Miracle-dz/UniFAR-FTUs huggingface dataset:
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

Motivation: Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections. Results: We developed a fully automatic, non-rigid but as-rigid-as-possible registration method for large tiled serial section microscopy stacks. We use the Scale Invariant Feature Transform (SIFT) to identify corresponding landmarks within and across sections and globally optimize the pose of all tiles in terms of least square displacement of these landmark correspondences. We evaluate the precision of the approach using an artificially generated dataset designed to mimic the properties of TEM data. We demonstrate the performance of our method by registering an ssTEM dataset of the first instar larval brain of Drosophila melanogaster consisting of 6885 images. Availability: This method is implemented as part of the open source software TrakEM2 (http://www.ini.uzh.ch/∼acardona/trakem2.html) and distributed through the Fiji project (http://pacific.mpi-cbg.de). Contact: tomancak@mpi-cbg.de
Health benefits of low glycaemic index foods, such as pulses, in diabetic patients and healthy individuals

The present paper covers the health benefits of low glycaemic index foods, such as pulses. Nutritional factors potentially play a crucial role in health and disease. A low-fat, high-carbohydrate diet is often recommended as a part of a healthy life-style. Historical works have shown that carbohydrate foods differ in their ability to affect post-ingestive glycaemia. The glycaemic index concept allows a ranking of carbohydrate-rich foods in terms of their blood glucose raising potential. Pulses are foods with very low glycaemic index values. Numerous studies have documented the health benefits that can be obtained by selecting foods of low glycaemic index. These benefits are of crucial importance in the dietary treatment of diabetes mellitus: glycaemic control is improved as well as several metabolic parameters, such as blood lipids. The results of human studies have been confirmed by animal experiments in the field of diabetes. Diets with low glycaemic index value improve the prevention of coronary heart disease in diabetic and healthy subjects. In obese or overweight individuals, low-glycaemic index meals increase satiety and facilitate the control of food intake. Selecting low glycaemic index foods has also demonstrated benefits for healthy persons in terms of post-prandial glucose and lipid metabolism. Several public health organizations have recently integrated consideration of the glycaemic index in their nutritional recommendations for patients with metabolic diseases and for the general population.
The inactivation of single‐chain urokinase‐type plasminogen activator by thrombin in a plasma milieu: effect of thrombomodulin

Thrombin cleaves single-chain urokinase-type plasminogen activator (scu-PA) into a virtually inactive two-chain form (tcu-PA/T), a process which may contribute to the maintenance of a fresh blood clot. We have examined the inactivation of scu-PA by thrombin in a plasma milieu to get more insight in the physiological relevance of this phenomenon. Citrated pooled normal plasma was treated with thrombin in the absence and presence of thrombomodulin. After an incubation period of 30 min the concentrations of scu-PA and tcu-PA/T were measured using specific bioimmunoassays. The inactivation of scu-PA in citrated plasma was found to be stimulated fourfold by thrombomodulin. Kinetic experiments showed that the inactivation of scu-PA by thrombin in the absence and presence of thrombomodulin occurred rapidly and declined within 1 min as a result of rapid inhibition by antithrombin III (ATIII) and other possible inhibitors. Calcium had no direct effect on the inactivation of scu-PA by exogenously added thrombin in the absence and presence of thrombomodulin. However, recalcification of plasma induced significant inactivation of scu-PA in plasma as a result of endogenous thrombin generation through the contact activation system. This calcium-induced inactivation of scu-PA was completely abolished in the presence of thrombomodulin, most likely as a result of activation of protein C by the complex formed between thrombomodulin and endogenously generated thrombin. Thrombomodulin thus appeared to play a dual role both by stimulating the inactivation of scu-PA by thrombin, and by inhibiting calcium-induced inactivation of scu-PA in plasma. In the plasma from a patient heterozygous for protein C deficiency, thrombomodulin could not prevent calcium-induced generation of tcu-PA/T, whereas the stimulating effect of thrombomodulin predominated instead. This result implied that disturbance of the protein C pathway may lead to the inactivation of substantial amounts of scu-PA in plasma under (patho)physiological circumstances and may provide an additional explanation for the association found between thromboembolism and deficiencies in the protein C pathway. This study shows that the amount of scu-PA that is inactivated in plasma depends mainly on the generation of thrombin and on thrombomodulin. We conclude that the inhibition of scu-PA-induced fibrinolysis appears to be regulated by activation of the coagulation system, providing a link between coagulation and fibrinolysis.
ON THE SIZE AND COMOVING MASS DENSITY EVOLUTION OF EARLY-TYPE GALAXIES

We present a simple, empirically motivated model that simultaneously predicts the evolution of the mean size and the comoving mass density of massive (>1011 M☉) early-type galaxies from z = 2 to the present. First, we demonstrate that some size evolution of the population can be expected simply due to the continuous emergence of early-type galaxies. The Sloan Digital Sky Survey (SDSS) data reveal that in the present-day universe more compact early-type galaxies with a given dynamical mass have older stellar populations. This implies that with increasing look-back time, the more extended galaxies will be more and more absent from the population. In contrast, at a given stellar velocity dispersion, SDSS data show that there is no relation between size and age, which implies that the velocity dispersion can be used to estimate the epoch at which galaxies stopped forming stars, turning into early-type galaxies. Based on this, we define an empirically motivated, redshift-dependent velocity dispersion threshold above which galaxies do not form stars at a significant rate, which we associate with the transformation into early-type galaxies. Applying this “formation” criterion to a large sample of nearby early-type galaxies, we predict the redshift evolution in the size distribution and the comoving mass density. The resulting evolution in the mean size is roughly half of the observed evolution. Then we include a prescription for the merger histories of galaxies between the “formation” redshift and the present, based on cosmological simulations of the assembly of dark matter halos. Such mergers after the transformation into an early-type galaxy are presumably dissipationless (“dry”), where the increase in size is expected to be approximately proportional to the increase in mass. This model successfully reproduces the observed evolution since z ∼ 2 in the mean size and in the comoving mass density of early-type galaxies with mass M > 1011 M☉. We conclude that the recently measured, substantial size evolution of early-type galaxies can be explained by the combined effect of the continuous emergence of galaxies as early types and their subsequent growth through dry merging.
SSERBC 2017: Sclera segmentation and eye recognition benchmarking competition

This paper summarises the results of the Sclera Segmentation and Eye Recognition Benchmarking Competition (SSERBC 2017). It was organised in the context of the International Joint Conference on Biometrics (IJCB 2017). The aim of this competition was to record the recent developments in sclera segmentation and eye recognition in the visible spectrum (using iris, sclera and peri-ocular, and their fusion), and also to gain the attention of researchers on this subject. In this regard, we have used the Multi-Angle Sclera Dataset (MASD version 1). It is comprised of2624 images taken from both the eyes of 82 identities. Therefore, it consists of images of 164 (82×2) eyes. A manual segmentation mask of these images was created to baseline both tasks. Precision and recall based statistical measures were employed to evaluate the effectiveness of the segmentation and the ranks of the segmentation task. Recognition accuracy measure has been employed to measure the recognition task. Manually segmented sclera, iris and peri-ocular regions were used in the recognition task. Sixteen teams registered for the competition, and among them, six teams submitted their algorithms or systems for the segmentation task and two of them submitted their recognition algorithm or systems. The results produced by these algorithms or systems reflect current developments in the literature of sclera segmentation and eye recognition, employing cutting edge techniques. The MASD version 1 dataset with some of the ground truth will be freely available for research purposes. The success of the competition also demonstrates the recent interests of researchers from academia as well as industry on this subject.
Glucose-6-phosphate dehydrogenase – beyond the realm of red cell biology

Abstract Glucose-6-phosphate dehydrogenase (G6PD) is critical to the maintenance of NADPH pool and redox homeostasis. Conventionally, G6PD deficiency has been associated with hemolytic disorders. Most biochemical variants were identified and characterized at molecular level. Recently, a number of studies have shone light on the roles of G6PD in aspects of physiology other than erythrocytic pathophysiology. G6PD deficiency alters the redox homeostasis, and affects dysfunctional cell growth and signaling, anomalous embryonic development, and altered susceptibility to infection. The present article gives a brief review of basic science and clinical findings about G6PD, and covers the latest development in the field. Moreover, how G6PD status alters the susceptibility of the affected individuals to certain degenerative diseases is also discussed.
Exploring the Role of Affect and Evaluative Beliefs in the Emergence of Workplace Attitude: The Case of Organizational Commitment

Affective events theory is used to examine the relationships between workplace events, affect and the emergence of attitude. We discuss the relationships between relational and transactional contracts, organizational commitment, and trust as a mediator. We propose that organizational commitment is a function of affective and belief antecedents that may influence attitude independently or together.
rpS6 regulates blood–testis barrier dynamics through Akt-mediated effects on MMP-9

ABSTRACT Mammalian target of rapamycin complex 1 (mTORC1) is an emerging regulator of blood–tissue barriers that utilizes ribosomal protein S6 (rpS6) as the downstream signaling molecule. To explore the role of rpS6 in blood–testis barrier (BTB) function, a constitutively active quadruple rpS6 phosphomimetic mutant was constructed in mammalian expression vector and overexpressed in Sertoli cells cultured in vitro that mimicked the BTB in vivo. Using this quadruple phosphomimetic mutant, phosphorylated (p)-rpS6 was shown to disrupt IGF-1/insulin signaling, thereby abolishing Akt phosphorylation, which led to an induction of MMP-9. This increase in MMP-9 secretion perturbed the Sertoli cell tight junction permeability barrier by proteolysis-mediated downregulation of tight junction proteins at the BTB. These findings were confirmed by the use of a specific MMP-9 inhibitor that blocked the disruption of the tight junction permeability barrier by the rpS6 mutant. Additionally, RNA interference (RNAi)-mediated Akt silencing was able to mimic the results of rpS6 mutant overexpression in Sertoli cells, further confirming this p-rpS6–Akt–MMP-9 signaling pathway. In conclusion, these data support a new concept of mTORC1-mediated BTB regulation, that is possibly also applicable to other blood–tissue barriers.
Deuterium studies in normal man. I. The rate of synthesis of serum cholesterol. II. Measurement of total body water and water absorption.

The rate of synthesis of serum cholesterol may be measured by determining the rate at which deuterium is incorporated into the serum cholesterol when an elevated deuterium concentration is maintained at a steady level in the body water. The rise in deuterium concentration in the serum cholesterol represents the appearance in the circulation of newly synthesized cholesterol molecules. The labeled cholesterol is formed from precursors which have derived their deuterium from the labeled body water (1). Previous studies have shown that about half of the stably bound hydrogen atoms of cholesterol synthesized in the body are derived from body water. When non-isotopic cholesterol is present in the diet, it will dilute the deuteriocholesterol formed in the body and result in a lower maximum isotope concentration in the serum cholesterol. This maximum isotope concentration is ascertained experimentally by determining the maximum isotope concentration which is reached on prolonged maintenance of a steady deuterium concentration in the body water. The time required to reach 50 per cent of this maximum deuterium concentration is the half life time, tt, of serum cholesterol, i.e. the time required for half the serum cholesterol molecules present in the circulation to be synthesized. In an individual in the steady state, the rate of cholesterol synthesis is equal to the rate of cholesterol degradation. Consequently, tt is also the time required for the disappearance of half the serum cholesterol molecules which have been formed at any one time. This report is concerned with the study of the rate of synthesis (and degradation) of serum cholesterol in a normal man. Previous studies in mice have revealed a tt for total body cholesterol of 15 to 25 days (1). By maintaining a steady concentration of deuterium in the body water and by measuring the time required for the serum cholesterol to attain 50 per cent of the maximum concentration of deuterium, a value of about 8 days for
MMT - A pathway modeling tool for data from rapid sampling experiments

The identification of metabolic regulation is a major concern in metabolic engineering. Metabolic regulation phenomena depend on intracellular compounds such as enzymes, metabolites and cofactors. A complete understanding of metabolic regulation requires quantitative information about these compounds under in vivo conditions. This quantitative knowledge in combination with the known network of metabolic pathways allows the construction of mathematical models that describe the dynamic changes in metabolite concentrations over time. Rapid sampling combined with pulse experiments is a useful tool for the identification of metabolic regulation owing to the transient data they provide. Enzymatic tests in combination with ESI-LC-MS (Electrospray Ionization Liquid Chromatographic Tandem Mass Spectrometry) and HPLC measurements have been used to identify up to 30 metabolites and nucleotides from rapid sampling experiments. A metabolic modeling tool (MMT) that is built on a relational database was developed specifically for analysis of rapid sampling experiments. The tool allows to construct complex pathway models with information stored in the relational database. Parameter fitting and simulation algorithms for the resulting system of Ordinary Differential Equations (ODEs) are part of MMT. Additionally explicit sensitivity functions are calculated. The integration of all necessary algorithms in one tool allows fast model analysis and comparison. Complex models have been developed to describe the central metabolic pathways of Escherichia coli during a glucose pulse experiment.
Serious games and emotion teaching in autism spectrum disorders: a comparison with LIFEisGAME project

We found 18 computer games, but only 6 showed empirically validated/published results. Majority had no reference to research work and no professionals of education or psychology were involved in game design. Technology is a useful resource for Autism Spectrum Disorders (Golan & Baron-Cohen 2006), but research in this topic is necessary to avoid the misuse of non-scientific tools as valid, that can lead to counter-productive intervention. LIFEisGAME has the advantage of being a computer game that is empirically and theoretically grounded, uses front line technology and includes a multidisciplinary team of professional in order to achieve scientific validation. 4. Results
ALTERED AUTONOMIC BALANCE IN NORMAL TENSION GLAUCOMA

Objective: To study autonomic imbalance if any in normal tension glaucoma (NTG)patients by heart rate variability (HRV)and head-up tilt (HUT)test. Methods: The study subjects of age between 45 and 65 years of either sex comprised 20 patients with NTG (Group ІІ)and 20 age- and sex-matched healthy controls (Group І). Different variables of time and frequency domain of HRV were analyzed at rest, during HUT and the recovery period. R esults: Highly significant decrease in value of root mean square successive difference observed in Group ІІ (p<0.000)in comparison to controls. The high-frequency variables (HF [nu]and HF [ms2])were significantly less (p<0.000)and low frequency (LF)/HF ratio was significantly high (p<0.000) in Group ІІ. C onclusion: During stress test, i.e., HUT there was the greater withdrawal of parasympathetic input to heart; hence, there was relatively over sympathetic activity due to sympatho-vagal imbalance. Ke ywords: Stress test, Sympatho-vagal imbalance, Autonomic function test.
1 Cancer patients ’ respect experiences in relation to perceived communication behaviours from hospital staff : analysis of the 2012-2013 National Cancer Patient Experience Survey . Running title : Cancer patients ’ respect experiences

Purpose: Respect experiences are poorly understood despite respect being central to professionalism in healthcare and patient well-being, and needed for optimal patient care. This study explores which patient-perceived communication behaviours from hospital staff contribute most to cancer patients’ respect experiences and account for variation in their experience by socio-demographic and clinical characteristics. Methods: Secondary analysis of data from the 2012-2013 National Cancer Patient Experience Survey of 45191 patients with a primary cancer diagnosis treated in English National Health Service trusts providing adult acute cancer services who provided data on experienced respect and dignity. Results: Both autonomy-supportive and caring/emotionally sensitive behaviours were associated with reported respect, although the latter showed stronger associations and accounted for most differences in reports of respect between patient groups. Differences in respect were found by gender, race/ethnicity, age, the presence of long-standing conditions, treatment response, time since first treated for cancer (p<.001), employment and type of cancer (p<.05). Conclusions: The study questions the tendency to conceptualise respect primarily in terms of autonomy-supportive behaviours and shows the relative contribution of autonomy-supportive and caring/emotionally sensitive behaviours in explaining disparities in respect experiences. More attention should be paid to affective communication behaviours from hospital staff to reduce disparities in respect experiences.
American Cancer Society Guideline for Human Papillomavirus (HPV) Vaccine Use to Prevent Cervical Cancer and Its Precursors

The American Cancer Society (ACS) has developed guidelines for the use of the prophylactic human papillomavirus (HPV) vaccine for the prevention of cervical intraepithelial neoplasia and cervical cancer. These recommendations are based on a formal review of the available evidence. They address the use of prophylactic HPV vaccines, including who should be vaccinated and at what age, as well as a summary of policy and implementation issues. Implications for screening are also discussed.
Performance assessment of morphological dynamic link architecture under optimal and real operating conditions

In this paper, the performance of morphological dynamic link architecture (MDLA) is assessed under optimal and real operating conditions. It is shown that MDLA achieves a very low equal error rate on the extended M2VTS database which contains 295 persons’ video data in 8 shots recorded under optimal conditions. However, its performance severely deteriorates, when it is applied to the IBERMATICA database that has been recorded under conditions simulating a real access-control to an automatic teller machine. The compensation for the image variations attributed to the variable recording conditions, i.e., changes in illumination, face size differences and varying face position, is addressed next. The use of simple and powerful pre-processing techniques aiming at compensating for the aforementioned variations prior to the application of MDLA is proposed. The first results obtained indicate that the proposed approach overcomes the image variations and stabilizes the performance of MDLA.
Understanding physical activity maintenance in breast cancer survivors.

OBJECTIVES To examine predictors of physical activity (PA) 6 months after a randomized controlled trial. METHODS Breast cancer survivors (N=377) completed assessments at baseline, postintervention, and 6 months after the intervention. Data were collected on demographic, medical, psychosocial, motivational, and behavioral variables at baseline, postintervention, and 6 months. RESULTS Survivors meeting PA guidelines at baseline (OR = 5.54, 95% CI = 2.99-9.82, P < 0.001) and postintervention (OR = 2.92, 95% CI = 1.63-5.23, P < 0.001) had a greater likelihood of meeting PA guidelines at 6 months follow-up. CONCLUSIONS Interventions promoting PA maintenance should focus on optimizing PA behavior, psychosocial functioning, and motivation.