Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Semaphorin‐3A and its receptors in endochondral ossification: Potential role in skeletal development and innervation

Bone tissue is densely innervated, and there is increasing evidence for a neural control of bone metabolism. Semaphorin‐3A is a very important regulator of neuronal targeting in the peripheral nervous system as well as in angiogenesis, and knockout of the Semaphorin‐3A gene induces abnormal bone and cartilage development. We analyzed the spatial and temporal expression patterns of Semaphorin‐3A signaling molecules during endochondral ossification, in parallel with the establishment of innervation. We show that osteoblasts and chondrocytes differentiated in vitro express most members of the Semaphorin‐3A signaling system (Semaphorin‐3A, Neuropilin‐1, and Plexins‐A1 and ‐A2). In vitro, osteoclasts express most receptor chains but not the ligand. In situ, these molecules are all expressed in the periosteum and by resting, prehypertrophic and hypertrophic chondrocytes in ossification centers before the onset of neurovascular invasion. They are detected later in osteoblasts and also osteoclasts, with differences in intensity and regional distribution. Semaphorin‐3A and Neuropilin‐1 are also expressed in the bone marrow. Plexin‐A3 is not expressed by bone cell lineages in vitro. It is detected early in the periosteum and hypertrophic chondrocytes. After the onset of ossification, this chain is restricted to a network of cell processes in close vicinity to the cells lining the trabeculae, similar to the pattern observed for neural markers at the same stages. After birth, while the density of innervation decreases, Plexin‐A3 is strongly expressed by blood vessels on the ossification front. In conclusion, Semaphorin‐3A signaling is present in bone and seems to precede or coincide at the temporal but also spatial level with the invasion of bone by blood vessels and nerve fibers. Expression patterns suggest Plexin‐A3/Neuropilin‐1 as a candidate receptor in target cells for the regulation of bone innervation by Semaphorin‐3A. Developmental Dynamics 234:393–403, 2005. © 2005 Wiley‐Liss, Inc.
The Perception of Stress Pattern in Young Cochlear Implanted Children: An EEG Study

Children with sensorineural hearing loss may (re)gain hearing with a cochlear implant—a device that transforms sounds into electric pulses and bypasses the dysfunctioning inner ear by stimulating the auditory nerve directly with an electrode array. Many implanted children master the acquisition of spoken language successfully, yet we still have little knowledge of the actual input they receive with the implant and specifically which language sensitive cues they hear. This would be important however, both for understanding the flexibility of the auditory system when presented with stimuli after a (life-) long phase of deprivation and for planning therapeutic intervention. In rhythmic languages the general stress pattern conveys important information about word boundaries. Infant language acquisition relies on such cues and can be severely hampered when this information is missing, as seen for dyslexic children and children with specific language impairment. Here we ask whether children with a cochlear implant perceive differences in stress patterns during their language acquisition phase and if they do, whether it is present directly following implant stimulation or if and how much time is needed for the auditory system to adapt to the new sensory modality. We performed a longitudinal ERP study, testing in bimonthly intervals the stress pattern perception of 17 young hearing impaired children (age range: 9–50 months; mean: 22 months) during their first 6 months of implant use. An additional session before the implantation served as control baseline. During a session they passively listened to an oddball paradigm featuring the disyllable “baba,” which was stressed either on the first or second syllable (trochaic vs. iambic stress pattern). A group of age-matched normal hearing children participated as controls. Our results show, that within the first 6 months of implant use the implanted children develop a negative mismatch response for iambic but not for trochaic deviants, thus showing the same result as the normal hearing controls. Even congenitally deaf children show the same developing pattern. We therefore conclude (a) that young implanted children have early access to stress pattern information and (b) that they develop ERP responses similar to those of normal hearing children.
Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata

Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis. Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata. We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms’ shared lifestyle as free-living anaerobes.
Title Volitional enhancement of firing synchrony and oscillation by neuronal operant conditioning: interaction with neurorehabilitation and brain-machine interface

Right © 2014 Sakurai, Song, Tachibana and Takahashi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Multicast via Satellite : A Survey by

Many of the emerging applications in the Internet, such as tele-conferencing, distance-learning, distributed games, software updates, and distributed computing would benefit from multicast services. In many of these applications, there is a need to distribute information to many sites that are widely dispersed from each other. Communication satellites are a natural technology option and are extremely well suited for carrying such services. Despite the potential of satellite multicast, there exists little support for satellite IP multicast services. Both Internet Engineering and Internet Research Task Forces (IETF and IRTF) have been involved in a research effort to identify the design space for a general purpose reliable multicast protocol and standardize certain protocol components as building blocks. However, for satellite multicast services, several of these components have a different design space. In this paper, we attempt to provide an overview of the design space and the ways in which the network deployment and application requirements affect the solution space. We maintain a similar taxonomy to that of the IETF efforts, and identify which key components of a general multicast protocol are affected by two of the most common satellite network deployment scenarios. We also highlight some of the issues which we think are critical in the development of next generation satellite IP multicast services.
Education, Technological Progress and Economic Growth

An important role of education - and the resultant accumulation of human capital - for a less-developed economy is to facilitate technology diffusion in order for it to catch up with developed economies. This paper presents a model linking education, the accumulation of physical capital and technological progress. In the model, investment in education and the accumulation of physical capital are complementary, and intertwine with the technology progress through related effects on technology diffusion and the expansion of the technology frontier. The allocation of effort to education, the optimal savings rate and the technology gap are endogenously determined in the steady-state balanced growth equilibrium.
Generalizable knowledge outweighs incidental details in prefrontal ensemble code over time

Memories for recent experiences are rich in incidental detail, but with time the brain is thought to extract latent rules and structures common across past experiences. We show that over weeks following the acquisition of two distinct associative memories, neuron firing in the rat prelimbic prefrontal cortex (mPFC) became less selective for perceptual features unique to each association and, with an apparently different time-course, became more selective for common relational features. We further found that during exposure to a novel experimental context, memory expression and neuron selectivity for relational features immediately generalized to the new situation. These neural patterns offer a window into the network-level processes by which the mPFC develops a knowledge structure of the world that can be adaptively applied to new experiences. DOI: http://dx.doi. org/10.7554/eLife.22177. 001
Automatic Expansion of a Social Judgment Lexicon for Sentiment Analysis

We present a new method for automatically enlarging a sentiment lexicon for mining social judgments from text, i.e., extracting opinions about human subjects. We use a two-step approach: first, we find which adjectives can be used as human modifiers, and then we assign their polarity attribute. To identify the human modifiers, we developed a set of hand-crafted lexicosyntactic rules representing elementary copular and adnominal constructions where such predicates can be found. These are applied to a large n-gram collection, gathering evidence about human/not-human adjective behavior. The adjective and rule frequencies are then used as input features to a statistical classifier. In the second and final stage, we assign polarities to human adjectives, by exploring the graph of synonyms. We calculate the shortest distances of each adjective with unknown polarity to the human adjectives of each sentiment class with prior polarity in the initial lexicon. The computed distances for each adjective are then used as the input features of a statistical polarity classifier. The application of the proposed method to a collection of manually annotated adjectives showed its effectiveness for developing a finegrained sentiment lexicon for social judgment, which can be seen as a human domain-specific alternative to general-purpose lexicons. We focus on the polarity classification of Portuguese human adjective predicates, but the studied method could be applied to other languages and semantic predicates. The lexicon of human adjectives with polarities produced with this method is now available as an open resource.
Molecular Analysis of the Retinoic Acid Induced 1 Gene (RAI1) in Patients with Suspected Smith-Magenis Syndrome without the 17p11.2 Deletion

Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder characterized by multiple congenital anomalies. The syndrome is primarily ascribed to a ∼3.7 Mb de novo deletion on chromosome 17p11.2. Haploinsufficiency of multiple genes likely underlies the complex clinical phenotype. RAI1 (Retinoic Acid Induced 1) is recognized as a major gene involved in the SMS phenotype. Extensive genetic and clinical analyses of 36 patients with SMS-like features, but without the 17p11.2 microdeletion, yielded 10 patients with RAI1 variants, including 4 with de novo deleterious mutations, and 6 with novel missense variants, 5 of which were familial. Haplotype analysis showed two major RAI1 haplotypes in our primarily Caucasian cohort; the novel RAI1 variants did not occur in a preferred haplotype. RNA analysis revealed that RAI1 mRNA expression was significantly decreased in cells of patients with the common 17p11.2 deletion, as well as in those with de novo RAI1 variants. Expression levels varied in patients with familial RAI1 variants and in non-17p11.2 deleted patients without identified RAI1 defects. No correlation between SNP haplotype and RAI1 expression was found. Two clinical features, ocular abnormalities and polyembolokoilomania (object insertion), were significantly correlated with decreased RAI1 expression. While not significantly correlated, the presence of hearing loss, seizures, hoarse voice, childhood onset of obesity and specific behavioral aspects and the absence of immunologic abnormalities and cardiovascular or renal structural anomalies, appeared to be specific for the de novo RAI1 subgroup. Recognition of the combination of these features will assist in referral for RAI1 analysis of patients with SMS-like features without detectable microdeletion of 17p11.2. Moreover, RAI1 expression emerged as a genetic target for development of therapeutic interventions for SMS.
Effectiveness of Random Search in SVM hyper-parameter tuning

Classification is one of the most common machine learning tasks. SVMs have been frequently applied to this task. In general, the values chosen for the hyper-parameters of SVMs affect the performance of their induced predictive models. Several studies use optimization techniques to find a set of hyper-parameter values that induces classifiers with good predictive performance. This paper investigates the hypothesis that a simple Random Search method is sufficient to adjust the hyper-parameters of SVMs. A set of experiments compared the performance of five tuning techniques: three meta-heuristics commonly used, Random Search and Grid Search. The experimental results show that the predictive performance of models using Random Search is equivalent to those obtained using meta-heuristics and Grid Search, but with a lower computational cost.
The Importance of Financial Market Development on the Relationship Between Loan Guarantees for SMEs and Local Market Employment Rates

We empirically examine whether a major government intervention in the small-firm credit market yields significantly better results in markets that are less financially developed. The government intervention that we investigate is SBA-guaranteed lending. The literature on financing small and medium size enterprises (SMEs) suggests that small firms may be exposed to a particular type of market failure associated with credit rationing. And SMEs in markets that are less financially developed will likely face a greater degree of this market failure. To test our hypothesis, we use the level of bank deposits per capita as our relative measure of financial market development, and we use local market employment rates as our measure of economic performance. After controlling for the appropriate cross-sectional market characteristics, we find that SBA-guaranteed lending has a significantly more (less) positive impact on the average annual level of employment when the local market is relatively less (more) financially developed. This result has important implications for public policy directives concerning where SBA-guaranteed lending should be directed.
The roles of scene priming and location priming in object-scene consistency effects

Presenting consistent objects in scenes facilitates object recognition as compared to inconsistent objects. Yet the mechanisms by which scenes influence object recognition are still not understood. According to one theory, consistent scenes facilitate visual search for objects at expected places. Here, we investigated two predictions following from this theory: If visual search is responsible for consistency effects, consistency effects could be weaker (1) with better-primed than less-primed object locations, and (2) with less-primed than better-primed scenes. In Experiments 1 and 2, locations of objects were varied within a scene to a different degree (one, two, or four possible locations). In addition, object-scene consistency was studied as a function of progressive numbers of repetitions of the backgrounds. Because repeating locations and backgrounds could facilitate visual search for objects, these repetitions might alter the object-scene consistency effect by lowering of location uncertainty. Although we find evidence for a significant consistency effect, we find no clear support for impacts of scene priming or location priming on the size of the consistency effect. Additionally, we find evidence that the consistency effect is dependent on the eccentricity of the target objects. These results point to only small influences of priming to object-scene consistency effects but all-in-all the findings can be reconciled with a visual-search explanation of the consistency effect.
Conservation of the Nrf2-Mediated Gene Regulation of Proteasome Subunits and Glucose Metabolism in Zebrafish

The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Besides the exogenous stress response, Nrf2 has been found to regulate numerous cellular functions, including protein turnover and glucose metabolism; however, the evolutionary origins of these functions remain unknown. In the present study, we searched for novel target genes associated with the zebrafish Nrf2 to answer this question. A microarray analysis of zebrafish embryos that overexpressed Nrf2 revealed that 115 candidate genes were targets of Nrf2, including genes encoding proteasome subunits and enzymes involved in glucose metabolism. A real-time quantitative PCR suggested that the expression of 3 proteasome subunits (psma3, psma5, and psmb7) and 2 enzymes involved in glucose metabolism (pgd and fbp1a) were regulated by zebrafish Nrf2. We thus next examined the upregulation of these genes by an Nrf2 activator, diethyl maleate, using Nrf2 mutant zebrafish larvae. The results of real-time quantitative PCR and whole-mount in situ hybridization showed that all of these 5 genes were upregulated by diethyl maleate treatment in an Nrf2-dependent manner, especially in the liver. These findings implied that the Nrf2-mediated regulation of the proteasome subunits and glucose metabolism is evolutionarily conserved among vertebrates.
The role of emotionality in the acquisition of new concrete and abstract words

A processing advantage for emotional words relative to neutral words has been widely demonstrated in the monolingual domain (e.g., Kuperman et al., 2014). It is also well-known that, in bilingual speakers who have a certain degree of proficiency in their second language, the effects of the affective content of words on cognition are not restricted to the native language (e.g., Ferré et al., 2010). The aim of the present study was to test whether this facilitatory effect can also be obtained during the very early stages of word acquisition. In the context of a novel word learning paradigm, participants were trained on a set of Basque words by associating them to their Spanish translations. Words’ concreteness and affective valence were orthogonally manipulated. Immediately after the learning phase and 1 week later, participants were tested in a Basque go-no go lexical decision task as well as in a translation task in which they had to provide the Spanish translation of the Basque words. A similar pattern of results was found across tasks and sessions, revealing main effects of concreteness and emotional content as well as an interaction between both factors. Thus, the emotional content facilitated the acquisition of abstract, but not concrete words, in the new language, with a more reliable effect for negative words than for positive ones. The results are discussed in light of the embodied theoretical view of semantic representation proposed by Kousta et al. (2011).
Corruption, Public Finances, and the Unofficial Economy

The authors found that, in post-communist economies, the unofficial economy's share of GDP is determined by the extent of control rights held by bureaucrats and politicians. Exploring in detail the role of taxation and bribery, and using data from an expanded data set of 49 Latin American, OECD, and transition economies, the authors find that the unofficial economy accounts for a larger share of GDP where there is great bureaucratic inefficiency and discretion, and where firms experience a greater tax and regulatory burden, as well as more bribery and corruption. The unofficial economy is also much larger where there is less state revenue and where the rule of law is weak. They also find that countries with a larger unofficial economy tend to grow more slowly. Thus, this framework suggests an additional channel whereby corruption and ineffective regulatory and tax administration can result in lower growth: the unofficial economy. Wealthy OECD economies and some Eastern European economies find themselves the"good equilibrium"of relatively low regulatory and tax burden (not necessarily low statutory tax rates), sizable revenue mobilization, good rule of law and control of corruption, and a small unofficial economy. Several countries in Latin America and the former Soviet Union exhibit characteristics consistent with a"bad equilibrium": the discretionary application of heavy regulatory and tax burdens, the weakrule of law, heavy bribery, and an active unofficial economy. In this large country sample (unlike in the earlier framework for transition economies only), the authors find that it is the ineffective and discretionary application of regulatory and tax regimes in many countries -- not higher tax rates by itself -- that increase the size of the unofficial economy. The tax burden reported by firms appears to be more a function of regulatory and bureaucratic inefficiency and discretion rather than of tax rates alone.
Entrepreneurial growth expectations and information flows in networks

The study analyzes entrepreneur’s expectations regarding future growth by analyzing the relationship between information flows from networks and the perceived risk of decisions associated with the future size of a firm. The main proposition is that growth expectations might be the outcome of superior judgment stemming from privileged information derived from networks. To provide evidence in support of this hypothesis a sample selection model is estimated using a two-step estimation procedure. Cross-section questionnaire data are used in the empirical analysis. Evidence is provided on the role of inter-firm contacts and relationships as a mechanism able to assist entrepreneurs in better assessing and even reduce the risk and uncertainty associated with their present and future decisions regarding firm growth. The study provides evidence on the factors affecting expected growth rates while it explicitly formulates and tests the hypothesis that expectations regarding growth might be the outcome of superior judgment stemming from privileged information derived from networks. Analysis indicates that networks are indeed information mechanisms, however, such information should be specific to problem solving firm processes. Better informed entrepreneurs are those that foresee higher growth in the future, yet they are not blocked in only local networking.