Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulating Organogenesis in COMSOL: Image-based Modeling

Mathematical Modelling has a long history in developmental biology. Advances in experimental techniques and computational algorithms now permit the development of increasingly more realistic models of organogenesis. In particular, 3D geometries of developing organs have recently become available. In this paper, we show how to use image-based data for simulations of organogenesis in COMSOL Multiphysics. As an example, we use limb bud development, a classical model system in mouse developmental biology. We discuss how embryonic geometries with several subdomains can be read into COMSOL using the Matlab LiveLink, and how these can be used to simulate models on growing embryonic domains. The ALE method is used to solve signaling models even on strongly deforming domains.
POSITION-INDEPENDENT INTERACTION FOR LARGE HIGH-RESOLUTION DISPLAYS

Since large, high-resolution displays (LHRD) are capable of visualizing a large amount of very detailed information, users have to move around in front of these displays to gain either in-depth knowledge or an overview. However, conventional input devices such as mouse and keyboard restrict users' mobility by requiring a stable surface on which to operate. We present a flexible and intuitive interaction technique based on an infrared laserpointer, a technique that allows identical use from any point and distance. In particular, our laserpointer interaction satisfies the demands of LHRD in the areas of mobility, accuracy, and interaction speed. The solution presented is technically designed as a generic interaction library whose flexibility and general applicability was verified by using it on two very different systems – a planar 221″ Powerwall and a curved 360° panoramic display. Furthermore, a comparative evaluation study with 16 participants was conducted on the Powerwall to compare the performances of a conventional mouse and our laserpointer by means of a unidirectional tapping test at varying distances (ISO 9241-9). The statistically significant performance advantage of the mouse (13%) appears marginal considering the intuitive and direct mode of interaction in using the laserpointer and the flexibility gained by its use, both of which are fundamental requirements for LHRDs. In comparison to previous systems and evaluations, we were able to reduce the laserpointer’s performance lag by over 50%. This result is achieved mainly by our precise tracking method, the minimized delay, and the effective jitter compensation.
Mechanical testing of a modified stabilisation method for tibial tuberosity advancement

Summary Objectives: This in vitro study evaluated three modified techniques of tibial tuberosity advancement (TTA). Loads to failure were calculated for each technique. Methods: A 9 mm TTA procedure was performed in the tibiae of dogs weighing between 32 and 38 kg. In group 1 (n = 12), the distal part of the tibial crest was left attached to the tibia by the cranial cortex, and a figure-of-eight wire was added for stabilisation. In group 2 (n = 12), the tibial crest was left attached but no additional device was used for stabilisation. In group 3 (n = 12), the tibial crest was completely separated from the tibia and fixed by a figure-of-eight wire so that, in this group, only the wire opposed avulsion of the tibial crest. Unidirectional axial force was applied via the patella to determine the maximal load to failure of the model. Results: There was no significant difference between group 1 and group 2. These two groups both had a significantly stronger construct than that of group 3. Clinical significance: We described modifications to the TTA procedure without plate fixation that warrant clinical investigation. When the crest is broken during its advancement, the tension sustained by the repair is significantly weaker from a biomechanical point of view and the use of such a repair clinically is not recommended by the authors.
Use of high potency statins and rates of admission for acute kidney injury: multicenter, retrospective observational analysis of administrative databases

Objective To quantify an association between acute kidney injury and use of high potency statins versus low potency statins. Design Retrospective observational analysis of administrative databases, using nine population based cohort studies and meta-analysis. We performed as treated analyses in each database with a nested case-control design. Rate ratios for different durations of current and past statin exposure to high potency or low potency statins were estimated using conditional logistic regression. Ratios were adjusted for confounding by high dimensional propensity scores. Meta-analytic methods estimated overall effects across participating sites. Setting Seven Canadian provinces and two databases in the United Kingdom and the United States. Participants 2 067 639 patients aged 40 years or older and newly treated with statins between 1 January 1997 and 30 April 2008. Each person hospitalized for acute kidney injury was matched with ten controls. Intervention A dispensing event was new if no cholesterol lowering drug or niacin prescription was dispensed in the previous year. High potency statin treatment was defined as ≥10 mg rosuvastatin, ≥20 mg atorvastatin, and ≥40 mg simvastatin; all other statin treatments were defined as low potency. Statin potency groups were further divided into cohorts with or without chronic kidney disease. Main outcome measure Relative hospitalization rates for acute kidney injury. Results Of more than two million statin users (2 008 003 with non-chronic kidney disease; 59 636 with chronic kidney disease), patients with similar propensity scores were comparable on measured characteristics. Within 120 days of current treatment, there were 4691 hospitalizations for acute kidney injury in patients with non-chronic kidney injury, and 1896 hospitalizations in those with chronic kidney injury. In patients with non-chronic kidney disease, current users of high potency statins were 34% more likely to be hospitalized with acute kidney injury within 120 days after starting treatment (fixed effect rate ratio 1.34, 95% confidence interval 1.25 to 1.43). Users of high potency statins with chronic kidney disease did not have as large an increase in admission rate (1.10, 0.99 to 1.23). χ2 tests for heterogeneity confirmed that the observed association was robust across participating sites. Conclusions Use of high potency statins is associated with an increased rate of diagnosis for acute kidney injury in hospital admissions compared with low potency statins. The effect seems to be strongest in the first 120 days after initiation of statin treatment.
Assessment of brain haemodynamic responses using optical topography modality

Neuroimaging studies have shown that negative mood states will impair the working memory (WM) functions that affect haemodynamic conditions at the prefrontal cortex (PFC) region. Compared to other neuroimaging tools, haemodynamic responses in surrounding brain surfaces can be assessed feasibly and with less constrained using Optical Topography (OT). This paper presents near infrared spectroscopy (NIRS) signal analysis technique and OT brain haemodynamic assessment methods to investigate sensorimotor and working memory tasks, without biasing of mood. The continuous OT measurements for finger-tapping task and N-back tasks should result in significant task activation on the lateral motor cortex region and PFC region respectively. Findings from the first study confirmed the phenomena of contralateral motor cortex activation. In the second study, it is found that larger haemodynamic responses are associated with N-back WM task with higher difficulty.
Observing and Interpreting Correlations in Metabolic Networks

MOTIVATION Metabolite profiling aims at an unbiased identification and quantification of all the metabolites present in a biological sample. Based on their pair-wise correlations, the data obtained from metabolomic experiments are organized into metabolic correlation networks and the key challenge is to deduce unknown pathways based on the observed correlations. However, the data generated is fundamentally different from traditional biological measurements and thus the analysis is often restricted to rather pragmatic approaches, such as data mining tools, to discriminate between different metabolic phenotypes. METHODS AND RESULTS We investigate to what extent the data generated networks reflect the structure of the underlying biochemical pathways. The purpose of this work is 2-fold: Based on the theory of stochastic systems, we first introduce a framework which shows that the emergent correlations can be interpreted as a 'fingerprint' of the underlying biophysical system. This result leads to a systematic relationship between observed correlation networks and the underlying biochemical pathways. In a second step, we investigate to what extent our result is applicable to the problem of reverse engineering, i.e. to recover the underlying enzymatic reaction network from data. The implications of our findings for other bioinformatics approaches are discussed.
The Effect of Bioactive Compounds on In Vitro and In Vivo Antioxidant Activity of Different Berry Juices

Background Berry fruit is known for its high contents of various bioactive compounds. The latter constitute of anthocyanins, flavonols and flavanols and posses high antioxidative activity. The highly dynamic antioxidant system can be evaluated in vitro and in vivo in several model organisms. These measurements represent a good approximation of the real potential of bioactive compounds in the cells of higher eucarions. The aim of the study was thus to determine in vitro and in vivo antioxidant activity of different berry juices, which reportedly contain high amounts of phenolics. Methodology/Principal Findings Five different berry species were collected from several locations in central Slovenia and juice was extracted from each species separately. Juice was assessed for their in vitro and in vivo antioxidant activity. Phenolic profiles of berries were determined with the use of a HPLC/MS system, in vitro antioxidant activity with the DPPH radical scavenging method and in vivo antioxidative activity using Saccharomyces cerevisiae. The highest diversity of individual phenols was detected for bilberry juice. The highest in vitro antioxidant capacity was determined for blackcurrant juice. A decrease in intracellular oxidation compared to control was observed in the following order: blackcurrant < chokeberry = blueberry < bilberry. The results indicate important differences in antioxidant activity of berry juices between in vitro and in vivo studies. Conclusion/Significance In addition to the total content of phenolic compounds entering the cells, a key factor determining antioxidative activity of berry juices is also the ratio between the compounds. Where high content levels of anthocyanins and very low content levels of flavonols and hydroxycinnamic acids were measured a lower intracellular oxidation has been detected. Specifically, intracellular oxidation increased with higher consumption of hydroxycinnamic acids and lower consumption of anthocyanins in the cells. Antioxidative activity also increased when the consumption of analyzed phenols was rather low.
Clinical demographics and long-term prognosis after stroke in patients on chronic haemodialysis. The Okinawa Dialysis Study (OKIDS) Group.

BACKGROUND Stroke is one of the leading causes of death in chronic dialysis patients. However, few epidemiological studies have reported on the demographics and long-term prognosis after stroke. METHODS We have observed the occurrence of stroke in the chronic dialysis population for the past 10 years in Okinawa, Japan. Definite cases of stroke were registered and categorized as cerebral haemorrhage (CB), cerebral infarction (CI), and subarachnoid hemorrhage (SAH). RESULTS Among 3741 chronic dialysis patients (2073 men, 1668 women), 271 patients (164 men, 107 women) had strokes (CB 162, CI 97, SAH 12) at least once during the study period from 1 April 1988 to 31 March 1998. The total duration of observation was 15 pound 748.8 patient-years (males 8990.5, females 6758.3). The incidence of stroke per 1000 patient-years was 17.2 overall, 10.3 for CB, 6.2 for CI, and 0.8 for SAH. Twenty-four per cent of stroke cases occurred within 1 year of starting dialysis therapy, and 57.7% occurred within 5 years after the beginning of therapy. The mean (SD) age at onset of stroke was 59.8 (13.0) years overall, 57.2 (12.6) for CB, 65.0 (12.1) for CI, and 53.6 (13.0) years for SAH. The survival rates after stroke were 53.4% at 1 month, 43.5% at 6 months, 35.7% at 12 months, and 23.2% at 60 months. Patients with diabetes mellitus (DM) had higher incidence of CI and a poorer prognosis than those without DM. CONCLUSION Incidence of stroke was high (17.2 per 1000 patient-years) in the dialysis population of our area and the long-term prognosis after stroke was poor.
A Bayesian framework for crowding effect

In crowding, neighboring distractors impair the visual perception of a presented ta get. We study influences by the configuration of distractors on the bias to perceive the orientation of a target. Our results show that: (a) when distractors are similar to each other but different from target, crowding is decreased; (b) when distractors form a subjective contour, crowding is also reduced. These results illustrate that crowding is weak whenever the target stands out from the context and strong when the target is grouped into the context as a part of a global percept. In addition, we show how a Bayesian model, based on the principle of spatial resolution of attention that is modulated by the large size of receptive fields, can account for the behavioral data.
Bayesian Optimization with Exponential Convergence

This paper presents a Bayesian optimization method with exponential convergence without the need of auxiliary optimization and without the δ-cover sampling. Most Bayesian optimization methods require auxiliary optimization: an additional non-convex global optimization problem, which can be time-consuming and hard to implement in practice. Also, the existing Bayesian optimization method with exponential convergence [1] requires access to the δ-cover sampling, which was considered to be impractical [1, 2]. Our approach eliminates both requirements and achieves an exponential convergence rate.
The Effects of Psychosis Risk Variants on Brain Connectivity: A Review

In light of observed changes in connectivity in schizophrenia and the highly heritable nature of the disease, neural connectivity may serve as an important intermediate phenotype for schizophrenia. However, how individual variants confer altered connectivity and which measure of brain connectivity is more proximal to the underlying genetic architecture (i.e., functional or structural) has not been well delineated. In this review we consider these issues and the relative sensitivity of imaging methodologies to schizophrenia-related changes in connectivity. We searched PubMed for studies considering schizophrenia risk genes AND functional or structural connectivity. Where data was available, summary statistics were used to determine an estimate of effect size (i.e., Cohen’s d). A random-effects meta-analysis was used to consider (1) the largest effect and (2) all significant effects between functional and structural studies. Schizophrenia risk variants involved in neurotransmission, neurodevelopment and myelin function were found to be associated with altered neural connectivity. On average, schizophrenia risk genes had a large effect on functional (mean d = 0.76) and structural connectivity (mean d = 1.04). The examination of the largest effect size indicated that the outcomes of functional and structural studies were comparable (Q = 2.17, p > 0.05). Conversely, consideration of effect size estimates for all significant effects suggest that reported effect sizes in structural connectivity studies were more variable than in functional connectivity studies, and that there was a significant lack of homogeneity across the modalities (Q = 6.928, p = 0.008). Given the more variable profile of effect sizes associated with structural connectivity, these data may suggest that structural imaging methods are more sensitive to a wider range of effects, as opposed to functional studies which may only be able to determine large effects. These conclusions are limited by methodological considerations, and require further investigation involving larger samples, multiple genes, and novel analysis techniques for confirmation.
Determining preferred spawning habitat of the endangered Rio Grande silvery minnow by hydrological manipulation of a conservation aquaculture facility and the implications for management

The endangered Rio Grande silvery minnow (Hybognathus amarus) was induced to spawn in both 2012 and 2013, using hydrological manipulation of a conservation aquaculture facility to create floodplain habitat. Fish responded to the flood by leaving the stream and entered both deep (20–97 cm) and shallow (14–18 cm) low‐velocity off‐channel habitats, spawning in the deep ones; fish did not spawn in the stream. When water level was brought down from flood stage, fry actively moved into the stream 2.5 weeks postspawn. This study supports the hypothesis that this species is a floodplain spawner. The results show that habitat restoration of the Rio Grande to create floodplains is needed for recovery of this species as floodplains are both spawning and nursery habitats. The study provides guidelines about how deep floodplain inundation must inundate for spawning to occur and for the duration of inundation so fry can actively swim with the water when flood waters recede. This project also shows that a conservation facility can be used for all stages of fish's life history. Equally important, it shows that a conservation aquaculture facility can be used to conduct hydrological experiments to determine how an endangered fish will respond to changes in river management.
Online privacy as a collective phenomenon

The problem of online privacy is often reduced to individual decisions to hide or reveal personal information in online social networks (OSNs). However, with the increasing use of OSNs, it becomes more important to understand the role of the social network in disclosing personal information that a user has not revealed voluntarily: How much of our private information do our friends disclose about us, and how much of our privacy is lost simply because of online social interaction? Without strong technical effort, an OSN may be able to exploit the assortativity of human private features, this way constructing shadow profiles with information that users chose not to share. Furthermore, because many users share their phone and email contact lists, this allows an OSN to create full shadow profiles for people who do not even have an account for this OSN. We empirically test the feasibility of constructing shadow profiles of sexual orientation for users and non-users, using data from more than 3 Million accounts of a single OSN. We quantify a lower bound for the predictive power derived from the social network of a user, to demonstrate how the predictability of sexual orientation increases with the size of this network and the tendency to share personal information. This allows us to define a privacy leak factor that links individual privacy loss with the decision of other individuals to disclose information. Our statistical analysis reveals that some individuals are at a higher risk of privacy loss, as prediction accuracy increases for users with a larger and more homogeneous first- and second-order neighborhood of their social network. While we do not provide evidence that shadow profiles exist at all, our results show that disclosing of private information is not restricted to an individual choice, but becomes a collective decision that has implications for policy and privacy regulation.
A Systematic Literature Review of Studies Analyzing Inequalities in Health Expectancy among the Older Population

Aim To collect, organize and appraise evidence of socioeconomic and demographic inequalities in health and mortality among the older population using a summary measure of population health: Health Expectancy. Methods A systematic literature review was conducted. Literature published in English before November 2014 was searched via two possible sources: three electronic databases (Web of Science, Medline and Embase), and references in selected articles. The search was developed combining terms referring to outcome, exposure and participants, consisting in health expectancy, socioeconomic and demographic groups, and older population, respectively. Results Of 256 references identified, 90 met the inclusion criteria. Six references were added after searching reference lists of included articles. Thirty-three studies were focused only on gender-based inequalities; the remaining sixty-three considered gender along with other exposures. Findings were organized according to two leading perspectives: the type of inequalities considered and the health indicators chosen to measure health expectancy. Evidence of gender-based differentials and a socioeconomic gradient were found in all studies. A remarkable heterogeneity in the choice of health indicators used to compute health expectancy emerged as well as a non-uniform way of defining same health conditions. Conclusions Health expectancy is a useful and convenient measure to monitor and assess the quality of ageing and compare different groups and populations. This review showed a general agreement of results obtained in different studies with regard to the existence of inequalities associated with several factors, such as gender, education, behaviors, and race. However, the lack of a standardized definition of health expectancy limits its comparability across studies. The need of conceiving health expectancy as a comparable and repeatable measure was highlighted as fundamental to make it an informative instrument for policy makers.
A High-Resolution Anisotropic Finite-Volume Head Model for EEG Source Analysis

Solution of the electroencephalogram (EEG) forward problem in a realistic head model is necessary for accurate source analysis. Realistic head models are usually derived from volumetric magnetic resonance images that provide a voxel resolution of about 1 mm3 . The availability of an electrical head model with this resolution would therefore be extremely advantageous. Head models with resolution in the millimeter range that incorporate the anisotropic properties of their elements have been formulated with the finite element method (FEM). However, these FEM models are fraught with complications related to irregular grids and meshes, along with the incumbent segmentation problems. Presented here is a finite volume method (FVM) formulation of the realistic head model in cubic elements that can ameliorate some of these problems, can incorporate tissue anisotropy, and is both physically intuitive and simple to implement