Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating motion from MRI data

INVITED PAPER: Magnetic resonance imaging (MRI) is an ideal imaging modality to measure blood flow and tissue motion. It provides excellent contrast between soft tissues, and images can be acquired at positions and orientations freely defined by the user. From a temporal sequence of MR images, boundaries and edges of tissues can be tracked by image processing techniques. Additionally, MRI permits the source of the image signal to be manipulated. For example, temporary magnetic tags displaying a pattern of variable brightness may be placed in the object using MR saturation techniques, giving the user a known pattern to detect for motion tracking. The MRI signal is a modulated complex quantity, being derived from a rotating magnetic field in the form of an induced current. Well-defined patterns can also be introduced into the phase of the magnetization, and could be thought of as generalized tags. If the phase of each pixel is preserved during image reconstruction, relative phase shifts can be used to directly encode displacement, velocity and acceleration. New methods for modeling motion fields from MRI have now found application in cardiovascular and other soft tissue imaging. In this review, we shall describe the methods used for encoding, imaging, and modeling motion fields with MRI.
Comparison of multiplex immunoassay platforms.

BACKGROUND Candidate biomarkers discovered with high-throughput proteomic techniques (along with many biomarkers reported in the literature) must be rigorously validated. The simultaneous quantitative assessment of multiple potential biomarkers across large cohorts presents a major challenge to the field. Multiplex immunoassays represent a promising solution, with the potential to provide quantitative data via parallel analyses. These assays also require substantially less sample and reagents than the traditional ELISA (which is further limited by its ability to measure only a single antigen). We have measured the reproducibility, reliability, robustness, accuracy, and throughput of commercially available multiplex immunoassays to ascertain their suitability for serum biomarker analysis and validation. METHODS Assay platforms MULTI-ARRAY (Meso Scale Discovery), Bio-Plex (Bio-Rad Laboratories), A(2) (Beckman Coulter), FAST Quant (Whatman Schleicher & Schuell BioScience), and FlowCytomix (Bender MedSystems) were selected as representative examples of technologies currently used for high-throughput immunoanalysis. All assays were performed according to protocols specified by the manufacturers and with the reagents (diluents, calibrators, blocking reagents, and detecting-antibody mixtures) included with their kits. RESULTS The quantifiable interval determined for each assay and antigen was based on precision (CV < 25%) and percentage recovery (measured concentration within 20% of the actual concentration). The MULTI-ARRAY and Bio-Plex assays had the best performance with the lowest limits of detection, and the MULTI-ARRAY system had the most linear signal output over the widest concentration range (10(5) to 10(6)). Cytokine concentrations in unspiked and cytokine-spiked serum samples from healthy individuals were further investigated with the MULTI-ARRAY and Bio-Plex assays. CONCLUSIONS The MULTI-ARRAY and Bio-Plex multiplex immunoassay systems are the most suitable for biomarker analysis or quantification.
The rise and fall of an opt-out system

Introduction: In Denmark, citizens participate in register-based research without the possibility of opting out. However, in 1995 it was made possible for Danish citizens to register an opt-out called ‘researcher protection’ [forskerbeskyttelse], which implied that researchers could not contact people to invite them to participate in research projects, such as clinical trials or questionnaries, based on their registrations in national registers. Data already registered could still be used for research. In 2014, this possibility of opt-out was revoked by law. Aims: The aims of this paper are to understand how the Danish researcher protection system came about, why it was terminated and what we can we learn from this example. Methods: We conducted a descriptive analysis of a copy of the former researcher protection register along with policies and media debate surrounding the rise and revocation of the researcher protection system. Results: Our results show how both the inception and the abolishment of researcher protection appear to be ad hoc and without specified criteria of success. An examination of the recorded entries in the researcher protection registry could have led to changes in its administration as an alternative to its total abolition. Conclusions: In future opt-out systems, there should be focus on monitoring register practices and the purpose and criteria for evaluation must be defined prior to implementation.
PUTTING THE SOCIAL IN PROSOCIAL BEHAVIOR: AN INTERACTIONS APPROACH TO ALTRUISM

While psychologically trained social psychologists have long been concerned with the issue of prosocial behavior, sociologically trained social psychologists have had relatively little to say on the matter. In this paper a symbolic interactionist approach to prosocial behavior is developed. First, the relevant work of George Herbert Mead is briefly examined. Next, Mead's concepts of social object, perspective, and the generalized other, are used to conceptualize pro social behavior as role behavior. The paper concludes with a discussion of the implications suggested by this particular sociological approach to altruism.
Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets

Significance We describe a method for identifying in distinct genetic datasets observations that represent the same person. By using correlations among genetic markers close to one another in the genome, the method can succeed even if the datasets contain no overlapping markers. We show that the method can link a dataset similar to those used in genomic studies with another dataset containing markers used for forensics. Our approach can assist in maintaining backward compatibility with databases of existing forensic genetic profiles as systems move to new marker types. At the same time, it illustrates that the privacy risks that can arise from the cross-linking of databases are inherent even for small numbers of markers. Combining genotypes across datasets is central in facilitating advances in genetics. Data aggregation efforts often face the challenge of record matching—the identification of dataset entries that represent the same individual. We show that records can be matched across genotype datasets that have no shared markers based on linkage disequilibrium between loci appearing in different datasets. Using two datasets for the same 872 people—one with 642,563 genome-wide SNPs and the other with 13 short tandem repeats (STRs) used in forensic applications—we find that 90–98% of forensic STR records can be connected to corresponding SNP records and vice versa. Accuracy increases to 99–100% when ∼30 STRs are used. Our method expands the potential of data aggregation, but it also suggests privacy risks intrinsic in maintenance of databases containing even small numbers of markers—including databases of forensic significance.
Preference-Based Solution Selection Algorithm for Evolutionary Multiobjective Optimization

Since multiobjective evolutionary algorithms (MOEAs) provide a set of nondominated solutions, decision making of selecting a preferred one out of them is required in real applications. However, there has been some research on MOEA in which the user's preferences are incorporated for this purpose. This paper proposes preference-based solution selection algorithm (PSSA) by which user can select a preferred one out of nondominated solutions obtained by any one of MOEAs. The PSSA, which is a kind of multiple criteria decision making (MCDM) algorithm, represents user's preference to multiple objectives or criteria as a degree of consideration by fuzzy measure and globally evaluates obtained solutions by fuzzy integral. The PSSA is also employed in each and every generation of evolutionary process to propose multiobjective quantum-inspired evolutionary algorithm with preference-based selection (MQEA-PS). To demonstrate the effectiveness of PSSA and MQEA-PS, computer simulations and real experiments on evolutionary multiobjective optimization for the fuzzy path planner of mobile robot are carried out. Computer simulation and experiment results show that the user's preference is properly reflected in the selected solution. Moreover, MQEA-PS shows improved performance for the DTLZ problems and fuzzy path planner optimization problem compared to MQEA with dominance-based selection and other MOEAs like NSGA-II and MOPBIL.
Dysregulation of the Peripheral and Adipose Tissue Endocannabinoid System in Human Abdominal Obesity

The endocannabinoid system has been suspected to contribute to the association of visceral fat accumulation with metabolic diseases. We determined whether circulating endocannabinoids are related to visceral adipose tissue mass in lean, subcutaneous obese, and visceral obese subjects (10 men and 10 women in each group). We further measured expression of the cannabinoid type 1 (CB1) receptor and fatty acid amide hydrolase (FAAH) genes in paired samples of subcutaneous and visceral adipose tissue in all 60 subjects. Circulating 2-arachidonoyl glycerol (2-AG) was significantly correlated with body fat (r = 0.45, P = 0.03), visceral fat mass (r = 0.44, P = 0.003), and fasting plasma insulin concentrations (r = 0.41, P = 0.001) but negatively correlated to glucose infusion rate during clamp (r = 0.39, P = 0.009). In visceral adipose tissue, CB1 mRNA expression was negatively correlated with visceral fat mass (r = 0.32, P = 0.01), fasting insulin (r = 0.48, P < 0.001), and circulating 2-AG (r = 0.5, P < 0.001), whereas FAAH gene expression was negatively correlated with visceral fat mass (r = 0.39, P = 0.01) and circulating 2-AG (r = 0.77, P < 0.001). Our findings suggest that abdominal fat accumulation is a critical correlate of the dysregulation of the peripheral endocannabinoid system in human obesity. Thus, the endocannabinoid system may represent a primary target for the treatment of abdominal obesity and associated metabolic changes.
Maternal Smoking and DNA Methylation in Newborns: In Utero Effect or Epigenetic Inheritance?

Background: Maternal smoking in pregnancy is associated with adverse health outcomes in children, including cancers; underlying mechanisms may include epigenetic modifications. Using Illumina's 450K array, we previously identified differential DNA methylation related to maternal smoking during pregnancy at 26 CpG sites (CpGs) in 10 genes in newborn cord bloods from the Norwegian Mother and Child Cohort Study (MoBa). Whether these methylation signals in newborns reflect in utero exposure only or possibly epigenetic inheritance of smoking-related modifications is unclear. Methods: We therefore evaluated the impact of the timing of mother's smoking (before or during pregnancy using cotinine measured at 18 weeks gestation), the father's smoking before conception, and the grandmother's smoking during her pregnancy with the mother on methylation at these 26 CpGs in 1,042 MoBa newborns. We used robust linear regression, adjusting for covariates, applying Bonferroni correction. Results: The strongest and only statistically significant associations were observed for sustained smoking by the mother during pregnancy through at least gestational week 18 (P < 1.6 × 10−5 for all 26 CpGs). We observed no statistically significant differential methylation due to smoking by the mother before pregnancy or that ceased by week 18, father's smoking before conception, or grandmother's smoking while pregnant with the mother. Conclusions: Differential methylation at these CpGs in newborns seems to reflect sustained in utero exposure rather than epigenetic inheritance. Impact: Smoking cessation in early pregnancy may negate effects on methylation. Analyses of maternal smoking during pregnancy and offspring health outcomes, including cancer, limited to ever smoking might miss true associations. Cancer Epidemiol Biomarkers Prev; 23(6); 1007–17. ©2014 AACR.
Cocaine causes deficits in radial migration and alters the distribution of glutamate and GABA neurons in the developing rat cerebral cortex

Prenatal cocaine exposure induces cytoarchitectural changes in the embryonic neocortex; however, the biological mechanisms and type of cortical neurons involved in these changes are not known. Previously, we found that neural progenitor proliferation in the neocortical ventricular zone (VZ) is inhibited by cocaine; here, we examine the changes in cortical neurogenesis and migration of glutamate and GABA neurons induced by prenatal cocaine exposure. Pregnant rats received 20 mg/kg of cocaine intraperitoneally twice at an interval of 12 h during three periods of neocortical neurogenesis. Neocortical area and distribution of developing neurons were examined by counting Tuj1+, glutamate+, or GABA+ cells in different areas of the cerebral cortex. Cocaine decreased neocortical area by reducing the size of the Tuj1+ layer, but only when administered during early periods of neocortical neurogenesis. The number of glutamatergic neurons was increased in the VZ but was decreased in the outer cortical laminae. Although the number of GABA+ neurons in the VZ of both the neocortex and ganglionic eminences was unchanged, GABA+ cells decreased in all other neocortical laminae. Tangential migration of GABA+ cells was also disrupted by cocaine. These findings suggest that in utero cocaine exposure disturbs radial migration of neocortical neurons, possibly because of decreased radial glia guiding support through enhanced differentiation of neocortical VZ progenitors. Cocaine interrupts radial migration of both glutamatergic and GABAergic neurons within the neocortex, in addition to the tangential migration of GABAergic neurons from the subcortical telecephalon. This may result in abnormal neocortical cytoarchitecture and concomitant adverse functional effects. Synapse 65:21–34, 2011. © 2010 Wiley‐Liss, Inc.
An efficient method for isolating mating‐competent cells from bottom‐fermenting yeast using mating pheromone‐supersensitive mutants

Crossbreeding is an effective approach to construct novel yeast strains with preferred characteristics; however, it is difficult to crossbreed strains of brewer's yeast, especially the bottom‐fermenting yeast Saccharomyces pastorianus, because of the relative inefficiency of the available methods to obtain mating‐competent cells (MCCs). Here, we describe a productive method for the isolation of MCCs without artificial genetic modification. We focused on the characteristics of two mating pheromone‐supersensitive mutants, Δbar1 and Δsst2, that show a growth defect in the presence of the mating pheromone. When MCCs secreting α‐factor and a‐factor were spotted on to a lawn of MATa Δbar1 and MATα Δsst2, a halo was observed around the respective MCCs. This plate assay was successful in identifying MCCs from bottom‐fermenting yeast strains. Furthermore, by selecting for cells that caused the growth defect in pheromone‐supersensitive cells on cultures plates, 40 α/α‐type and six a/a‐type meiotic segregants of bottom‐fermenting yeast strains were successfully isolated and crossed with tester strains to verify their mating type. This method of isolation is expected to be applicable to other industrial yeast strains, including wine, sake and distiller's yeasts, and will enable MCCs without genetic modifications to be obtained. As a result, it will be a useful tool for more convenient and efficient crossbreeding of industrial yeast strains that can be applied to practical brewing. Copyright © 2017 John Wiley & Sons, Ltd.
Medical migration: A qualitative exploration of the atypical path of Japanese international medical graduates

Abstract Background: International Medical Graduates (IMGs) are commonly understood to move from low to high resource countries with motivations including improved financial situations and cultures of emigration. A presumable exception to the above themes would be the Japanese IMG population. The aim of this study was to develop an understanding of the Japanese IMG experience. Methods: Using a grounded theory approach, we interviewed 19 Japanese IMGs working in the US and 16 Japanese IMGs working in Japan who had completed US clinical training. Questions addressed decision-making to pursue US clinical training, goals for the training, and career decision-making upon completing the training. Data collection and constant comparative analysis were conducted iteratively to identify emerging themes. Results: The emerging model of the Japanese IMG experience is focused around pivotal experiences that often include dissatisfaction with the quality of Japanese clinical training and personal exposures to US clinical education. Further decision-making in the pursuit of US residency is influenced by educator training quality, and clinical training and career opportunities. The desire to improve Japanese clinical training commonly influences career decision-making after US training. Conclusions: The Japanese IMG experience contrasts numerous perceptions of international physician migration and, in turn, enhances understanding of this paradigm.
Comment on “Drug Screening for ALS Using Patient-Specific Induced Pluripotent Stem Cells”

Egawa et al. recently showed the value of patient-specific induced pluripotent stem cells (iPSCs) for modeling amyotrophic lateral sclerosis in vitro. Their study and our work highlight the need for complementary assays to detect small, but potentially important, phenotypic differences between control iPSC lines and those carrying disease mutations.
Expanding the Nomological Net of the Pathological Narcissism Inventory: German Validation and Extension in a Clinical Inpatient Sample

The Pathological Narcissism Inventory (PNI) is a multidimensional measure for assessing grandiose and vulnerable features in narcissistic pathology. The aim of the present research was to construct and validate a German translation of the PNI and to provide further information on the PNI’s nomological net. Findings from a first study confirm the psychometric soundness of the PNI and replicate its seven-factor first-order structure. A second-order structure was also supported but with several equivalent models. A second study investigating associations with a broad range of measures (DSM Axis I and II constructs, emotions, personality traits, interpersonal and dysfunctional behaviors, and well-being) supported the concurrent validity of the PNI. Discriminant validity with the Narcissistic Personality Inventory was also shown. Finally, in a third study an extension in a clinical inpatient sample provided further evidence that the PNI is a useful tool to assess the more pathological end of narcissism.
University Students' Risk for Disordered Eating

KEYWORDS Eating Disorders. Disordered Eating. Anorexia Nervosa. Bulimia Nervosa. University. Student ABSTRACT 144 usable EAT-26 surveys were returned at one point in time in order to determine disordered eating characteristics amongst college age students at one university in California. This study examined the presence of disordered eating, as evidenced by the EAT-26, in a university population. In addition, demographic data, as well as behaviors known to be related to disordered eating were collected. Risk for disordered eating was much higher than expected with 23.6% of the females in this population scoring above 20 on the EAT- 26. When other risk factors for disordered eating are factored in, 42.5% of the female population in this particular class showed a risk for an eating disorder. This study demonstrates the importance of an eating disorder intervention at the college campus. In addition, it is speculated that some campuses, for a variety of reasons, may have a higher population of eating disordered females. A presentation on the risks of disordered eating followed the survey. Resources, and referrals were distributed; appointments with the faculty and health center were encouraged.
Neonatal thyroid hormone levels in association with autism spectrum disorder

Thyroid hormones (TH) are critical in early neurodevelopment, but few studies have examined whether neonatal TH levels influence risk of autism spectrum disorder (ASD). This study linked California neonatal screening data with live birth and Department of Developmental Services records to examine newborn TH levels in relation to ASD. Thyroxine (T4) and thyroid‐stimulating hormone (TSH) levels were measured in newborn bloodspots as part of routine screening, in 1996 and 2002, respectively. Mean levels of T4 and TSH were compared between ASD cases and non‐cases. Four hundred forty‐seven thousand, fifty‐nine screened, singleton births from 1996 and 446,424 from 2002 were examined, including 4,818 ASD cases. Binomial regression, using categories of T4 and TSH percentiles was used to calculate crude and adjusted risk ratios (RR). Covariates included maternal and child factors, gestational age, and age at blood draw. No significant associations were found with TSH levels and ASD in crude or adjusted analyses. ASD cases had significantly lower mean T4 levels than non‐cases, but this association was no longer significant in adjusted analyses (RR in individuals in lowest 5th percentile of T4 levels = 1.13, 95% 0.93–1.37). However, this association appeared stronger in certain subgroup analyses, particularly among neonates with blood draw ≥48 hr from birth (RR = 1.67, 95% CI 1.08, 2.60), when TH levels become more stable. Thus, results from this large, population‐based study did not suggest strong associations between neonatal TH and ASD, but certain subgroups of newborns with the lowest T4 levels may have modestly increased ASD risk. Autism Res 2016. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. Autism Res 2017, 10: 585–592. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.
Rate-adaptive polar codes for distributed source coding

In this paper, we consider how polar codes can be used for distributed source coding configuration regardless of the statistical dependency of correlated binary sources. The polar code encoder transmits the syndrome bits which have high entropy first to the decoder for optimal compression. However, the optimal order for transmitting syndrome bits varies with the dependency of correlated sources. It means that the encoder needs to know the correlation of sources for optimal compression. In this point of view, we propose the construction method of the optimal sequence for syndrome bits. The sequence constructed with the proposed method shows the optimal compression rate without knowledge of correlation of sources at the polar code encoder.