Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatic approaches for identification and characterization of olfactomedin related genes with a potential role in pathogenesis of ocular disorders.

PURPOSE To identify olfactomedin domain containing proteins, which are expressed in the eye and have similarity to myocilin, to test as potential candidates for eye diseases. Most of the mutations in myocilin causing primary open angle glaucoma are located in the olfactomedin domain. In vitro experiments demonstrated interaction between optimedin and myocilin through the conserved olfactomedin domains of the proteins in rats, and it was speculated that optimedin might have a role in the pathogenesis of ocular disorders. Hence, we aimed to identify myocilin related human proteins having conserved olfactomedin domains with potential to interact between them and examine the expression patterns in the eye by bioinformatics approaches. This endeavor would have the potential to identify new candidate genes for eye diseases in general and glaucoma in particular to be tested by wet-lab experiments. METHODS Proteins with homology to myocilin were selected by BLASTp at the NCBI server. cDNA sequences and corresponding genomic contigs were retrieved. Pairwise BLAST was done to investigate the gene structure. The human EST database and NEIBank were searched against the selected cDNAs to look for tissue specific expression of the transcripts. RESULTS The study led to the identification of three groups of proteins encoded by three different genes; Noelin 1 (9q34.3), Noelin 2 (19p13.2), and Noelin 3 (1p22) encompassing 45,575 bp, 82,679 bp, and 1,93,421 bp of the genomic sequence, respectively. Genomic structures, alternate usage of exons, and molecular evolution of the Noelins were determined. Similar structures of the genes, splicing patterns and high levels of homology shed light on the relatedness and molecular evolution of this group of olfactomedin related proteins. Strikingly, however, Noelin 1 and Noelin 3 were found to be expressed as multiple splice variants while only a single spliced transcript could be identified for Noelin 2. A human EST database search suggested the expression of all three Noelin genes in the brain but only two (Noelin 1 and Noelin 2) in the eye despite experimental evidence for expression of Noelin 3 in ocular tissue. Myocilin was determined to have similar levels (60-61%) of homology with all three Noelin gene products (Noelin 1_v1, Noelin 2_v1, and Noelin 3_v1) at the conserved olfactomedin domains. CONCLUSIONS Mammalian Noelin 1 evolved from its precursor, followed by evolution of Noelin 3 and Noelin 2 by gene duplication events. Myocilin might have evolved from Noelin 2 by gene duplication followed by exon fusion. Noelin 1 and Noelin 2 could be tested as candidate genes for eye diseases based on their expressions in the eye and shared olfactomedin domains with Myocilin in the C-termini of the respective proteins.
CONSISTENT DISCRETIZATION AND CANONICAL, CLASSICAL AND QUANTUM REGGE CALCULUS

We apply the "consistent discretization" technique to the Regge action for (Euclidean and Lorentzian) general relativity in arbitrary number of dimensions. The result is a well-defined canonical theory that is free of constraints and where the dynamics is implemented as a canonical transformation. In the Lorentzian case, the framework appears to be naturally free of the "spikes" that plague traditional formulations. It also provides a well-defined recipe for determining the integration measure for quantum Regge calculus.
Role of GABAA inhibition in modulation of pyramidal tract neuron activity during postural corrections

In a previous study we demonstrated that the activity of pyramidal tract neurons (PTNs) of the motor cortex is modulated in relation to postural corrections evoked by periodical tilts of the animal. The modulation included an increase in activity in one phase of the tilt cycle and a decrease in the other phase. It is known that the motor cortex contains a large population of inhibitory GABAergic neurons. How do these neurons participate in periodic modulation of PTNs? The goal of this study was to investigate the role of GABAA inhibitory neurons of the motor cortex in the modulation of postural‐related PTN activity. Using extracellular electrodes with attached micropipettes, we recorded the activity of PTNs in cats maintaining balance on a tilting platform both before and after iontophoretic application of the GABAA receptor antagonists gabazine or bicuculline. The tilt‐related activity of 93% of PTNs was affected by GABAA receptor antagonists. In 88% of cells, peak activity increased by 75 ± 50% (mean ± SD). In contrast, the trough activity changed by a much smaller value and almost as many neurons showed a decrease as showed an increase. In 73% of the neurons, the phase position of the peak activity did not change or changed by no more than 0.1 of a cycle. We conclude that the GABAergic system of the motor cortex reduces the posture‐related responses of PTNs but has little role in determining their response timing.
Role of Cortico-Cancellous Heterologous Bone in Human Periodontal Ligament Stem Cell Xeno-Free Culture Studied by Synchrotron Radiation Phase-Contrast Microtomography

This study was designed to quantitatively demonstrate via three-dimensional (3D) images, through the Synchrotron Radiation Phase-Contrast Microtomography (SR-PhC-MicroCT), the osteoinductive properties of a cortico-cancellous scaffold (Osteobiol Dual Block—DB) cultured with human Periodontal Ligament Stem Cells (hPDLSCs) in xeno-free media. In vitro cultures of hPDLSCs, obtained from alveolar crest and horizontal fibers of the periodontal ligament, were seeded onto DB scaffolds and cultured in xeno-free media for three weeks. 3D images were obtained by SR-PhC-microCT after one and three weeks from culture beginning. MicroCT data were successively processed with a phase-retrieval algorithm based on the Transport of Intensity Equation (TIE). The chosen experimental method, previously demonstratively applied for the 3D characterization of the same constructs in not xeno-free media, quantitatively monitored also in this case the early stages of bone formation in basal and differentiating conditions. Interestingly, it quantitatively showed in the xeno-free environment a significant acceleration of the mineralization process, regardless of the culture (basal/differentiating) medium. This work showed in 3D that the DB guides the osteogenic differentiation of hPDLSCs in xeno-free cultures, in agreement with 2D observations and functional studies previously performed by some of the authors. Indeed, here we fully proved in 3D that expanded hPDLSCs, using xeno-free media formulation, not only provide the basis for Good Manufacturing Practice (preserving the stem cells’ morphological features and their ability to differentiate into mesenchymal lineage) but have to be considered, combined to DB scaffolds, as interesting candidates for potential clinical use in new custom made tissue-engineered constructs.
Effect of alanine on D‐galactosamine‐induced acute liver failure in rats

The effect of high‐dose alanine on survival and liver function in rats with acute liver failure caused by a lethal dose of D‐galactosamine (D‐gal) was studied. Greater than 90% of control animals died within 5 days after D‐gal injection, but alanine significantly decreased mortality, even when treatment was started at 12 hours after D‐gal injection. Alanyl‐glutamine had a slight effect, but glucose produced no improvement. There was marked elevation of the plasma aspartate transaminase (AST) level, prolongation of the prothrombin time, and a decrease of the arterial ketone body ratio (AKBR) and hepatic adenosine triphosphate (ATP) content within 12 hours after D‐gal injection. The AKBR decreased in parallel with the decrease of the hepatic ATP content. These parameters were significantly improved in alanine‐ treated rats at 48 hours after the induction of liver damage, which was just before control rats began to die. The hepatic ATP content was significantly greater in alanine‐treated rats than in the other rats (including normal controls), but glucose pretreatment had no effect. It was also found that the liver labeling index of partially hepatectomized rats was significantly elevated by alanine administration at 3 hours before measurement. In conclusion, alanine is effective for the treatment of experimental acute liver failure, probably caused by promotion of ATP synthesis. Ala may be a good candidate for clinical application because of its preventive effect on hepatocyte necrosis and its promotive effect on liver regeneration.
Natural Narrowing as a General Unied Mechanism for Programming and Proving

Although originally introduced as a theorem proving method to solve equational unification problems, narrowing was soon recognized as a key mechanism to unify functional and logic programming. In fact, in a declarative setting where programming and proving can be seamlessly integrated, narrowing serves as a unified mechanism for both evaluation and deduction. For narrowing to be an efficient evaluation mechanism, several lazy narrowing strategies have been proposed, although typically for the restricted case of left-linear constructor-based rewrite systems. These assumptions, while reasonable for functional programming applications, are too restrictive for a much broader range of applications to which narrowing can be fruitfully applied. In this paper, we propose an efficient lazy narrowing strategy called natural narrowing which can be applied to a larger class of rewrite systems without the above assumptions. This strategy is more efficient than all previously know strategies when applied to the class of left-linear constructor-based rewrite systems. An important consequence of this generalization is the wide range of applications that can now be efficiently supported by narrowing. We highlight a few such applications including symbolic model checking, theorem proving, and partial evaluation. What thus emerges is a general and efficient unified mechanism based on narrowing, that seamlessly integrates a very wide range of applications in programming and proving.
Critical roles of Bcl11b in T‐cell development and maintenance of T‐cell identity

Summary: T‐cell development primarily occurs in the thymus and involves in the interactions of many important transcription factors. Until recently, no single transcription factor has been identified to be essential for T‐cell lineage commitment or maintenance of T‐cell identity. Recent studies have now identified the zinc finger transcription factor Bcl11b to be essential for T‐cell development and for maintenance of T‐cell identity. Remarkably, T cells acquire NK cell properties upon Bcl11b deletion. These reprogrammed cells have unique properties in proliferation, cytokine dependency and killing target cells, and may therefore provide a new cell source for some cell‐based therapies.
The glutamate receptor ion channels.

The ionotropic glutamate receptors are ligand-gated ion channels that mediate the vast majority of excitatory neurotransmission in the brain. The cloning of cDNAs encoding glutamate receptor subunits, which occurred mainly between 1989 and 1992 ([Hollmann and Heinemann, 1994][1]), stimulated this
Social and Emotional Learning in Preschool: An Evaluation of Strong Start Pre-K

Social and Emotional Learning in Preschool: An Evaluation of Strong Start Pre-K Leslie Gunter Department of Counseling Psychology and Special Education, BYU Educational Specialist in School Psychology Young children face unique social challenges, and they need social and emotional resilience skills in order to navigate their way through school. Many of the children who need the most help are in family situations where parents are not able to teach these skills. Students can become more resilient through social and emotional learning (SEL) in the classroom. SEL teaches children to identify the emotions of themselves and others, to communicate their emotions in a nonviolent way, and to be good friends. By teaching SEL at a young age, teachers can help children become more adept as they make friends and learn how to interact in social situations, thus bolstering their relationships with friends and adults. Improved social and emotional skills help students succeed in academics and with their peers as they form social connections. Strong Start Pre-K, a social and emotional learning curriculum, was evaluated in a local preschool program. Using a nonequivalent control group design, two preschool teachers taught the curriculum in their classrooms, and a third classroom was the control. Both before and after the implementation of the curriculum, data were gathered from classroom teachers on their students’ emotional regulation, internalizing behaviors, and the teachers’ perceived relationships with their students. Results indicated a slight increase in emotional regulation and a significant decrease in internalizing behaviors in the treatment groups. Student-teacher relationships improved, specifically with a decrease on the subscale of Conflict. Treatment fidelity indicated that teachers were able to implement most or all of the components of each lesson 90% of the time. Social validity measurements indicated that the teachers would recommend the curriculum to other educators.
Pentoxifylline and propentofylline prevent proliferation and activation of the mammalian target of rapamycin and mitogen activated protein kinase in cultured spinal astrocytes

Astrocyte activation is an important feature in many disorders of the central nervous system, including chronic pain conditions. Activation of astrocytes is characterized by a change in morphology, including hypertrophy and increased size of processes, proliferation, and an increased production of proinflammatory mediators. The xanthine derivatives pentoxifylline and propentofylline are commonly used experimentally as glial inhibitors. These compounds are generally believed to attenuate glial activity by raising cyclic AMP (cAMP) levels and inhibiting glial tumor necrosis factor (TNF) production. In the present study, we show that these substances inhibit TNF and serum‐induced astrocyte proliferation and signaling through the mammalian target of rapamycin (mTOR) pathway, demonstrated by decreased levels of phosphorylated S6 kinase (S6K), commonly used as a marker of mTOR complex (mTORC) activation. Furthermore, we show that pentoxifylline and propentofylline also inhibit JNK and p38, but not ERK, activation induced by TNF. In addition, the JNK antagonist SP600125, but not the p38 inhibitor SB203580, prevents TNF‐induced activation of S6 kinase, suggesting that pentoxifylline and propentofylline may regulate mTORC activity in spinal astrocytes partially through inhibition of the JNK pathway. Our results suggest that pentoxifylline and propentofylline inhibit astrocyte activity in a broad fashion by attenuating flux through specific pathways. © 2012 Wiley Periodicals, Inc.
Singular perturbation based solution to optimal microalgal growth problem and its infinite time horizon analysis

The problem of the optimal microalgal growth is considered here. The objective is to maximize the specific growth rate of microalgae by manipulating the irradiance. The model describing the growth of microalgae is based on the mechanistic description in the form of the so called photosynthetic factory (PSF) resulting into the second order bilinear system which is, nevertheless, known in biotechnological literature to comprise many important features of microalgal growth. To obtain the solution of optimal control problem, the singular perturbation approach is used here to reduce fast components of system dynamics leading to a less dimensional system with more complex performance index which allows a nice analytical solution. Its infinite horizon analysis shows that the optimal solution on large time intervals tends to the optimal steady state of PSF thereby supporting the hypothesis often mentioned in the biotechnological literature. Finally, the numerical algorithm to compute optimal control is applied to the original non-reduced system giving very similar results as the reduction based approach.
Coupled Prediction Classification for Robust Visual Tracking

This paper addresses the problem of robust template tracking in image sequences. Our work falls within the discriminative framework in which the observations at each frame yield direct probabilistic predictions of the state of the target. Our primary contribution is that we explicitly address the problem that the prediction accuracy for different observations varies, and in some cases, can be very low. To this end, we couple the predictor to a probabilistic classifier which, when trained, can determine the probability that a new observation can accurately predict the state of the target (that is, determine the “relevance” or “reliability” of the observation in question). In the particle filtering framework, we derive a recursive scheme for maintaining an approximation of the posterior probability of the state in which multiple observations can be used and their predictions moderated by their corresponding relevance. In this way, the predictions of the “relevant” observations are emphasized, while the predictions of the “irrelevant” observations are suppressed. We apply the algorithm to the problem of 2D template tracking and demonstrate that the proposed scheme outperforms classical methods for discriminative tracking both in the case of motions which are large in magnitude and also for partial occlusions.
Attentional Bias Modification: Impact on Mood in College Students with Anxiety Symptoms

The current investigation examined the effects of a differential attentional training task on subsequent emotional reactivity in response to a task that was aimed to either induce positive or negative affectivity. Specifically, the study employed a dot-probe attentional training paradigm to train attention toward positive images (Attend-Positive condition), toward neutral images (Attend-Neutral condition), or to not train attention at all (Control condition). The hypothesis was that individuals whose attention was trained toward positive images would exhibit faster response times toward positive images (compared to the Attend-Neutral and Control conditions) at post assessment, individuals whose attention was trained toward neutral images would exhibit faster response times toward neutral images (compared to the Attend-Positive and Control conditions) at post assessment, and individuals in the Control condition would maintain similar response times from baseline to post assessment, aside from general practice effects. It was also hypothesized that those in the Attend-Positive condition would better regulate emotion, as measured by less negative affect in response to a stress task and more positive affect in response to a positive mood induction task, compared to individuals who have engaged in a control task involving no attentional bias training (Control condition). It was also hypothesized that those in the Attend-Neutral condition would better regulate emotion, as measured by less negative affect in response to a stress task and more positive affect in response to a positive mood induction task, compared to individuals who have engaged in a control task involving no attentional bias training (Control condition). Last, it was hypothesized that individuals in the Attend-Positive condition would report differentially less negative affect in response to the stress task (failure anagrams) than those in the Attend-Neutral condition, and that individuals in the Attend-Positive condition would report differentially more positive affect in response to the positive mood induction task (success anagrams) than those in the Attend-Neutral condition. In all conditions, the dotprobe attentional training did not effectively modify biases in the hypothesized directions. While there was differential affectivity change for individuals who underwent a Failure Anagram task versus a Success Anagram task, there is no way to definitively interpret the meaning of these changes given the failure of the attentional manipulation. The findings from the current investigation provide no evidence for single-session dot-probe attentional bias modification procedures to manipulate attentional bias toward positive stimuli or toward neutral stimuli. Possible explanations for these results, including lack of reliability of the dotprobe task, are discussed.
A self-powered power management circuit for energy harvested by a piezoelectric cantilever

This paper presents development of a self-powered power management circuit for energy harvested by a piezoelectric cantilever. A full-wave rectifier followed by a buck-boost converter running in the discontinuous conduction mode rectifies the AC output, matches the source impedance, and generates a regulated DC output provided the input power is sufficient to charge up the load. A low power microcontroller unit is used for the maximum power point tracking and the output voltage regulation. Experimental results show that the circuit can harvest up to 3.5 mW with a 50×31.8 mm2 piezoelectric cantilever under 0.5g (rms) base acceleration. Detailed loss analysis is presented for efficiency enhancement in the future.
Endophytic bacteria in rice seeds inhibit early colonization of roots by Azospirillum brasilense

From the rhizoplane of Oryza sativa, vars. Morelos A-88 and Apatzingan, rice plantlets, we isolated two bacterial strains: Corynebacterium ̄avescens and Bacillus pumilus. By scanning electron microscopy, endophytic bacteria were frequently identi®ed at the base of secondary roots, between the epidermis and the mucilaginous layer. Endophytes were also identi®ed in the intercellular spaces when the mucilaginous layer was disrupted. These endophytic bacteria were not pathogenic when assayed on tobacco leaves. Plantlets from the rice varieties cultured gnotobiotically under hydroponic conditions were inoculated with Azospirillum brasilense, 6-81 or UAP-154 strains. Control experiments were performed using non-inoculated plantlets or plantlets previously treated with nalidixic acid. Comparison of the length of inoculated or nalidixic acid-treated plantlets, with non-inoculated plantlets revealed a signi®cant p , 0:05 promotion of the growth of the shoots at 15 days of culture in plantlets colonized exclusively by endophytes. A. brasilense seems to be excluded from the rhizoplane by the endophytic bacteria, suggesting that endophytes compete with Azospirillum, and also that A. brasilense inhibits growth of rice. Our results indicate that endophytic bacteria could participate in the growth and development of rice plants. q 2001 Elsevier Science Ltd. All rights reserved.
On The Modeling of OpenFlow-based SDNs: The Single Node Case

OpenFlow is one of the most commonly used protocols for communication between the controller and the forwarding element in a software defined network (SDN). A model based on M/M/1 queues is proposed in [1] to capture the communication between the forwarding element and the controller. Albeit the model provides useful insight, it is accurate only for the case when the probability of expecting a new flow is small. Secondly, it is not straight forward to extend the model in [1] to more than one forwarding element in the data plane. In this work we propose a model which addresses both these challenges. The model is based on Jackson assumption but with corrections tailored to the OpenFlow based SDN network. Performance analysis using the proposed model indicates that the model is accurate even for the case when the probability of new flow is quite large. Further we show by a toy example that the model can be extended to more than one node in the data plane.