Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated information for large complex networks

How does one quantify dynamic complexity in large stochastic networks? While measures of integrated information serve as a good start to address these issues, all existing versions of the measure have been plagued with normalization ambiguities and combinatorial explosions which has hindered applications to large-scale networks. In this paper, we propose a new version of integrated information which resolves all these problems and brings us a step closer to addressing complexity in large biological networks. We also show that our measure is the only one which accounts for the total integrated information of a network. We apply this measure to prototypical networks and interestingly find the existence of complexity resonances in the solutions, which suggests a new way of looking at the informational spectrum of complex dynamical systems. Finally, as a proof of principle, we compute how much information is integrated by the anatomical connectivity network of the human cerebral cortex.
The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments

Abstract During the EUROCarbDB project our group developed the GlycanBuilder and GlycoWorkbench glycoinformatics tools. This short communication summarizes the capabilities of these two tools and updates which have been made since the original publications in 2007 and 2008. GlycanBuilder is a tool that allows for the fast and intuitive drawing of glycan structures; this tool can be used standalone, embedded in web pages and can also be integrated into other programs. GlycoWorkbench has been designed to semi-automatically annotate glycomics data. This tool can be used to annotate mass spectrometry (MS) and MS/MS spectra of free oligosaccharides, N and O-linked glycans, GAGs (glycosaminoglycans) and glycolipids, as well as MS spectra of glycoproteins.
Sulfo- and Oxy-analogues of Arginine: Synthesis, Analysis and Preliminary Biological Screening

A novel methodology for the synthesis of sulfo- and oxy-modified amino acid analogues of arginine (Arg) has been developed using both conventional and polymer assisted synthesis from ready available amino acid precursor. Introduction of guanidine group was made also by the MWA synthesis. The in vitro inhibitory effect of the amino acid analogues on the growth of murine erythroleukemia cells, clone F4N in culture was also studied. (doi: 10.5562/cca1780)
A 60 GHz Frequency Generator Based on a 20 GHz Oscillator and an Implicit Multiplier

This paper proposes a mm-wave frequency generation technique that improves its phase noise (PN) performance and power efficiency. The main idea is that a fundamental 20 GHz signal and its sufficiently strong third harmonic at 60 GHz are generated simultaneously in a single oscillator. The desired 60 GHz local oscillator (LO) signal is delivered to the output, whereas the 20 GHz signal can be fed back for phase detection in a phase-locked loop. Third-harmonic boosting and extraction techniques are proposed and applied to the frequency generator. A prototype of the proposed frequency generator is implemented in digital 40 nm CMOS. It exhibits a PN of -100 dBc/Hz at 1 MHz offset from 57.8 GHz and provides 25% frequency tuning range (TR). The achieved figure-of-merit (FoM) is between 179 and 182 dBc/Hz.
A Fully Automated Robotic System for Microinjection of Zebrafish Embryos

As an important embodiment of biomanipulation, injection of foreign materials (e.g., DNA, RNAi, sperm, protein, and drug compounds) into individual cells has significant implications in genetics, transgenics, assisted reproduction, and drug discovery. This paper presents a microrobotic system for fully automated zebrafish embryo injection, which overcomes the problems inherent in manual operation, such as human fatigue and large variations in success rates due to poor reproducibility. Based on computer vision and motion control, the microrobotic system performs injection at a speed of 15 zebrafish embryos (chorion unremoved) per minute, with a survival rate of 98% (n = 350 embryos), a success rate of 99% (n = 350 embryos), and a phenotypic rate of 98.5% (n = 210 embryos). The sample immobilization technique and microrobotic control method are applicable to other biological injection applications such as the injection of mouse oocytes/embryos and Drosophila embryos to enable high-throughput biological and pharmaceutical research.
The latency-associated transcript of herpes simplex virus type 1 promotes survival and stimulates axonal regeneration in sympathetic and trigeminal neurons

Herpes simplex virus type 1 (HSV-1) primarily infects mucoepithelial tissues of the eye, the orofacial region, and to a lesser extent the genitalia. The virus is retrogradely transported through the axons of sensory and sympathetic neurons to their cell bodies to establishe a life-long latent infection. Throughout this latency period, the viral genome is transcriptionally silent except for a single region encoding the latency-associated transcript (LAT). The function of LAT is still largely unknown. To understand how HSV-1 latency might affect neurons, the authors transfected primary cultures of sympathetic neurons and trigeminal sensory neurons obtained from rat embryos with LAT-expressing plasmids. LAT increased the survival of both sympathetic and trigeminal neurons after induction of cell death by nerve growth factor (NGF) deprivation. Because HSV-1 is transported through axons both after initial infection and during reactivation, the authors considered the possibility that LAT may affect axonal growth. They found that LAT expression increased axonal regeneration by twofold in both types of neurons. Inhibition of the mitogen-activated protein kinase (MAPK) pathway reverses stimulation of both neuronal survival and axonal regeneration, which indicates that these effects are mediated through the MAPK pathway. These data provide evidence that HSV-1 LAT promotes survival of sympathetic as well as trigeminal neurons. The authors show for the first time that LAT stimulates axonal regeneration in both sympathetic and trigeminal neurons.
The RIP1–RIP3 Complex Mediates Osteocyte Necroptosis after Ovariectomy in Rats

Osteocyte apoptosis has been reported to play a central role in bone remodeling. In addition to apoptosis, other mechanisms may be involved in osteocyte loss. This study aimed to investigate the effect of necroptosis on osteocytes in ovariectomized (OVX) rats. Ninety-six female Sprague-Dawley rats were randomly divided into an OVX group and a sham group. At 0, 4, 8 and 12 weeks after surgery, specimens from each group (n = 12 each) were harvested. Bone mineral density (BMD) and body weight were measured. Transmission electron microscopy (TEM) and micro-CT were used to observe the changes in cellular morphology and bone microarchitecture induced by estrogen deficiency. Osteocyte apoptosis and necroptosis were evaluated via TUNEL and immunofluorescence staining for active caspase-3. At 8 weeks after ovariectomy, a greater number of osteocytes with typical necrotic morphological features were TUNEL positive but negative for active caspase-3. Western blotting, quantitative real-time PCR and immunofluorescence assessments demonstrated that the levels of receptor-interacting serine/threonine protein kinase 1 (RIP1) and RIP3 in osteocytes were significantly increased at 8 weeks after ovariectomy. These data are the first to suggest that necroptosis accelerates osteocyte loss under conditions of estrogen deficiency-induced osteoporosis in OVX rats. These findings provide evidence of a potential mechanism through which osteocyte necroptosis is associated with postmenopausal osteoporosis.
In defense of orthonormality constraints for nonrigid structure from motion

In factorization approaches to nonrigid structure from motion, the 3D shape of a deforming object is usually modeled as a linear combination of a small number of basis shapes. The original approach to simultaneously estimate the shape basis and nonrigid structure exploited ortho-normality constraints for metric rectification. Recently, it has been asserted that structure recovery through ortho-normality constraints alone is inherently ambiguous and cannot result in a unique solution. This assertion has been accepted as conventional wisdom and is the justification of many remedial heuristics in literature. Our key contribution is to prove that ortho-normality constraints are in fact sufficient to recover the 3D structure from image observations alone. We characterize the true nature of the ambiguity in using ortho-normality constraints for the shape basis and show that it has no impact on structure reconstruction. We conclude from our experimentation that the primary challenge in using shape basis for nonrigid structure from motion is the difficulty in the optimization problem rather than the ambiguity in ortho-normality constraints.
Able But Not Willing? Teamwork Aptitude and Interest Meet Head-on

In student teams, teamwork aptitude was negatively related to teamwork interest and satisfaction with groups’ project success. Teamwork aptitude was unrelated to overall satisfaction at the team level. These unexpected results from an ongoing study of student teams suggest student teams should be carefully monitored and trained. If you are an instructor who has used group projects in classes, you have probably been met with a range of reactions to the announcement that students would be required to form teams to complete an assignment. Some students smile, some frown, and some wince and groan. Apart from possible individual differences in the expression of emotions, why are there such varying responses to the prospect of working with others? Certainly, teams have become a staple in American organizations; instructors who use group projects in their classes are endeavoring to provide students opportunities to practice working in teams. And, when asked about their work with other students on course assignments, students from different universities queried in a qualitative study reported they had learned about communication, task sharing and conflict resolution in group projects (Colbeck, Campbell, & Bjorklund, 2000). So, why the groans? In this paper, I describe a serendipitous finding from an ongoing research project studying class teams that may operationalize some of the groans and the smiles of students from classroom team projects. This paper reports an unexpected finding from an ongoing research project studying the composition of class teams and the satisfaction of the members of class teams. The original intent of the research project was to assess how surface level (i.e., gender, ethnicity) and deep level (i.e., Big Five personality) diversity would affect team project process and outcomes (e.g., Phillips, Northcraft, & Neale, 2006). This paper does not report on the larger study but on unforeseen results that emerged in early data analysis of the larger data set: Teamwork aptitudes were negatively correlated with measures of attitudes toward teamwork and a self rating of project success; teamwork aptitude was unrelated to the final measure of group satisfaction. This paper describes these findings.
Nonlinear mapping from multi-view face patterns to a Gaussian distribution in a low dimensional space

We investigate into a nonlinear mapping by which multi-view face patterns in the input space are mapped into invariant points in a low dimensional feature space. The invariance to both illumination and view is achieved in two-stages. First, a nonlinear mapping from the input space to a low dimensional feature space is learned from multi-view face examples to achieve illumination invariance. The illumination invariant feature points of face patterns across views are on a curve parameterized by the view parameter, and the view parameter of a face pattern can be estimated from the location of the feature point on the curve by using least squares fit. Then the second nonlinear mapping, which is from the illumination invariant feature space to another feature space of the same dimension, is performed to achieve invariance to both illumination and view. This amounts to do a normalization based on the view estimate. By the two stage nonlinear mapping, multi-view face patterns are mapped to a zero mean Gaussian distribution in the latter feature space. Properties of the nonlinear mappings and the Gaussian face distribution are explored and supported by experiments.
Role of Oxygen Vacancies at the TiO2/HfO2 Interface in Flexible Oxide‐Based Resistive Switching Memory

Flexible memory is highly desirable for data storage in portable wearable electronics. Here, a flexible bilayer TiO2/HfO2‐architecture‐based resistive random access memory (RRAM) is fabricated a on polyethylene naphthalate (PEN) substrate, and exhibits outstanding uniformity, high durability, and excellent mechanical flexibility. The coefficients of variations for high and low resistance state are ≈3.2% and ≈3%, respectively. No performance degradation is observed under mechanical stress with bending radius ranging from 70 to 10 mm. Interestingly, the performance degradation after long‐term stability tests can be recovered. An asymmetric hourglass‐shaped oxygen vacancy (Vo) distribution at the HfO2/TiO2 interface plays a key role in high performance of this flexible RRAM device. The proposed flexible RRAM devices have potential applications in wearable electronics.
Relationship between polymorphism of insulin receptor gene, and adiponectin gene with PCOS

Background: Polycystic ovary syndrome (PCOS) is a complex disease having both genetic and environmental components and candidate genes on obesity and insulin metabolism have been hypothesized to be involved in its etiology. Objective: We examined the possible association of adiponectin and insulin receptor gene polymorphisms with PCOS. Materials and Methods: A total of 186 women with PCOS using NIH criteria and 156 healthy women were recruited. Their samples were genotyped for the polymorphism in exon 17 and 8 of the insulin receptor gene or exon and intron 2 of the adiponectin gene. Results: The distributions of genotypes and alleles of both polymorphisms were not different in women with PCOS and controls. There was no significant differences on the anthropometric and hormonal profiles of various adiponectin and insulin receptor genes polymorphisms among both groups. Conclusion: Adiponectin and insulin receptor gene polymorphisms are not associated with PCOS in a sample of Iranian population.
MARKET OVERLAP AND THE DIRECTION OF EXPORTS - a new approach of assessing the Linder hypothesis

The Linder hypothesis states that countries will trade more intensively with countries that have similar structures of demand. We suggest an alternative method of assessing the hypothesis, incorporating the distribution of income within a country. The variables that we develop capture the similarity in demand structures between two trading partners and the size of the market for which the market overlap is identified. These variables are included in a one-sided gravity model. Results show that similarity in structure of demand act as a catalyst of trade flows between countries and that similarities are more important for the differentiated goods than homogenous goods.
The impact of cardiac feedback on human cognition

Afferent feedback from arterial baroreceptors modulates sensorimotor responses, but it is unknown whether it can also interfere with high-order cognition. In Study One, electrocutaneous stimuli (ranging from non-painful to very painful) were randomly delivered across the cardiac cycle. Pain ratings were highest at R+300 ms, whereas nociceptive reflex responses did not vary. Study Two followed up these findings by presenting the stimuli in blocks of either ascending or descending intensities. Nociceptive responses to painful stimuli were attenuated during systole; pain ratings did not vary regardless of stimulus intensity. Study Three compared both schedules of stimulation independently of cardiac cycle timings. When unpredictable, shocks elicited hypoalgesia but also the highest nociceptive responses, indicating that pain dissociates from nociception under stress. The fourth study examined the effects of moderate exercise-induced cardiovascular arousal on attention control and working memory. Two experiments revealed that working memory and attention are facilitated by moderate exercise. Finally, Study Five assessed Sternberg task performance across the cardiac cycle. Probes presented during systole produced the highest intercept but the shallowest slope. In sum, these studies (a) provide further support for the afferent feedback hypothesis; and (b) extend previous findings obtained with sensorimotor responses to high-order cognition.
Emotional Acuity in Children With and Without Autism Spectrum Disorder

The present study investigated the ability of young children with and without Autism Spectrum Disorder (ASD) to identify emotion in photographs as well as their response to a distress event. Since communication is a core aspect of the disability, alternate methods of assessment were employed in order to investigate emotion understanding and emotion response in children with and without ASD. Thirty-one children with ASD (mean age 48 months) and forty typically developing children (mean age 53 months) participated. A sorting procedure was used to determine participants' ability to identify happy, sad and angry emotions in photographs with and without contextual information. Results suggest that context had no effect on either group. Children with ASD were significantly less likely to correctly sort emotional faces. When witnessing the experimenter in distress, children with ASD showed similar levels of affect matching and a similar pattern in heart rate. Significant differences were found in the eye gaze pattern of the two groups; the typically developing children were more likely to look at the face of the experimenter during the distress event. By reducing the language component required for the emotion identification task and including behavioral and physiological outcome measures to the response to distress paradigm, this study seeks to investigate the unique characteristics of children with ASD without the impediment of their communicative difficulties. These results provide insight into the emotional lives of children with ASD and may shed light on why these children respond differently to emotion than their typically developing peers.
The Nature of Age-Related Decline on the Reading Span Task

We examined the effect of age on working memory with a reading span task (RST) together with other verbal span tasks. Sixty-two participants were divided into three subgroups (young, middle-aged, and elderly). The RST performances were significantly different among all the subgroups. To elucidate which component of the working memory system is affected by age, we performed an analysis of covariance with the scores of simple and complex verbal span tasks as covariates. From the results, we conclude that the difference of the RST performance between the middle-aged and elderly groups reflects a decline in the capacity of the phonological loop, and the difference between the young and middle-aged groups reflects malfunctioning of the central executive system.
A functional analysis of Notch mutations in Drosophila.

The Notch gene encodes a receptor protein that is involved in many processes during development. Its best understood role is during neurogenesis in a process called "lateral inhibition. " However, it has been proposed that Notch also has a role in defining the proneural clusters in the first place. This raises the possibility that the Notch protein is acting as a multifunctional receptor. To test this hypothesis, we have carried out a genetic analysis of molecularly characterized Notch alleles to identify alleles that affect only one of the two proposed functions. Here we present evidence that Notch alleles can be identified that appear to affect the function of Notch during either lateral inhibition or the definition of proneural clusters. In addition our results indicate that there may be discrete regions of the Notch protein required for each function.
Towards a Better Understanding of Bidirectional Search

Three admissible bidirectional search algorithms have been described in the literature: A Cartesian product approach due to Doran, Pohl's BHPA, and Champeaux and Sint's BHFFA2. This paper describes an algorithm, GP, which contains the latter two and others. New admissibility results are obtained. A first order analysis is made comparing the run times of Cartesian product search, two versions of GP, and unidirectional A. The goal is to gain insight on when bidirectional search is useful and direction for seeking better bidirectional search algorithms.
Current perspectives on attachment disorders: Rejoinder and synthesis

Several commentators (e.g., Byrne, Green, Minde, van Ijzendoorn and BakersmanKranenberg) noted the conceptual and practical difficulties in differentiating behaviours associated with Reactive Attachment Disorder from (a) other forms of very insecure behaviour, such as Disorganized attachment, and (b) a variety of clinical phenomena, particularly problems in social and attachment relationships and difficulty in talking and thinking about these relationships (i.e., problems in ‘mentalizing’). With respect to the former, several commentators endorsed the potential conceptual advantages of placing attachment disorder and attachment disorganization on the same spectrum. An advantage of this approach would be to more explicitly link attachment disorders with attachment research on individual differences in normal and high-risk samples. However, although it may be helpful to construct such a spectrum for heuristic purposes, this does not mean that there is a single continuum of disturbance ranging from Secure on one end to a diagnosis of Attachment Disorder on the opposite end. There are two reasons for rejecting, or at least being suspicious about, this particular continuum notion (as distinct from the somewhat looser concept of a spectrum). The first is that we simply do not have the necessary information on how Attachment Disorders connect with individual differences in attachment quality – and indeed if a direct connection can be made. More specifically, several features of the diagnostic formulation of Attachment Disorder are incompatible with the research and theoretical tradition developed by Bowlby, Ainsworth, and others. These incompatibilities need to be resolved, if possible. A second reason for being wary of a continuum is the impression from clinical and research experience that children with an attachment disorder (e.g., defined according to DSM-IV criteria) are, at least in some respects, qualitatively different from those classified as having a Secure or Insecure (even Disorganized) attachment. Most critically, the central concern here is whether or not a selective or discriminating attachment relationship exists between the child and his/her caregiver. This has been posed as a distinction between disorders of attachment vs. disorders of nonattachment (Lieberman & Zeanah, 1995). On the other hand, it would be incorrect to say that this supposed qualitative distinction is evident in all cases. This is the point made by many contributors. Indeed, a real dilemma arises because children with a Disorganized attachment may show similar behavioural features to children with