Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Analysis of Nocturnin, a Circadian Deadenylase, at Maternal-to-zygotic Transition in Mice

Abstract Degradation of maternally stored mRNAs after fertilization is an essential process for mammalian embryogenesis. Maternal mRNA degradation depending on deadenylases in mammalian early embryos has been mostly speculated, rather than directly demonstrated. Previously, we found that gene expression of nocturnin, which functions as a circadian clock-controlled deadenylase in mammalian cells, was clearly changed during the maternal-to-zygotic transition (MZT). Here, we investigated the possible role of nocturnin during mouse MZT. First, we examined the expression profile and localization of nocturnin in mouse oocytes and early embryos. The abundance of Nocturnin mRNA level was significantly decreased from the MII to 4-cell stages and slightly increased from the 8-cell to blastocyst stages, whereas the Nocturnin protein level was almost stable in all examined cells including GV and MII oocytes and early embryos. Nocturnin was localized in both the cytoplasm and the nucleus of all examined cells. We then examined the effect of loss or gain of Nocturnin function on early embryonic development. Knockdown of Nocturnin by injection of Nocturnin antisense expression vector into 1-cell embryos resulted in the delay of early embryonic development to the early blastocyst stage. Moreover, Nocturnin-overexpressed embryos by injection of Nocturnin expression vector impaired their development from the 1-cell to 2-cell or 4-cell stages. These results suggest that precise expression of nocturnin is critical to proper development of early mouse embryos. Functional analysis of nocturnin may contribute to the understanding of the possible role of the deadenylase at mouse MZT.
Attention approximation of mobile users towards their environment

Public environments are increasingly equipped with interactive features, such as electronic maps for way finding, dynamic information displays or animated advertisements. Understanding the attention patterns of users within these environments is important for the design and evaluation of such interactive elements. We present a modelling approach based on dynamic adaptation of the users' field-of-view, bottom-up visual saliency calculation and task-dependent semantic interest modeling that allows approximating the attention of users with regard to a photorealistic 3D-model. This improved availability of attention information can help to design more usable navigation systems, identify problems for user groups with special needs and support the design of seamless attention switches between information elements.
Hysteresis and transient behavior in current–voltage measurements of hybrid-perovskite absorber solar cells

Hybrid organo-metal halide perovskites are an exciting new class of solar absorber materials and have exhibited a rapid increase in solar cell efficiencies throughout the past two years to over 17% in both meso-structured and thin-film device architectures. We observe slow transient effects causing hysteresis in the current–voltage characterization of these devices that can lead to an over- or underestimation of the solar cell device efficiency. We find that the current–voltage (IV) measurement scan direction, measurement delay time, and light and voltage bias conditions prior to measurement can all have a significant impact upon the shape of the measured IV light curves and the apparent device efficiency. We observe that hysteresis-free light IV curves can be obtained at both extremely fast and slow voltage scan rates but only in the latter case are quasi-steady-state conditions achieved for a valid power conversion efficiency measurement. Hysteretic effects are also observed in devices utilizing alternative selective contacts but differ in magnitude and time scale, suggesting that the contact interfaces have a big effect on transients in perovskite-absorber devices. The transient processes giving rise to hysteresis are consistent with a polarization response of the perovskite absorber that results in changes in the photocurrent extraction efficiency of the device. The strong dependence of the hysteresis on light and voltage biasing conditions in thin film devices for a period of time prior to the measurement suggests that photo-induced ion migration may additionally play an important role in device hysteresis. Based on these observations, we provide recommendations for correct measurement and reporting of IV curves for perovskite solar cell devices.
Is Sickle Cell Anemia a Neglected Tropical Disease?

Governments and philanthropic organizations collectively pour hundreds of millions of dollars annually into the prevention and treatment of a select group of life-threatening infectious diseases that includes malaria, HIV/AIDS, and tuberculosis. The merits of these high-profile programs are indisputable, yet emerging interest in traditionally neglected tropical diseases (NTDs) suggests that the lights of global awareness and medical treatment are now shining more brightly on lesser-known infections, which remain scourges for more than a billion persons worldwide [1]. More recently, noncommunicable diseases also have garnered attention and funding as causes of serious morbidity and mortality, including diabetes, cardiovascular disease, and cancer [2]. Standing awkwardly alone between these traditionally communicable and noncommunicable diseases, however, is sickle cell anemia (SCA). As a congenital but noninfectious disease with high childhood mortality, SCA is a serious health condition that represents a silent killer of children with enormous global burden. Only with improved recognition and a concerted worldwide effort can we begin to address this disparity and offer life-saving interventions to millions of affected children. Should SCA be considered an NTD? From the viewpoint of this hematologist, an NTD can be operationally defined as any serious medical affliction with the following characteristics: (1) worldwide distribution, typically affecting millions; (2) highest burden among the most impoverished and disadvantaged populations; (3) serious morbidity, diminished quality of life, and even mortality; (4) comorbidity for other life-threatening diseases; (5) relatively simple diagnostic testing; and (6) inexpensive treatment options. Although NTDs are usually infectious and communicable, perhaps those should not be strict requirements. Indeed, based on these criteria, SCA is long overdue for membership in this elite but tragic club of global medical maladies. Perhaps ironically, such a designation of SCA may allow this currently “invisible” lethal disease to become more noticeable as a “neglected” disease.
Lutein and Brain Function

Lutein is one of the most prevalent carotenoids in nature and in the human diet. Together with zeaxanthin, it is highly concentrated as macular pigment in the foveal retina of primates, attenuating blue light exposure, providing protection from photo-oxidation and enhancing visual performance. Recently, interest in lutein has expanded beyond the retina to its possible contributions to brain development and function. Only primates accumulate lutein within the brain, but little is known about its distribution or physiological role. Our team has begun to utilize the rhesus macaque (Macaca mulatta) model to study the uptake and bio-localization of lutein in the brain. Our overall goal has been to assess the association of lutein localization with brain function. In this review, we will first cover the evolution of the non-human primate model for lutein and brain studies, discuss prior association studies of lutein with retina and brain function, and review approaches that can be used to localize brain lutein. We also describe our approach to the biosynthesis of 13C-lutein, which will allow investigation of lutein flux, localization, metabolism and pharmacokinetics. Lastly, we describe potential future research opportunities.
Word2Image: towards visual interpreting of words

Besides the traditional textual semantic description to convey the meanings of a certain concept or word, visual illustration is a complementary, yet important and more intuitive way to interpret the word. Thus the technique that converts word to image is desirable though it is very difficult. Since a word usually has different semantic aspects, we need several correct and semantic-rich images to represent the word. In this paper, we explore how to leverage the web image collections to fulfill such task and develop a novel multimedia application system, Word2Image. Various techniques, including the correlation analysis, semantic and visual clustering are adapted into our system to produce sets of high quality, precise, diverse and representative images to visually translate a given word. The objective and subjective evaluations show the feasibility and effectiveness of our approach.
A biologically inspired controller for fast eye movements

We describe and test a non-linear control algorithm inspired by the behavior of motor neurons in humans and other animals during extremely fast saccadic eye movements. The algorithm is implemented on a robotic eye, which includes a stiff camera cable, similar to the optic nerve, which adds a complicated non-linear stiffness to the plant. For high speed movement, our “pulse-step” controller operates open-loop using an internal model of the eye plant learned from past measurements. We show that the controller approaches the performance seen in the human eye, producing fast movements with little overshoot. Interestingly, the controller reproduces the main sequence relationship observed in animal eye movements.
Magnetic field configuration and field-aligned acceleration of energetic ions during substorm onsets

In this paper, we present an interpretation of the observed field-aligned acceleration events measured by GEOS-2 near the night-side synchronous orbit at substorm onsets (Chen et al., 2000). We show that field-aligned ac- celeration of ions (with pitch angle asymmetry) is closely related to strong short-lived electric fields in the Ey direc- tion. The acceleration is associated with either rapid dipo- larization or further stretching of local magnetic field lines. Theoretical analysis suggests that a centrifugal mechanism is a likely candidate for the parallel energization. Equatorward or anti-equatorward energization occurs when the tail cur- rent sheet is thinner tailward or earthward of the spacecraft, respectively. The magnetic field topology leading to anti- equatorward energization corresponds to a situation where the near-Earth tail undergoes further compression and the in- ner edge of the plasma sheet extends inwards as close as the night-side geosynchronous altitudes.
Optimizing the learning of binary mappings

When training simple sigmoidal feed-forward neural networks on binary mappings using gradient descent algorithms with a sum-squared-error cost function, the learning algorithm often gets stuck with some outputs totally wrong. This is because the weight updates depend on the derivative of the output sigmoid which goes to zero as the output approaches maximal error. Common solutions to this problem include offsetting the output targets, offsetting the sigmoid derivatives, and using a different cost function. Comparisons are difficult because of the different optimal parameter settings for each case. In this paper I use an evolutionary approach to optimize and compare the different approaches.
Texturing Faces

We present a number of techniques to facilitate the generation of textures for facial modeling. In particular, we address the generation of facial skin textures from uncalibrated input photographs as well as the creation of individual textures for facial components such as eyes or teeth. Apart from an initial feature point selection for the skin texturing, all our methods work fully automatically without any user interaction. The resulting textures show a high quality and are suitable for both photo-realistic and real-time facial animation.
Exploiting Distributional Semantic Models in Question Answering

This paper investigates the role of Distributional Semantic Models (DSMs) in Question Answering (QA), and specifically in a QA system called Question Cube. Question Cube is a framework for QA that combines several techniques to retrieve passages containing the exact answers for natural language questions. It exploits Information Retrieval models to seek candidate answers and Natural Language Processing algorithms for the analysis of questions and candidate answers both in English and Italian. The data source for the answer is an unstructured text document collection stored in search indices. In this paper we propose to exploit DSMs in the Question Cube framework. In DSMs words are represented as mathematical points in a geometric space, also known as semantic space. Words are similar if they are close in that space. Our idea is that DSMs approaches can help to compute relatedness between users' questions and candidate answers by exploiting paradigmatic relations between words. Results of an experimental evaluation carried out on CLEF2010 QA dataset, prove the effectiveness of the proposed approach.
Heuristic Twists and Ontological Creeds - Road Map for Evolutionary Economics

What is special about the evolutionary approach? This question is given quite different, and partly incommensurable, answers in evolutionary economics. The present paper shows how the different answers correspond with, on the one hand, the particular heuristic twists by which the corresponding authors arrive at their hypotheses (e.g. by borrowing analogies from evolutionary biology). On the other hand, the answers hinge on different ontological assumption (i.e. on whether or not evolution in nature and in the economy are viewed as belonging to the same sphere of reality and, hence, as mutually dependent processes). By distinguishing these two dimensions a road map for evolutionary economics is drawn up that helps to better understand where, and why, the competing interpretations differ. In order to assess their achievements and their potential for future research, some results of an opinion poll among evolutionary economists are presented and discussed.
The CXCR4 and adhesion molecule expression of CD34+ hematopoietic cells mobilized by “on-demand” addition of plerixafor to granulocyte–colony-stimulating factor

Granulocyte–colony‐stimulating factor (G‐CSF) is routinely used for mobilization of hematopoietic stem and progenitor cells preceding autologous transplantation after high‐dose chemotherapy in hematologic malignancies. However, due to high mobilization failure rates, alternative mobilization strategies are required.
Geometrical structures of FIR manifold and their application to multichannel blind deconvolution

We study geometrical structures on the manifold of FIR filters and their application to multichannel blind deconvolution. First we introduce the Lie group and Riemannian metric to the manifold of FIR filters. Then we derive the natural gradient on the manifold using the isometry of the Riemannian metric. Using the natural gradient, we present a novel learning algorithm for blind deconvolution based on the minimization of mutual information. We also study properties of the learning algorithm, such as equivariance and stability. Simulations are given to illustrate the effectiveness and validity of the proposed algorithm.
Caldesmon Regulates Axon Extension through Interaction with Myosin II*

Background: Axon extension, an essential step for creating neural circuits, is regulated by cytoskeletal dynamics. Results: Caldesmon is a regulator of the actin cytoskeleton and enhances axon extension through direct interaction with myosin II. Conclusion: Caldesmon binding to myosin II inhibits myosin II function, resulting in the enhancement of axon extension. Significance: This study elucidates how caldesmon-regulated actin-myosin system is involved in axon extension. To begin the process of forming neural circuits, new neurons first establish their polarity and extend their axon. Axon extension is guided and regulated by highly coordinated cytoskeletal dynamics. Here we demonstrate that in hippocampal neurons, the actin-binding protein caldesmon accumulates in distal axons, and its N-terminal interaction with myosin II enhances axon extension. In cortical neural progenitor cells, caldesmon knockdown suppresses axon extension and neuronal polarity. These results indicate that caldesmon is an important regulator of axon development.
Congestive heart failure in type 2 diabetes: prevalence, incidence, and risk factors.

OBJECTIVE To estimate the prevalence and incidence of congestive heart failure (CHF) in populations with and without type 2 diabetes and to identify risk factors for diabetes-associated CHF. RESEARCH DESIGN AND METHODS We searched the inpatient and outpatient electronic medical records of 9,591 individuals diagnosed with type 2 diabetes before 1 January 1997 and those of an age- and sex-matched control group without diabetes for a diagnosis of CHF. Among those without a baseline diagnosis of CHF, we searched forward for 30 months for incident cases of CHF. We constructed multiple logistic regression models to identify risk factors for both prevalent and incident CHF. RESULTS CHF was prevalent in 11.8% (n = 1,131) of diabetic subjects and 4.5% (n = 435) of control subjects at baseline. We observed incident cases of CHF in 7.7% of diabetic subjects free of CHF at baseline (650 of 8,460) and in 3.4% of control subjects (314 of 9,156). In diabetic subjects, age, diabetes duration, insulin use, ischemic heart disease, and elevated serum creatinine were independent risk factors for both prevalent and incident CHF. Better glycemic control at baseline, and improved glycemic and blood pressure control at follow-up predicted the development of CHF. CONCLUSIONS Despite controlling for age, duration of diabetes, presence of ischemic heart disease, and presence of hypertension, insulin use was associated with both prevalent and incident CHF. Why insulin use and better glycemic control both at baseline and follow-up independently predicted CHF deserves further study.
Analyzing the Scaling of Connectivity in Neuromorphic Hardware and in Models of Neural Networks

In recent years, neuromorphic hardware systems have significantly grown in size. With more and more neurons and synapses integrated in such systems, the neural connectivity and its configurability have become crucial design constraints. To tackle this problem, we introduce a generic extended graph description of connection topologies that allows a systematical analysis of connectivity in both neuromorphic hardware and neural network models. The unifying nature of our approach enables a close exchange between hardware and models. For an existing hardware system, the optimally matched network model can be extracted. Inversely, a hardware architecture may be fitted to a particular model network topology with our description method. As a further strength, the extended graph can be used to quantify the amount of configurability for a certain network topology. This is a hardware design variable that has widely been neglected, mainly because of a missing analysis method. To condense our analysis results, we develop a classification for the scaling complexity of network models and neuromorphic hardware, based on the total number of connections and the configurability. We find a gap between several models and existing hardware, making these hardware systems either impossible or inefficient to use for scaled-up network models. In this respect, our analysis results suggest models with locality in their connections as promising approach for tackling this scaling gap.
Optimistic Update for Positive Life Events? An Unbiased Test

A large body of research has documented a valence dependent asymmetry in belief updating. Specifically, participants update their beliefs to a greater extent when receiving desirable information compared to undesirable information. Here, we ask whether asymmetric belief updating is observed for predictions regarding everyday positive and negative life events. First, using simulations, we show that an artificial bias in updating would be observed if a skewed distribution of base rates is utilized without controlling for estimation errors. This artificial bias is flipped for positive and negative life events. We then go on to use normally distributed base rates, for which the simulation does not produce an artificial bias. Our human data reveal an optimistic update bias when predicting everyday life events and provides evidence that the pattern is similar regardless if one is estimating a positive or negative event.
Towards a texture naming system: Identifying relevant dimensions of texture

Recently, researchers have started using texture for data visualization. The rationale behind this is to exploit the sensitivity of the human visual system to texture in order to overcome the limitations inherent in the display of multidimensional data. A fundamental issue that must be addressed is what textural features are important in texture perception, and how they are used. We designed an experiment to help identify the relevant higher order features of texture perceived by humans. We used twenty subjects, who were asked to rate 56 pictures from Brodatz's album on 12 nine-point Likert scales. We applied the techniques of hierarchical cluster analysis, non-parametric multidimensional scaling (MDS), classification and regression tree analysis (CART), discriminant analysis, and principal component analysis to data gathered from the subjects. Based on these techniques, we identified three orthogonal dimensions for texture to be repetitive vs. non-repetitive; high-contrast and non-directional vs. low-contrast and directional; granular, coarse and low-complexity vs. non-granular, fine and high-complexity. <<ETX>>
Compensatory signals associated with the activation of human GC 5′ splice sites

GC 5′ splice sites (5′ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5′ss activated by a mutation in BTK intron 3. This GC 5′ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5′ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5′ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5′ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5′ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5′ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5′ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.