Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Annotation of Populus trichocarpa microRNAs from Diverse Tissue Sets

Populus trichocarpa is an important woody model organism whose entire genome has been sequenced. This resource has facilitated the annotation of microRNAs (miRNAs), which are short non-coding RNAs with critical regulatory functions. However, despite their developmental importance, P. trichocarpa miRNAs have yet to be annotated from numerous important tissues. Here we significantly expand the breadth of tissue sampling and sequencing depth for miRNA annotation in P. trichocarpa using high-throughput smallRNA (sRNA) sequencing. miRNA annotation was performed using three individual next-generation sRNA sequencing runs from separate leaves, xylem, and mechanically treated xylem, as well as a fourth run using a pooled sample containing vegetative apices, male flowers, female flowers, female apical buds, and male apical and lateral buds. A total of 276 miRNAs were identified from these datasets, including 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Importantly, we identified several xylem-enriched miRNAs predicted to target genes known to be important in secondary growth, including the critical reaction wood enzyme xyloglucan endo-transglycosylase/hydrolase and vascular-related transcription factors. This study provides a thorough genome-wide annotation of miRNAs in P. trichocarpa through deep sRNA sequencing from diverse tissue sets. Our data significantly expands the P. trichocarpa miRNA repertoire, which will facilitate a broad range of research in this major model system.
Finding Motifs in a Database of Shapes

The problem of efficiently finding images that are similar to a target image has attracted much attention in the image processing community and is rightly considered an information retrieval task. However, the problem of finding structure and regularities in large image datasets is an area in which data mining is beginning to make fundamental contributions. In this work, we consider the new problem of discovering shape motifs, which are approximately repeated shapes within (or between) image collections. As we shall show, shape motifs can have applications in tasks as diverse as anthropology, law enforcement, and historical manuscript mining. Brute force discovery of shape motifs could be untenably slow, especially as many domains may require an expensive rotation invariant distance measure. We introduce an algorithm that is two to three orders of magnitude faster than brute force search, and demonstrate the utility of our approach with several real world datasets from diverse domains.
The effect of calcium ions on the binomial statistic parameters that control acetylcholine release at preganglionic nerve terminals.

1. A study has been made of the effects of changing [Ca]O and [Mg]O on the binomial statistic parameters p and n that control the average quantal content (m) of the excitatory post‐synaptic potential (e.p.s.p.) due to acetylcholine release at preganglionic nerve terminals. 2. When [Ca]O was increased in the range from 0‐2 to 0‐5 mM, p increased as the first power of [Ca]O whereas n increased as the 0‐5 power of [Ca]O; when [Mg]O was increased in the range from 5 to 200 mM, p decreased as the first power of [Mg]O whereas n decreased as the 0‐5 power of [Mg]O. 3. The increase in quantal release of a test impulse following a conditioning impulse was primarily due to an increase in n; the increase in quantal content of successive e.p.s.p.s in a short train was due to an increase in n and p, and the increase in n was quantitatively described in terms of the accumulation of a Ca‐receptor complex in the nerve terminal. 4. The decrease in quantal content of successive e.p.s.p.s during long trains of impulses over several minutes was primarily due to a decrease in n. These results are discussed in terms of an hypothesis concerning the physical basis of n and p in the release process.
A high frequency radio study of G11.2 0.3, a historical supernova remnant with a flat spectrum core

We present radio maps of the historical supernova remnant G11.2 0.3 in the frequency range from 4.85 GHz to 32 GHz. The integrated spectrum with = 0:50 (S ) is dominated by its steep spectrum shell emission ( 0:57), although a flat spectrum core structure classies G11.2 0.3 as a composite supernova remnant. A radial magnetic eld structure is observed. An analysis of the multi{frequency polarization data results in highly varying rotation measures along the shell. The percentage polarization is rather low (2%) and we conclude that G11.2 0.3 is in the transient phase from free to adiabatic expansion. The central flat spectrum component is partly resolved. A compact radio source with an inverted spectrum likely coincides with the previously detected X{ray pulsar (Torii et al. 1997). Two symmetric structures with flat radio spectra possibly indicate a bipolar outflow. Combining available X{ray and radio data we conclude that G11.2 0.3 is likely the remnant of a type II supernova explosion with an early type B progenitor star.
Permeability measurements from free-space technique and theoretical simulation in millimeter-wave frequency range

Real part of permeability of Yttrium Gadolinium Iron Oxide (Gd-YIG) has been observed in the frequency range from 30 to 120 GHz by using a free-space quasi-optical millimeter-wave spectrometer. The simulation results from both Schlöemann's and Soohoo's equation have also been studied. The comparison between the simulation and experimental result, and the standard deviation have been performed and calculated through the whole frequency range.
From broadcast news to spontaneous dialogue transcription: portability issues

Reports on experiments of porting the ITC-irst Italian broadcast news recognition system to two spontaneous dialogue domains. The trade-off between performance and the required amount of task specific data was investigated. Porting was experimented by applying supervised adaptation methods to acoustic and language models. By using two hours of manually transcribed speech, word error rates of 26.0% and 28.4% were achieved by the adapted systems. Two reference systems, developed on a larger training corpus, achieved word error rates of 22.6% and 21.2%, respectively.
Non-Synonymous Single Nucleotide Polymorphisms in the P2X Receptor Genes: Association with Diseases, Impact on Receptor Functions and Potential Use as Diagnosis Biomarkers

P2X receptors are Ca2+-permeable cationic channels in the cell membranes, where they play an important role in mediating a diversity of physiological and pathophysiological functions of extracellular ATP. Mammalian cells express seven P2X receptor genes. Single nucleotide polymorphisms (SNPs) are widespread in the P2RX genes encoding the human P2X receptors, particularly the human P2X7 receptor. This article will provide an overview of the non-synonymous SNPs (NS-SNPs) that have been associated with or implicated in altering the susceptibility to pathologies or disease conditions, and discuss the consequences of the mutations resulting from such NS-SNPs on the receptor functions. Disease-associated NS-SNPs in the P2RX genes have been valuable in understanding the disease etiology and the receptor function, and are promising as biomarkers to be used for the diagnosis and development of stratified therapeutics.
Effect of Preschool Working Memory, Language, and Narrative Abilities on Inferential Comprehension at School-Age in Children with Spina Bifida Myelomeningocele and Typically Developing Children

Abstract Children with spina bifida myelomeningocele (SBM) are more likely to display a pattern of good-decoding/poor comprehension than their neurologically intact peers. The goals of the current study were to (1) examine the cognitive origins of one of the component skills of comprehension, bridging inferences, from a developmental perspective and (2) to test the effects of those relations on reading comprehension achievement. Data from a sample of children with SBM and a control group (n = 78) who participated in a longitudinal study were taken from age 36-month and 9.5-year time points. A multiple mediation model provided evidence that three preschool cognitive abilities (working memory/inhibitory control, oral comprehension, narrative recall), could partially explain the relation between group and bridging inference skill. A second mediation model supported that each of the 36-month abilities had an indirect effect on reading comprehension through bridging inference skill. Findings contribute to an understanding of both typical and atypical comprehension development, blending theories from the developmental, cognitive, and neuropsychological literature. (JINS, 2013, 19, 1–10)
Interest And Its Development

This chapter focuses on interest as a cognitive and affective motivational variable that develops and can be supported to develop. Interest and interest development as described by Midi and Renninger’s (2006) Four-Phase Model of Interest Development are (a) defined and then (b) contextualized in light of other conceptualizations that focus on specific aspects of interest (such as emotion, experience, task features, value, and vocational interest) and issues pertaining to the operationalization and measurement of interest. Following this, research addressing the development of interest is overviewed, with particular attention to (a) the triggering of interest in both earlier and later phases of interest, (b) maintaining interest once it has been triggered, (c) fluctuations in interest, and (d) shifts between phases in the development of interest. Finally, a Punnett square is employed to suggest next steps and open questions in the study of interest development.
Psychosocial Factors Associated with Knowledge about Affective Disorders in Patients with Depression

Background: Increasing importance is attributed to the knowledge that patients have concerning their illness. For psychiatric disorders, imparting information about the illness has become a standard part of treatment. Despite the great clinical relevance of knowledge about depression, only few empirical studies on this subject have been carried out. This study aimed to identify psychosocial factors associated with greater or lesser knowledge about affective disorders. Methods: Sixty-one in-patients with depression were recruited and tested with the Knowledge about Depression and Mania Inventory. Results: Almost all patients sought specific information about their disorder prior to admission to hospital. There were large differences in patients’ knowledge about the disorder and their choice of information source. Older and less educated patients had less knowledge about affective disorders. Patients with less illness knowledge also have a less favourable illness concept, poorer interpersonal relationships and more passive coping strategies. Conclusions: The results show that knowledge about affective disorders is a central illness characteristic that has numerous implications for the ability to cope with the disorder, as well as for psychotherapeutic management. The results contribute to a clarification of the relationship between psychoeducation and psychotherapy.
Project 01 : Random walk models on graphs and groups Update , January 2015

Research interests of W. Woess The central topic of the research of W. Woess is “Random Walks on Infinite Graphs and Groups”, which is also the title of the quite successful monograph [7]. Here, Random Walks are understood as Markov chains whose transition probabilities are adapted to an algebraic, geometric, resp. combinatorial structure of the underlying state space. The main theme is the interplay between probabilisitc, analytic and potential theoretic properties of those random processes and the structural properties of that state space. From the probabilistic viewpoint, the question is what impact the particular type of structure has on various aspects of the behaviour of the random walk, such as transience/recurrence, decay and asymptotic behaviour of transition probabilities, rate of escape, convergence to a boundary at infinity and harmonic functions. Vice versa, random walks may also be seen as a nice tool for classifying, or at least describing the structure of graphs, groups and related objects. The work of W. Woess is not limited to those aspects that concentrate on the link between random walks and structure theory. One one side, there is also a body of more “pure” work on infinite graphs, group actions, and also formal languages (which entered the scene via the free group). This comprises past and current collaboration with T. Ceccherini-Silberstein. On another side, some recent and less recent work concerns locally compact groups and their actions in relation with the computation of norms of transition operators, and harmonic functions on certain spaces that arise as so–called horocyclic products: past and current collaboration with S. Brofferio, M. Salvatori, L. Saloff-Coste and A. Bendikov. Woess’ research is interdisciplinary between several Mathematical areas: Probability – Graph Theory – Geometric Group Theory – Discrete Geometry – Discrete Potential Theory – Harmonic Analysis and Spectral Theory.
Nuclear localization is required for function of the essential clock protein FRQ

The frequency (frq) gene in Neurosporaencodes central components of a circadian oscillator, a negative feedback loop involving frq mRNA and two forms of FRQ protein. Here we report that FRQ is a nuclear protein and nuclear localization is essential for its function. Deletion of the nuclear localization signal (NLS) renders FRQ unable to enter into the nucleus and abolishes overt circadian rhythmicity, while reinsertion of the NLS at a novel site near the N‐terminus of FRQ restores its function. Each form of FRQ enters the nucleus soon after its synthesis in the early subjective day; there is no evidence for regulated sequestration in the cytoplasm prior to nuclear entry. The kinetics of the nuclear entry are consistent with previous data showing rapid depression of frq transcript levels following the synthesis of FRQ, and suggest that early in each circadian cycle, when FRQ is synthesized, it enters the nucleus and depresses the level of its own transcript.
Variability of in vivo fluid dose distribution in mouse airways is visualized by high-speed synchrotron X-ray imaging.

BACKGROUND The manner in which fluid instillations into mouse nose and lung distribute through the airways is poorly understood. Many agents are delivered in this way for testing as therapeutics, or as challenges designed to establish infections or create systemic drug delivery effects. These agents are delivered into mouse airways with little knowledge of the manner in which doses move through the airways, how long they reside in each region, and where the instilled materials eventually reach. METHODS Synchrotron phase-contrast X-ray imaging (PCXI) was used to elucidate the primary controlling characteristics of mouse airway fluid dosing. High-speed image acquisition was used to track the movement of a range of bolus doses of an iodine-based contrast fluid through the nose (n=15) and lungs (n=10) of live anesthetized mice. For the lung studies, the mice were ventilated and paralyzed to control animal movement. Post-experiment image processing was used to visualize the fluid movement. RESULTS The maximum dose that could be retained in only the anterior nose was ∼7.5 μL (20 g mouse), and a range of dynamic dose behaviors was documented after delivery. In the lung, the use of mechanical ventilation in combination with a paralytic agent prevented confounding artifactual movement, improving visualization of fluid progression through the airways. In the lung, optimized image analysis using the high image capture rate revealed the presence of respiratory pauses that could not be visualized at slower acquisition rates. The variability in the outcome of identical dose deliveries in different animals indicates that uniform lung distribution cannot be expected to occur with tracheal fluid delivery. CONCLUSIONS With adequate imaging rate and fluid dose parameters, this study shows the utility of synchrotron PCXI for determining the post-delivery behavior and fate of fluid doses such as those used in in vivo gene transfer or pharmaceutical studies.
Neuronal population activity and functional imaging

Human functional brain imaging detects blood flow changes that are thought to reflect the activity of neuronal populations and, thus, the responses of neurons that carry behaviourally relevant information. Since this relationship is poorly understood, we explored the link between the activity of single neurons and their neuronal population. The functional imaging results were in good agreement with levels of population activation predicted from the known effects of sensory stimulation, learning and attention on single cortical neurons. However, the nature of the relationship between population activation and single neuron firing was very surprising. Population activation was strongly influenced by those neurons firing at low rates and so was very sensitive to the baseline or ‘spontaneous’ firing rate. When neural representations were sparse and neurons were tuned to several stimulus dimensions, population activation was hardly influenced by the few neurons whose firing was most strongly modulated by the task or stimulus. Measures of population activation could miss changes in information processing given simultaneous changes in neurons' baseline firing, response modulation or tuning width. Factors that can modulate baseline firing, such as attention, may have a particularly large influence on population activation. The results have implications for the interpretation of functional imaging signals and for cross–calibration between different methods for measuring neuronal activity.
WHY ANIMALS COME TOGETHER, WITH THE SPECIAL CASE OF MIXED-SPECIES BIRD FLOCKS

Group living is a widespread, ubiquitous biological phenomenon in the animal kingdom that has attracted considerable attention in many different contexts. The availability of food and the presence of predators represent the two main factors believed to favor group life. In this review, major theories supporting grouping behavior in animals are explored, providing an explanation of animal grouping. This review is divided in two sections. First, major theories as well as potential mechanisms behind the benefit of grouping are described. Later, a special case on the widespread animal social system of mixed-species avian flocks is presented, exploring the available information in relation to the potential causes that bring birds together into this particular social aggregation.
Identifying Output Interactions Among Is Projects - A Text Mining Approach

In the literature, there is anecdotal as well as empirical evidence for the existence and the business impact of output interactions among information systems projects. While a lot of sophisticated optimization models have been suggested which already provide for the consideration of output interactions when selecting information systems project portfolios, the necessary data required for their application in business practice are usually not available to the planner. There is a lack of techniques in the literature on how to identify output interactions already at the time, a portfolio is planned. We attribute this lack to the rather semantical nature of output interactions. We contribute to filling the identified gap by conferring semantic clustering - a technique originating in the text mining literature - to the field of information systems project portfolio selection. A prototypical decision support system is developed that uses latent semantic analysis and hierarchical clustering to identify potential output interactions among information systems project proposals based on semantic similarities within their goal descriptions. This paper focuses on the design of the developed prototype and argues that latent semantic analysis represents a very promising technique for the identification of output interactions among information systems projects.
Cloning of the Sodium-dependent, Broad-scope, Neutral Amino Acid Transporter Bo from a Human Placental Choriocarcinoma Cell Line*

We have isolated a cDNA from a human placental choriocarcinoma cell cDNA library which, when expressed in HeLa cells, induces a Na+-dependent amino acid transport system with preference for zwitterionic amino acids. Anionic amino acids, cationic amino acids, imino acids, and N-methylated amino acids are excluded by this system. These characteristics are identical to those described for the amino acid transporter Bo. When expressed in Xenopus laevis oocytes that do not have detectable endogenous activity of the amino acid transporter Bo, the cloned transporter increases alanine transport in the oocytes severalfold and induces alanine-evoked inward currents in the presence of Na+. The cDNA codes for a polypeptide containing 541 amino acids with 10 putative transmembrane domains. Amino acid sequence homology predicts this transporter (hATBo) to be a member of a superfamily consisting of the glutamate transporters, the neutral amino acid transport system ASCT, and the insulin-activable neutral/anionic amino acid transporter. Chromosomal assignment studies with somatic cell hybrid analysis and fluorescent in situ hybridization have located the ATBo gene to human chromosome 19q13.3.
Differential effects of estrogen and prolactin on autoimmune disease in the NZB/NZW F1 mouse model of systemic lupus erythematosus

Estrogen and prolactin have been shown to modulate autoimmunity in the NZB/NZW F1 (B/W) mouse model of systemic lupus erythematosus (SLE). However, estrogen stimulates prolactin secretion. The goal of this study was to examine differential effects of estrogen and prolactin in the female B/W mouse model of SLE. B/W females were manipulated to create combinations of low and high concentrations of serum estrogen and prolactin. Hyperprolactinemic mice with either low or high serum estrogen levels had accelerated development of albuminuria at 24 and 32 weeks of age compared to normal and hypoprolatinemic mice. High estrogen/high prolactin mice also had a higher percentage of anti-DNA antibodies compared to mice in the low estrogen/low prolactin and the high estrogen/low prolactin groups. IgG levels were not significantly different between groups. Mean survival was shortest in the high estrogen/high prolactin group (34 1.0 weeks) and longest in the high estrogen/low prolactin group (42 1.2 weeks; P < 0.05). High levels of serum estrogen were associated with depressed in vitro lymphoproliferation and IL-2 production. This study suggests that high prolactin levels in either high or low serum estrogen states are associated with accelerated autoimmunity in the B/W mouse. This study further demonstrates that high estrogen levels do not accelerate murine SLE when the prolactin-stimulating property of estrogen is suppressed by bromocriptine. Further investigation of hormonal interactions in autoimmunity will provide a better understanding of hormonal immunoregulation and, perhaps, lead to improved clinical application of hormonal immunomodulation.