Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian period lengths of lipid synthesis mutants (cel, chol-1) of Neurospora show defective temperature, but intact pH-compensation

The influence of extracellular pH on the circadian sporulation rhythm of Neurospora crassa has been investigated for the mutants chol-1 and cel. Both mutants have a defect in the lipid synthesis pathway and require either choline or palmitate, respectively, as supplements for normal growth. The chol-1 and cel mutants also show an impaired temperature-compensation when growing on minimal medium. We investigated the possible correlation between loss of temperature- and pH-compensation in cel and chol-1 similar to the correlation found earlier for the frq7 mutant. Our results show that the cel and the chol-1 mutants, although defective in temperature-compensation have an intact pH-compensation of their circadian rhythms. At present, the products of the frq-locus are the only components of the clock that affect the sporulation rhythm of Neurospora both through pH- and temperature-compensation.
An implementation of spatial algorithm to estimate the focus map from a single image

In this paper, the implementation to estimate the focus map spatially based on the intentional reblur of one image, which is the only input data, is presented. This enables flexible computation in the spatial domain, rather than the frequency domain. The gradient magnitude term widely used in image processing was used to derive a ratio map. The pixels closer to the focal point of the camera were on the thinner edge in the proposed ratio map. Oppositely, The edge was wider the when the pixels were far from the focal point. The core of proposed algorithm is introduced and the experimental results demonstrate the enhanced effectiveness, quality, and precision of the proposed algorithm.
The Domain of the Replicators

Do cultural phenomena undergo evolutionary change, in a Darwinian sense? If so, is evolutionary game theory (EGT) the best way to study them? Opinion on these questions is sharply divided. Proponents of EGT argue that it offers a unified theoretical framework for the social sciences, while critics even deny that Darwinian models are appropriately applied to culture. To evaluate these claims, we examine three facets of cultural evolution: (i) cultural traits that evolve by Darwinian selection, (ii) cultural traits that affect biological fitness, and (iii) coevolution of culture and biology, where selection in one affects evolutionary outcomes in the other. For each of these cases, the relevance of EGT depends on whether its assumptions are met. Those assumptions are quite restrictive: selection is constant, time horizons are deep, the external environment is not part of the game, and neutral processes such as drift are irrelevant. If these conditions are not met, other evolutionary models such as neutrality, coalescence theory, or niche construction may prove more appropriate. We conclude that Darwinian processes can occur in all three types of cultural or biological change. However, exclusive reliance on EGT can obscure the respective roles of selective and neutral processes.
H3N2 influenza viruses in humans: Viral mechanisms, evolution, and evaluation

ABSTRACT Annual seasonal influenza vaccines are composed of two influenza A strains representing the H1N1 and H3N2 subtypes, and two influenza B strains representing the Victoria and Yamagata lineages. Strains from these Influenza A and Influenza B viruses currently co-circulate in humans. Of these, strains associated with the H3N2 subtype are affiliated with severe influenza seasons. H3N2 influenza viruses pre-dominated during 3 of the last 5 quite severe influenza seasons. During the 2016/2017 flu season, the H3N2 component of the influenza vaccine exhibited a poor protective efficacy (∼28–42%) against preventing infection of co-circulating strains. Since their introduction to the human population in 1968, H3N2 Influenza viruses have rapidly evolved both genetically and antigenically in an attempt to escape host immune pressures. As a result, these viruses have added numerous N-linked glycans to the viral hemagglutinin (HA), increased the overall net charge of the HA molecule, changed their preferences in receptor binding, and altered the ability of neuraminidase (NA) to agglutinate red blood cells prior to host entry. Over time, these adaptations have made characterizing these viruses increasingly difficult. This review investigates these recent changes in modern H3N2 influenza viruses and explores the methods that researchers are currently developing in order to study these viruses.
Revisiting the vicious circle of dry eye disease: a focus on the pathophysiology of meibomian gland dysfunction

Meibomian gland dysfunction (MGD) is the most frequent cause of dry eye disease (DED). Eyelid inflammation, microbial growth, associated skin disorders as well as potentially severe corneal complications culminate to make MGD a complex multifactorial disorder. It is probable that MGD is a heterogeneous condition arising from any combination of the following five separate pathophysiological mechanisms: eyelid inflammation, conjunctival inflammation, corneal damage, microbiological changes and DED resulting from tear film instability. The pathogenesis of both MGD and DED can be described in terms of a ‘vicious circle’: the underlying pathophysiological mechanisms of DED and MGD interact, resulting in a double vicious circle. The MGD vicious circle is self-stimulated by microbiological changes, which results in increased melting temperature of meibum and subsequent meibomian gland blockage, reinforcing the vicious circle of MGD. Meibomian gland blockage, dropout and inflammation directly link the two vicious circles. MGD-associated tear film instability provides an entry point into the vicious circle of DED and leads to hyperosmolarity and inflammation, which are both a cause and consequence of DED. Here we propose a new pathophysiological scheme for MGD in order to better identify the pathological mechanisms involved and to allow more efficient targeting of therapeutics. Through better understanding of this scheme, MGD may gain true disease status rather than being viewed as a mere dysfunction.
Subjective Well-Being Is Modulated by Circadian Phase, Sleep Pressure, Age, and Gender

Subjective well-being largely depends on mood, which shows circadian rhythmicity and can be linked to rhythms in many physiological circadian markers, such as melatonin and cortisol. In healthy young volunteers mood is influenced by an interaction of circadian phase and the duration of time awake. The authors analyzed this interaction under differential sleep pressure conditions to investigate age and gender effects on subjective well-being. Sixteen healthy young (8 women, 8 men; 20-35 years) and 16 older volunteers (8 women, 8 men; 55-75 years) underwent a 40-h sleep deprivation (high sleep pressure) and a 40-h nap protocol (low sleep pressure) in a balanced crossover design under constant routine conditions. Mood, tension, and physical comfort were assessed by visual analogue scales during scheduled wakefulness, and their average formed a composite score of well-being. Significant variations in well-being were determined by the factors “age,” “sleep pressure,” and “circadian phase. ” Well-being was generally worse under high than low sleep pressure. Older volunteers felt significantly worse than the young under both experimental conditions. Significant interactions were found between “sleep pressure” and “age,” and between “sleep pressure” and “gender. ” This indicated that older volunteers and women responded with a greater impairment in well-being under high compared with low sleep pressure. The time course of well-being displayed a significant circadian modulation, particularly in women under high sleep pressure conditions. The results demonstrate age- and/or gender-related modifications of well-being related to sleep deprivation and circadian phase and thus point to specific biological components of mood vulnerability.
Echocardiographic Evaluation of Cardiac Structural and Functional Changes in Hepatitis C Positive Non-Alcoholic Liver Cirrhosis Patients and Their Plasma NT-ProBNP Levels

Background: Cirrhotic cardiomyopathy (CC) refers to cardiac structural, functional, and electrophysiological changes in liver cirrhosis (LC) patients. Emerging role of natruretic peptides in screening LC patients for development of CC was suggested. The aim of this study was to assess structural and functional cardiac changes in hepatitis C positive nonalcoholic (LC) patients and Nterminal pro brain natriuretic peptides (NTproBNP) blood levels in these patients. Methods: Forty hepatitis C positive LC patients classified according to their child Pugh score underwent transthorathic echocardiographic assessment of cardiac chambers dimensions, and left ventricular functions. Estimation of plasma NT-proBNP levels of these patients and 10 healthy age and gender matched healthy control subjects was done. Results: Child-Pugh C LC patients have significantly higher mean left ventricular end diastolic (LVEDD) and end systolic dimensions (LVESD) compared to those of ChildPugh A and B LC patients. LV systolic function was preserved in the three ChildPugh groups, while diastolic dysfunction was detected in 78.5% of ChildPugh C patients. Mean plasma NT-proBNP level was significantly higher in Child-Pugh C patients compared to mean plasma levels in ChildPugh A and B patients. ProBNP plasma levels correlated significantly with serum albumin, bilirubin, creatinine, international normalized ratio, Child-Pugh score, LVESD, LVEDD, left atrial and right ventricular diameters. Conclusion: Child-Pugh C LC patients suffered of cardiac structural changes associated with diastolic dysfunction and raised mean ProBNP plasma level but preserved systolic function. NT-ProBNP levels correlated significantly with echocardiographic changes and ChildPugh score. [Manal Eldeeb, Ragai M. F. R. Fouda, Mona M.R. Hammady and Laila Rashed. Echocardiographic Evaluation of Cardiac Structural and Functional Changes in Hepatitis C Positive Non-Alcoholic Liver Cirrhosis Patients and Their Plasma NT-Probnp Levels. Life Science Journal 2012; 9(1):786-792]. (ISSN: 1097-8135). http://www.lifesciencesite. com.113
SetCoLa: High-Level Constraints for Graph Layout

Constraints enable flexible graph layout by combining the ease of automatic layout with customizations for a particular domain. However, constraint-based layout often requires many individual constraints defined over specific nodes and node pairs. In addition to the effort of writing and maintaining a large number of similar constraints, such constraints are specific to the particular graph and thus cannot generalize to other graphs in the same domain. To facilitate the specification of customized and generalizable constraint layouts, we contribute SetCoLa: a domain-specific language for specifying high-level constraints relative to properties of the backing data. Users identify node sets based on data or graph properties and apply high-level constraints within each set. Applying constraints to node sets rather than individual nodes reduces specification effort and facilitates reapplication of customized layouts across distinct graphs. We demonstrate the conciseness, generalizability, and expressiveness of SetCoLa on a series of real-world examples from ecological networks, biological systems, and social networks. CCS Concepts •Human-centered computing → Graph drawings;
A Meta-Analysis of Component Treatment Studies: Are the Parts as Good as the Whole?

A META-ANALYSIS OF COMPONENT TREATMENT STUDIES: ARE THE PARTS AS GOOD AS THE WHOLE? by Erin Jane Clarke December 2011 Psychotherapy has been proven effective in treating a variety of mental health issues. However, there is disagreement in psychotherapy research about whether or not factors common to all psychotherapies or specific ingredients within a treatment package are responsible for successful treatment outcomes. Component studies are research designs specifically aimed at identifying the mechanisms of change in a full treatment package. Component studies do this by comparing the differences in outcome among dismantled treatment components and the full treatment protocol. The present metaanalytic review of component studies examined whether or not differences between these two treatment groups generally exist. Fifty-nine component studies were analyzed to determine the difference in the outcome between dismantled treatments and full treatment packages. Studies were coded on a number of variables including sample size, intervention type, treatment problem, gender, and age. As hypothesized, results from 59 comparisons of post-treatment score differences revealed that there are not differences between the full treatment package and the component treatment (d = -.005). These results mirrored the findings from Ahn and Wampold’s (2001) original meta-analysis of 20 component studies. However, there was significant heterogeneity among these studies, with treatment effectiveness moderated by age (i.e., older clients benefiting more from
Medical schools should be prioritising nutrition and lifestyle education

Would you expect a junior doctor to be confident giving basic advice and care for the most common and fatal diseases? Of course you would. The National Institute for Health and Care Excellence guidelines state that a first line intervention for diabetes, obesity, and high cholesterol is to give ‘lifestyle advice’—but this phrase is so vague that it is left up to doctors and patients to define it and, potentially, ignore it. In 2008 and 2009, more than 75% of American junior physicians felt inadequately trained to counsel patients on diet and physical activity.1 The picture is reportedly similar in the UK.2 In Tomorrow’s Doctors, the General Medical Council requires qualifying medical students to understand the role of diet in health promotion and disease prevention, which includes being nutritionally competent. Internationally, this knowledge is lacking in medical training. Just 27% of US medical schools provided the agreed minimum of 25 hours of nutrition education in 2008.3 A recent study of European medical schools was slightly more optimistic, suggesting that nutrition education was a requirement in 68.8% of …
Quantum correlations in a clusterlike system

We discuss a clusterlike one-dimensional system with triplet interaction. We study the topological properties of this system. We find that the degeneracy depends on the topology of the system and is well protected against external local perturbations. All these facts show that the system is topologically ordered. We also find a string order parameter to characterize the quantum phase transition. Besides, we investigate two-site correlations including entanglement, quantum discord, and mutual information. We study the different divergence behaviors of the correlations. The quantum correlation decays exponentially in both topological and magnetic phases, and diverges in reversed power law at the critical point. And we find that in topological order systems, the global difference of topology induced by dimension can be reflected in local quantum correlations.
Quantification of Elemental Distribution in Spherical Core-Shell Nanoparticles Measured by STEM-EDX

Quantum dots exhibit many interesting and useful size-dependent optoelectronic properties and are used extensively in fields ranging from optical displays to biological imaging. By adding shell structures to these quantum dots, many properties may be improved, including mitigation of surface effects, reduction in blinking, and control of spacing between deposited particles. Alternatively, core/shell structures can be fabricated to create various types of band alignment between the core and shell materials: one example is type-II confinement, which has been studied systems such as Ge/Si and CdTe/CdSe core/shell particles. The optical properties of these systems are affected by the quality of the interface between the two materials. As such, interfacial broadening between the core and shell is an important parameter to measure and control in these systems. This elemental distribution, while important, has proven to be difficult to accurately assess. In this study, we use plasma-grown spherical Ge/Si core/shell nanoparticles as a test case for scanning transmission electron microscopy–energy dispersive X-ray (STEM-EDX) analysis of the core/shell elemental distribution.
Use of Super-resolution Immunofluorescence Microscopy to Analyze Tight Junction Protein Interactions in situ

Sites of intercellular contact are regulated by structures known as junctions. Among the several classes of intercellular junctions are tight junctions that enable epithelia to form barriers by controlling the permeability of soluble molecules, water and ions across extracellular contacts between cells [1]. Tight junctions are composed of a complex of transmembrane proteins linked to the actin cytoskeleton by cytoplasmic scaffold proteins. Paracellular permeability is directly controlled by transmembrane proteins called claudins [2]. There are about two dozen different human claudin genes; tissue-specific expression of claudins confers distinct permeability to different epithelia. Most claudins directly bind to the scaffold protein zonula occludens-1 (ZO-1) that, in turn, binds to cortical actin which promotes tight junction formation [3]. This is just one of the many protein-protein interactions that are required to form fully functional junctions.
Eye Movements in Risky Choice

Abstract We asked participants to make simple risky choices while we recorded their eye movements. We built a complete statistical model of the eye movements and found very little systematic variation in eye movements over the time course of a choice or across the different choices. The only exceptions were finding more (of the same) eye movements when choice options were similar, and an emerging gaze bias in which people looked more at the gamble they ultimately chose. These findings are inconsistent with prospect theory, the priority heuristic, or decision field theory. However, the eye movements made during a choice have a large relationship with the final choice, and this is mostly independent from the contribution of the actual attribute values in the choice options. That is, eye movements tell us not just about the processing of attribute values but also are independently associated with choice. The pattern is simple—people choose the gamble they look at more often, independently of the actual numbers they see—and this pattern is simpler than predicted by decision field theory, decision by sampling, and the parallel constraint satisfaction model. © 2015 The Authors. Journal of Behavioral Decision Making published by John Wiley & Sons Ltd.
ICSV 14 Cairns • Australia 9-12 July , 2007 NON LINEAR RESPONSE OF BEAMS USING FINITE ELEMENT METHOD WITH SYMPLECTIC INTEGRATION SCHEME

The beam finite element matrices are formed with the assumption that it is subjected to large deflection with small strain and rotation. The finite element equations are represented in Hamiltonian form and are solved by the appropriate symplectic integration scheme. The induced axial forces are not averaged and the first second and third order stiffness matrices are formed to incorporate the effect of axial force. All conservative laws are observed during the numerical integration. The response of the beam is studied for free and forced vibration with un-damping cases.
Qualitative Tracking Performance Evaluation without Ground-Truth

We present a qualitative tracking performance evaluation algorithm without ground-truth, where several representative frames are automatically selected and visualized in a principled way. Although tracking algorithms are typically evaluated by quantitative scores based on predefined measures, qualitative evaluation is also useful especially when the ground-truth of a target state is unavailable or unreliable. However, there is no prior study on how to present frames for better qualitative evaluation of tracking algorithms. Motivated by this fact, we propose an unbiased frame selection technique, where salient and unique features in tracking results are captured effectively. Our method identifies a set of representative frames by 1) analyzing the sequence structure using manifold learning, and 2) selecting frames by formulating the task as a facility location problem. By presenting the manifold and the selected frames, one can understand the sequence structure as well as the characteristics of tracking results. The effectiveness of our method is illustrated with single and multiple tracking results for sequences without ground-truth.
Essential Nutrient Interactions: Does Low or Suboptimal Magnesium Status Interact with Vitamin D and/or Calcium Status?

Although much is known about magnesium, its interactions with calcium and vitamin D are less well studied. Magnesium intake is low in populations who consume modern processed-food diets. Low magnesium intake is associated with chronic diseases of global concern [e.g., cardiovascular disease (CVD), type 2 diabetes, metabolic syndrome, and skeletal disorders], as is low vitamin D status. No simple, reliable biomarker for whole-body magnesium status is currently available, which makes clinical assessment and interpretation of human magnesium research difficult. Between 1977 and 2012, US calcium intakes increased at a rate 2–2.5 times that of magnesium intakes, resulting in a dietary calcium to magnesium intake ratio of >3.0. Calcium to magnesium ratios <1.7 and >2.8 can be detrimental, and optimal ratios may be ∼2.0. Background calcium to magnesium ratios can affect studies of either mineral alone. For example, US studies (background Ca:Mg >3.0) showed benefits of high dietary or supplemental magnesium for CVD, whereas similar Chinese studies (background Ca:Mg <1.7) showed increased risks of CVD. Oral vitamin D is widely recommended in US age-sex groups with low dietary magnesium. Magnesium is a cofactor for vitamin D biosynthesis, transport, and activation; and vitamin D and magnesium studies both showed associations with several of the same chronic diseases. Research on possible magnesium and vitamin D interactions in these human diseases is currently rare. Increasing calcium to magnesium intake ratios, coupled with calcium and vitamin D supplementation coincident with suboptimal magnesium intakes, may have unknown health implications. Interactions of low magnesium status with calcium and vitamin D, especially during supplementation, require further study.