STrengthening the Reporting of OBservational studies in Epidemiology: Molecular Epidemiology STROBE-ME. An extension of the STROBE statement

Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility, and clinical outcomes are used as proxies for investigating the interactions between external and/or endogenous agents and the body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as STrengthening Reporting of Observational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE Statement implementing 9 existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.

Representations of the Human/ Nonhuman Primate Divide: the Influence of Science, Fiction, and Science-Fiction on the Concept of 'Being Human'

For as far back as human history can be traced, mankind has questioned what it means to be human. One of the most common approaches throughout Western culture's intellectual tradition in attempts to answering this question has been to compare humans with or against other animals. I argue that it was not until Charles Darwin's publication of The Descent of Man and Selection in Relation to Sex (1871) that Western culture was forced to seriously consider human identity in relation to the human/ nonhuman primate line. Since no thinker prior to Charles Darwin had caused such an identity crisis in Western thought, this interdisciplinary analysis of the history of how the human/ nonhuman primate line has been understood focuses on the reciprocal relationship of popular culture and scientific representations from 1871 to the Human Genome Consortium in 2000. Focusing on the concept coined as the "Darwin-Müller debate," representations of the human/ nonhuman primate line are traced through themes of language, intelligence, and claims of variation throughout the popular texts: Descent of Man, The Jungle Books (1894), Tarzan of the Apes (1914), and Planet of the Apes (1963). Additional themes such as the nature versus nurture debate and other comparative phenotypic attributes commonly used for comparison between man and apes are also analyzed. Such popular culture representations are compared with related or influential scientific research during the respective time period of each text to shed light on the reciprocal nature of Western intellectual tradition, popular notions of the human/ nonhuman primate line, and the development of the field of primatology. Ultimately this thesis shows that the Darwin-Müller debate is indeterminable, and such a lack of resolution makes man uncomfortable. Man's unsettled response and desire for self-knowledge further facilitates a continued search for answers to human identity. As the Human Genome Project has led to the rise of new debates, and primate research has become less anthropocentric over time, the mysteries of man's future have become more concerning than the questions of our past. The human/ nonhuman primate line is reduced to a 1% difference, and new debates have begun to overshadow the Darwin-Müller debate. In conclusion, I argue that human identity is best represented through the metaphor of evolution: both have an unknown beginning, both have an indeterminable future with no definite end, and like a species under the influence of evolution, what it means to be human is a constant, indeterminable process of change.

A NOVEL AND SIMPLE RULE OF THUMB FOR MULTIPLICITY CONTROL IN EQUIVALENCE TESTING USING TWO ONE-SIDED TESTS

Equivalence testing is growing in use in scientific research outside of its traditional role in the drug approval process. Largely due to its ease of use and recommendation from the United States Food and Drug Administration guidance, the most common statistical method for testing (bio)equivalence is the two one-sided tests procedure (TOST). Like classical point-null hypothesis testing, TOST is subject to multiplicity concerns as more comparisons are made. In this manuscript, a condition that bounds the family-wise error rate (FWER) using TOST is given. This condition then leads to a simple solution for controlling the FWER. Specifically, we demonstrate that if all pairwise comparisons of k independent groups are being evaluated for equivalence, then simply scaling the nominal Type I error rate down by (k - 1) is sufficient to maintain the family-wise error rate at the desired value or less. The resulting rule is much less conservative than the equally simple Bonferroni correction. An example of equivalence testing in a non drug-development setting is given.

PENALIZED FUNCTIONAL REGRESSION

We develop fast fitting methods for generalized functional linear models. An undersmooth of the functional predictor is obtained by projecting on a large number of smooth eigenvectors and the coefficient function is estimated using penalized spline regression. Our method can be applied to many functional data designs including functions measured with and without error, sparsely or densely sampled. The methods also extend to the case of multiple functional predictors or functional predictors with a natural multilevel structure. Our approach can be implemented using standard mixed effects software and is computationally fast. Our methodology is motivated by a diffusion tensor imaging (DTI) study. The aim of this study is to analyze differences between various cerebral white matter tract property measurements of multiple sclerosis (MS) patients and controls. While the statistical developments proposed here were motivated by the DTI study, the methodology is designed and presented in generality and is applicable to many other areas of scientific research. An online appendix provides R implementations of all simulations.

Cadaver dogs--a study on detection of contaminated carpet squares

INTRODUCTION: Cadaver dogs are known as valuable forensic tools in crime scene investigations. Scientific research attempting to verify their value is largely lacking, specifically for scents associated with the early postmortem interval. The aim of our investigation was the comparative evaluation of the reliability, accuracy, and specificity of three cadaver dogs belonging to the Hamburg State Police in the detection of scents during the early postmortem interval. MATERIAL AND METHODS: Carpet squares were used as an odor transporting media after they had been contaminated with the scent of two recently deceased bodies (PMI<3h). The contamination occurred for 2 min as well as 10 min without any direct contact between the carpet and the corpse. Comparative searches by the dogs were performed over a time period of 65 days (10 min contamination) and 35 days (2 min contamination). RESULTS: The results of this study indicate that the well-trained cadaver dog is an outstanding tool for crime scene investigation displaying excellent sensitivity (75-100), specificity (91-100), and having a positive predictive value (90-100), negative predictive value (90-100) as well as accuracy (92-100).

Non-intrusive pressure measurement in microchannels

A non-intrusive interferometric measurement technique has been successfully developed to measure fluid compressibility in both gas and liquid phases via refractive index (RI) changes. The technique, consisting of an unfocused laser beam impinging a glass channel, can be used to separate and quantify cell deflection, fluid flow rates, and pressure variations in microchannels. Currently in fields such as microfluidics, pressure and flow rate measurement devices are orders of magnitude larger than the channel cross-sections making direct pressure and fluid flow rate measurements impossible. Due to the non-intrusive nature of this technique, such measurements are now possible, opening the door for a myriad of new scientific research and experimentation. This technique, adapted from the concept of Micro Interferometric Backscatter Detection (MIBD), boasts the ability to provide comparable sensitivities in a variety of channel types and provides quantification capability not previously demonstrated in backscatter detection techniques. Measurement sensitivity depends heavily on experimental parameters such as beam impingement angle, fluid volume, photodetector sensitivity, and a channel’s dimensional tolerances. The current apparatus readily quantifies fluid RI changes of 10-5 refractive index units (RIU) corresponding to pressures of approximately 14 psi and 1 psi in water and air, respectively. MIBD reports detection capability as low as 10-9 RIU and the newly adapted technique has the potential to meet and exceed this limit providing quantification in the place of detection. Specific device sensitivities are discussed and suggestions are provided on how the technique may be refined to provide optimal quantification capabilities based on experimental conditions.

An immunohistochemical procedure to detect patients with paraganglioma and phaeochromocytoma with germline SDHB, SDHC, or SDHD gene mutations: a retrospective and prospective analysis

BACKGROUND: Phaeochromocytomas and paragangliomas are neuro-endocrine tumours that occur sporadically and in several hereditary tumour syndromes, including the phaeochromocytoma-paraganglioma syndrome. This syndrome is caused by germline mutations in succinate dehydrogenase B (SDHB), C (SDHC), or D (SDHD) genes. Clinically, the phaeochromocytoma-paraganglioma syndrome is often unrecognised, although 10-30% of apparently sporadic phaeochromocytomas and paragangliomas harbour germline SDH-gene mutations. Despite these figures, the screening of phaeochromocytomas and paragangliomas for mutations in the SDH genes to detect phaeochromocytoma-paraganglioma syndrome is rarely done because of time and financial constraints. We investigated whether SDHB immunohistochemistry could effectively discriminate between SDH-related and non-SDH-related phaeochromocytomas and paragangliomas in large retrospective and prospective tumour series. METHODS: Immunohistochemistry for SDHB was done on 220 tumours. Two retrospective series of 175 phaeochromocytomas and paragangliomas with known germline mutation status for phaeochromocytoma-susceptibility or paraganglioma-susceptibility genes were investigated. Additionally, a prospective series of 45 phaeochromocytomas and paragangliomas was investigated for SDHB immunostaining followed by SDHB, SDHC, and SDHD mutation testing. FINDINGS: SDHB protein expression was absent in all 102 phaeochromocytomas and paragangliomas with an SDHB, SDHC, or SDHD mutation, but was present in all 65 paraganglionic tumours related to multiple endocrine neoplasia type 2, von Hippel-Lindau disease, and neurofibromatosis type 1. 47 (89%) of the 53 phaeochromocytomas and paragangliomas with no syndromic germline mutation showed SDHB expression. The sensitivity and specificity of the SDHB immunohistochemistry to detect the presence of an SDH mutation in the prospective series were 100% (95% CI 87-100) and 84% (60-97), respectively. INTERPRETATION: Phaeochromocytoma-paraganglioma syndrome can be diagnosed reliably by an immunohistochemical procedure. SDHB, SDHC, and SDHD germline mutation testing is indicated only in patients with SDHB-negative tumours. SDHB immunohistochemistry on phaeochromocytomas and paragangliomas could improve the diagnosis of phaeochromocytoma-paraganglioma syndrome. FUNDING: The Netherlands Organisation for Scientific Research, Dutch Cancer Society, Vanderes Foundation, Association pour la Recherche contre le Cancer, Institut National de la Santé et de la Recherche Médicale, and a PHRC grant COMETE 3 for the COMETE network.

Semiotic Analysis in the Study of Social Work

Research and professional practices have the joint aim of re-structuring the preconceived notions of reality. They both want to gain the understanding about social reality. Social workers use their professional competence in order to grasp the reality of their clients, while researchers’ pursuit is to open the secrecies of the research material. Development and research are now so intertwined and inherent in almost all professional practices that making distinctions between practising, developing and researching has become difficult and in many aspects irrelevant. Moving towards research-based practices is possible and it is easily applied within the framework of the qualitative research approach (Dominelli 2005, 235; Humphries 2005, 280). Social work can be understood as acts and speech acts crisscrossing between social workers and clients. When trying to catch the verbal and non-verbal hints of each others’ behaviour, the actors have to do a lot of interpretations in a more or less uncertain mental landscape. Our point of departure is the idea that the study of social work practices requires tools which effectively reveal the internal complexity of social work (see, for example, Adams & Dominelli & Payne 2005, 294 – 295). The boom of qualitative research methodologies in recent decades is associated with much profound the rupture in humanities, which is called the linguistic turn (Rorty 1967). The idea that language is not transparently mediating our perceptions and thoughts about reality, but on the contrary it constitutes it was new and even confusing to many social scientists. Nowadays we have got used to read research reports which have applied different branches of discursive analyses or narratologic or semiotic approaches. Although differences are sophisticated between those orientations they share the idea of the predominance of language. Despite the lively research work of today’s social work and the research-minded atmosphere of social work practice, semiotics has rarely applied in social work research. However, social work as a communicative practice concerns symbols, metaphors and all kinds of the representative structures of language. Those items are at the core of semiotics, the science of signs, and the science which examines people using signs in their mutual interaction and their endeavours to make the sense of the world they live in, their semiosis. When thinking of the practice of social work and doing the research of it, a number of interpretational levels ought to be passed before reaching the research phase in social work. First of all, social workers have to interpret their clients’ situations, which will be recorded in the files. In some very rare cases those past situations will be reflected in discussions or perhaps interviews or put under the scrutiny of some researcher in the future. Each and every new observation adds its own flavour to the mixture of meanings. Social workers have combined their observations with previous experience and professional knowledge, furthermore, the situation on hand also influences the reactions. In addition, the interpretations made by social workers over the course of their daily working routines are never limited to being part of the personal process of the social worker, but are also always inherently cultural. The work aiming at social change is defined by the presence of an initial situation, a specific goal, and the means and ways of achieving it, which are – or which should be – agreed upon by the social worker and the client in situation which is unique and at the same time socially-driven. Because of the inherent plot-based nature of social work, the practices related to it can be analysed as stories (see Dominelli 2005, 234), given, of course, that they are signifying and told by someone. The research of the practices is concentrating on impressions, perceptions, judgements, accounts, documents etc. All these multifarious elements can be scrutinized as textual corpora, but not whatever textual material. In semiotic analysis, the material studied is characterised as verbal or textual and loaded with meanings. We present a contribution of research methodology, semiotic analysis, which has to our mind at least implicitly references to the social work practices. Our examples of semiotic interpretation have been picked up from our dissertations (Laine 2005; Saurama 2002). The data are official documents from the archives of a child welfare agency and transcriptions of the interviews of shelter employees. These data can be defined as stories told by the social workers of what they have seen and felt. The official documents present only fragmentations and they are often written in passive form. (Saurama 2002, 70.) The interviews carried out in the shelters can be described as stories where the narrators are more familiar and known. The material is characterised by the interaction between the interviewer and interviewee. The levels of the story and the telling of the story become apparent when interviews or documents are examined with the use of semiotic tools. The roots of semiotic interpretation can be found in three different branches; the American pragmatism, Saussurean linguistics in Paris and the so called formalism in Moscow and Tartu; however in this paper we are engaged with the so called Parisian School of semiology which prominent figure was A. J. Greimas. The Finnish sociologists Pekka Sulkunen and Jukka Törrönen (1997a; 1997b) have further developed the ideas of Greimas in their studies on socio-semiotics, and we lean on their ideas. In semiotics social reality is conceived as a relationship between subjects, observations, and interpretations and it is seen mediated by natural language which is the most common sign system among human beings (Mounin 1985; de Saussure 2006; Sebeok 1986). Signification is an act of associating an abstract context (signified) to some physical instrument (signifier). These two elements together form the basic concept, the “sign”, which never constitutes any kind of meaning alone. The meaning will be comprised in a distinction process where signs are being related to other signs. In this chain of signs, the meaning becomes diverged from reality. (Greimas 1980, 28; Potter 1996, 70; de Saussure 2006, 46-48.) One interpretative tool is to think of speech as a surface under which deep structures – i.e. values and norms – exist (Greimas & Courtes 1982; Greimas 1987). To our mind semiotics is very much about playing with two different levels of text: the syntagmatic surface which is more or less faithful to the grammar, and the paradigmatic, semantic structure of values and norms hidden in the deeper meanings of interpretations. Semiotic analysis deals precisely with the level of meaning which exists under the surface, but the only way to reach those meanings is through the textual level, the written or spoken text. That is why the tools are needed. In our studies, we have used the semiotic square and the actant analysis. The former is based on the distinctions and the categorisations of meanings, and the latter on opening the plotting of narratives in order to reach the value structures.

Open Data and Earth Observations The Case of Opening Up Access to and Use of Earth Observation Data Through the Global Earth Observation System of Systems

Earth observations (EO) represent a growing and valuable resource for many scientific, research and practical applications carried out by users around the world. Access to EO data for some applications or activities, like climate change research or emergency response activities, becomes indispensable for their success. However, often EO data or products made of them are (or are claimed to be) subject to intellectual property law protection and are licensed under specific conditions regarding access and use. Restrictive conditions on data use can be prohibitive for further work with the data. Global Earth Observation System of Systems (GEOSS) is an initiative led by the Group on Earth Observations (GEO) with the aim to provide coordinated, comprehensive, and sustained EO and information for making informed decisions in various areas beneficial to societies, their functioning and development. It seeks to share data with users world-wide with the fewest possible restrictions on their use by implementing GEOSS Data Sharing Principles adopted by GEO. The Principles proclaim full and open exchange of data shared within GEOSS, while recognising relevant international instruments and national policies and legislation through which restrictions on the use of data may be imposed.The paper focuses on the issue of the legal interoperability of data that are shared with varying restrictions on use with the aim to explore the options of making data interoperable. The main question it addresses is whether the public domain or its equivalents represent the best mechanism to ensure legal interoperability of data. To this end, the paper analyses legal protection regimes and their norms applicable to EO data. Based on the findings, it highlights the existing public law statutory, regulatory, and policy approaches, as well as private law instruments, such as waivers, licenses and contracts, that may be used to place the datasets in the public domain, or otherwise make them publicly available for use and re-use without restrictions. It uses GEOSS and the particular characteristics of it as a system to identify the ways to reconcile the vast possibilities it provides through sharing of data from various sources and jurisdictions on the one hand, and the restrictions on the use of the shared resources on the other. On a more general level the paper seeks to draw attention to the obstacles and potential regulatory solutions for sharing factual or research data for the purposes that go beyond research and education.

Mössbauer, X-ray and Magnetic Studies of Black Sand from the Italian Mediterranean Sea

The study of natural magnetic sands is instrumental to investigate the geological aspects of their formation and of the origin of their territory. In particular, Mössbauer spectroscopy provides unique information on their iron content and on the oxidation state of iron in their mineral composition. The Italian coast on the Mediterranean Sea near Rome is known for the presence of highly magnetic black sands of volcanic origin. A study of the room temperature Mössbauer spec- trum, powder X-ray diffraction, energy dispersive X-ray spectroscopy, and magnetic measurements of a sample of black magnetic sand collected on the seashore of the town of Ladispoli is performed. This study reveals magnetite as main constituent with iron in both tetrahedral and octahedral sites. Minor constituents are the iron minerals hematite and ilmenite, the iron containing minerals diopsite, gossular, and allanite, as well as ubiquitous sanidine, quartz, and calcite.

Conception Rate Using the Select-Synch Protocol in Combination with a Lower Dose Progesterone-Releasing Intravaginal Insert (1.38 g) in Swiss Dairy Cows

Background: Synchronization programs have become standard in the dairy industry. In Switzerland, these programs are used but newly. The objective of this study was A) to estimate the pregnancy rate after a Select-Synch protocol in- cluding a low dosage of progesterone in CIDR (1.38 g). As a second step B) this pregnancy rate should be compared to cows from another Swiss study that used a Select-Synch protocol with the 1.9 g insert (Rudolph et al., 2011). Methods: A) 196 cows were included in the study. Cows received a CIDR 1.38 g and 2.5 ml of buserelin i.m. on d 0. On d 7, the CIDR insert was removed and 5 ml of dinoprost was administered i.m. On d 0 a milk sample for progesterone analysis was taken. Pregnancy was determined at or more than 35 days after artificial insemination. B) The 1.38 g group and the 1.9 g group were compared as to cow and farm factors, number of preceding AI’s, gynecological and uterine pretreat- ment and treatment itself. A forward selection procedure was used (test result considered significant if p-value  0.05). Results: A) The pregnancy rate, using the Select-Synch protocol with the CIDR 1.38 g was 44.4%. B) The CIDR 1.9 g Select-Synch group revealed a pregnancy rate of 50.4% (Rudolph et al., 2011). Significant differences between the groups were not found. Conclusion: The 1.38 g CIDR-Select-Synch protocol may be recommended for multiparous dairy cows. The pregnancy rate compared to the 1.9 g CIDR-Select-Synch protocol was 8% lower, but this difference was not significant.