaterial named P558 is a new austenitic stainless steel (SS) with a negligible amount of Ni (<0.20%). In previous in vitro and in vivo studies it was compared with conventional SS and Ti6Al4V and shown to be a promising material in orthopedics. Because osteoporosis is a type of pathology very often encountered in implanted patients and can be studied with in vitro models, the purpose of the present study was to evaluate P558 in vitro through comparison of normal (nOB) with osteopenic (oOB) bone-derived primary rat osteoblasts. Osteoblasts were cultured directly on P558 and polystyrene as controls for 72 h. Osteoblast proliferation, adhesion, and activity (ALP, OC, TGF-beta1, and IL-6) were evaluated at 24 and 72 h. Results demonstrated that the growth of nOB and oOB cultured on P558 was not affected negatively when compared to control. Cells on P558 did not show any alteration in terms of adhesion, proliferation, and metabolic marker production in nOB and oOB cultures, and a significant increase in ALP, OC, and TGF-beta1 production was observed. SEM images revealed no alteration in cell morphology. The current findings demonstrate that P558 promotes osteoblast proliferation, activation, and differentiation not only in normal bone, but also in osteopenic bone-derived osteoblasts.

MEDIANOVO - a media database for medical education, research and health care

MEDIANOVO provides a high quality, scientifically indexed multi-media database with comfortable authoring and download functions through a web-based frontend. Currently, MEDIANOVO is used by medical teachers as a repository for storing and sharing media for educational purposes. However a database was created which could also serve with training and further education, in computer based learning systems as well as medical publishers and for individual patient information. Through the web-frontend the content is available worldwide.

A flexible architecture for constructing and executing tutoring processes

The tutoring process of conventional case-oriented medical training systems can be characterised as either guided or unguided. In contrast to that, the aim of the system "Docs'n Drugs" is to distinguish between different levels of guidance. The author can realise the tutoring case as a guided, a half guided or an unguided tutoring process. The system architecture distinguishes between an authoring system and a tutoring system. Fundaments of these are the tutoring process model and the case data model. This structure allows the reuse of elements of existing tutoring cases. The tutoring cases can be realised in different languages, e.g. German and English.

"Docs 'n drugs--the virtual polyclinic": an intelligent tutoring system for web-based and case-oriented training in medicine

Since the beginning of the year 2000 medical students of the University of Ulm are working in their curriculum with the web-based and case-oriented tutoring system "Docs 'n Drugs - The Virtual Polyclinic". The system consists of different subsystems and services. One subsystem is the Training System. It is based on three models: the Tutoring Process Model, the Case Knowledge Model and the Medical Knowledge Model. They describe the tutoring process as a series of nodes and steps, depict the structure of the medical cases, and provide the medical knowledge respectively. Case knowledge and medical knowledge form the expert knowledge of the medical domain. Together with the tutoring process, they build the basis for automatic intelligent tutoring. After giving a deeper insight into the system architecture and the training case structure, an informal evaluation shows a first feedback of the learners.

Formal classification of medical concept descriptions: graph-oriented operators

A crucial component of a medical concept representation system is the classifier. It requires features that are not sufficiently supported by current logic based formalisms like description logics and conceptual graphs. Those features are, for instance, the representation of partitive and spatial relations and their impact on subsumption. This paper introduces graph oriented classification operators for a concept representation language with normal forms. Emphasis is on the separation of generic and partitive relations and on the mutual interdependence of subsumption and part-whole. For that purpose operators are given for formal subsumption, formal part-whole, subsumptive part-whole and part-sensitive subsumption. These operators are based on the formal structure of concept descriptions and on explicitly introduced generic and partitive relationships between their constituents.

TSMI: a CEN/TC251 standard for time specific problems in healthcare informatics and telematics

Time is the most important variable in healthcare, and standards are needed about how to represent information with explicit references to time. In this paper, the European Prestandard 'TSMI: time standards for healthcare specific problems' (CEN/TC251 preENV 12381) is presented which aims to be the first contribution to this harmonisation process, focusing on 'representation' and 'explicit reference' of temporal information in healthcare. The prestandard is mainly composed of two parts. First, the basic building blocks for modelling time-related information are introduced, and a formal representation scheme proposed. In a second part, conformance rules and principles for Healthcare Data and Information as well as for Healthcare Information Systems, are covered.

The compositional approach for representing medical concept systems

The representation of patient-specific information in the computer-based medical record requires an expressive formalism, which supports computational services particularly with respect to subsumption. These demands are not sufficiently met by conventional medical terminology and classification systems. This paper investigates the weaknesses of conventional systems, which are primarily coding systems and contain a certain amount of implicit knowledge. The alternatives are logic-based formalisms, particularly languages of the KL-ONE-family and conceptual graphs, which are based on the formal representation of meanings. Principles of these approaches are reported and compared to the concept representation language developed in the GALEN project. Finally, an overview on the BERNWARD model is given, which aims at the formal description, classification, and composition of medical concepts. In BERNWARD subsumption and part-whole relation are treated in a symmetrical manner. There are explicit and formal criteria for supporting the inference of generic and partitive relations.

Subsumption principles underlying medical concept systems and their formal reconstruction

Conventional medical concept systems represent generic concept relations by hierarchical coding principles. Often, these coding principles constrain the concept system and reduce the potential for automatical derivation of subsumption. Formal reconstruction of medical concept systems is an approach that bases on the conceptual representation of meanings and that allows for the application of formal criteria for subsumption. Those criteria must reflect intuitive principles of subordination which are underlying conventional medical concept systems. Particularly these are: The subordinate concept results (1) from adding a specializing criterion to the superordinate concept, (2) from refining the primary category, or a criterion of the superordinate concept, by a concept that is less general, (3) from adding a partitive criterion to a criterion of the superordinate, (4) from refining a criterion by a concept that is less comprehensive, and finally (5) from coordinating the superordinate concept, or one of its criteria. This paper introduces a formalism called BERNWARD that aims at the formal reconstruction of medical concept systems according to these intuitive principles. The automatical derivation of hierarchical relations is primarily supported by explicit generic and explicit partititive hierarchies of concepts, secondly, by two formal criteria that base on the structure of concept descriptions and explicit hierarchical relations between their elements, namely: formal subsumption and part-sensitive subsumption. Formal subsumption takes only generic relations into account, part-sensitive subsumption additionally regards partive relations between criteria. This approach seems to be flexible enough to cope with unforeseeable effects of partitive criteria on subsumption.

Differential adherence of the human monocyte subsets 27E10 and RM3/1 to cytokine- or glucocorticoid-treated endothelial cells

Monocyte-endothelial interactions are of particular importance in the regulation of inflammation. The aim of the present study was to investigate the adhesion of functional different monocyte subsets to human umbilical vein endothelial cells treated with various cytokines or a glucocorticoid. The adherence of monocyte subset 27E10, which is associated with inflammatory processes, increased after endothelial activation with interleukin-1 beta (IL-1 beta), interferon-gamma (IFN gamma), tumor necrosis factor-alpha (TNF alpha), and the glucocorticoid prednylidene (Pred). The adherence at IFN gamma-treated endothelial cells was strong after a coculture duration of 10 min with a slight increase up to 60 min. The peak value after TNF alpha stimulation was reached after 15 min, thereafter quickly decreasing. IL-1 and Pred treatment caused a maximal adherence between 15 and 30 min followed by a slow decrease. TNF alpha and particularly interleukin-6 (IL-6) enhanced the endothelial adhesion of the monocyte subtype RM3/1, which is associated with the downregulation of inflammation. The maximal adherence was found after 15 and 30 min of coculture, respectively. The results show that, through modulation of the adhesive properties of endothelial cells, cytokines and glucocorticoids affect the adherence of monocyte subsets differently. They also suggest that IL-6 plays a role in the downregulation of acute inflammation.

Models for representation of terminologies and coding systems in medicine

Unification of medical coding systems is a perceived need involving a long-term task. Standards will support convergence of present coding systems towards a coherent set of tools. The Project Team "Model for Representation of Semantics" (CEN/TC251/PT003-MOSE) modeled existing tools to obtain a vocabulary apt to describe coding systems and terminologies. Requirements on faithfulness and safety, usefulness and purposiveness, coherence and integration were worked out, and the MOSE's 10 key principles for Standards in Medical Semantics were established.

An interactive report generator for bone scan studies

An interactive report generator for bone scintigraphy will be demonstrated. It comprises a controlled reporting vocabulary, an adaptive user interface, and a text generator. The controlled vocabulary represents the relevant concepts for bone scan reports: anatomical sites, scintigraphical phenomena, and diagnoses, and various attributes for these concept domains. Within the vocabulary selectional constraints are defined that restricts to meaningful combination of concepts. The interface provides intelligent views on the vocabulary, and presents only those terms that are relevant in a certain context. Through the interface the user may choose appropriate terms and combine them to complex findings. A German text generator for a restricted finding language transforms the entered data into morpho-syntactic surface structures and produces acceptable reports.

Conceptual graphs as an operational model for descriptive findings

Clinical findings are often based on impression and expressed by verbal descriptions. For their structured documentation a coherent and consistent representation model is demanding. The proposed approach is an attempt to take conceptual graphs as a formal notation for findings. Conceptual graphs are finite, connected, and bipartite graphs consisting of concept nodes that are linked by conceptual relation nodes. Concepts are organized in a type hierarchy. A subclass of conceptual graphs, called conceptual finding graphs, will be introduced that capture descriptive findings with well-defined characteristics. It will be shown, how conceptual finding graphs can serve as a coherent and consistent basis for data acquisition, database storage, and verbalization of descriptive findings. The data entry of findings can be supported by the definition of selectional constraints for conceptual relations. Database storage can be achieved by mapping conceptual finding graphs into a relational database schema. Findings can be verbalized by a text generator which takes conceptual finding graphs as input and produces morpho-syntactic surface structures. The model has been applied to an interactive report generator for bone scan studies. It provides the user with a controlled reporting vocabulary on an adaptive graphical interface, and allows the assembling of complex findings by term selection and combination based on selectional constraints. The entered findings can be stored without loss of structure. A text generation produces acceptable German reports.