Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyperactive BMP signaling induced by ALK2R206H requires type II receptor function in a Drosophila model for classic fibrodysplasia ossificans progressiva

Background: Fibrodysplasia Ossificans Progressiva (FOP) is an autosomal dominant disorder characterized by episodic deposition of heterotopic bone in place of soft connective tissue. All FOP‐associated mutations map to the BMP type I receptor, ALK2, with the ALK2R206H mutant form found in the vast majority of patients. The mechanism(s) regulating the expressivity of hyperactive ALK2R206H signaling throughout a patient's life is not well understood. Results: In Drosophila, human ALK2R206H receptor induces hyperactive BMP signaling. As in vertebrates, elevated signaling associated with ALK2R206H in Drosophila is ligand‐independent. We found that a key determinant for ALK2R206H hyperactivity is a functional type II receptor. Furthermore, our results indicate that like its Drosophila ortholog, Saxophone (Sax), wild‐type ALK2 can antagonize, as well as promote, BMP signaling. Conclusions: The dual function of ALK2 is of particular interest given the heterozygous nature of FOP, as the normal interplay between such disparate behaviors could be shifted by the presence of ALK2R206H receptors. Our studies provide a compelling example for Drosophila as a model organism to study the molecular underpinnings of complex human syndromes such as FOP. Developmental Dynamics 241:200–214, 2012. © 2011 Wiley Periodicals, Inc.
Cut-elimination and the decidability of reachability in alternating pushdown systems

We propose a new approach to formalize alternating pushdown systems as natural-deduction style inference systems. In this approach, the decidability of reachability can be proved as a simple consequence of a cut-elimination theorem for the corresponding inference system. Then, we show how this result can be used to extend an alternating pushdown system into a complete system where, for every configuration $A$, either $A$ or $\neg A$ is provable. The key idea is that cut-elimination permits to build a system where a proposition of the form $\neg A$ has a co-inductive (hence possibly infinite) proof if and only if it has an inductive (hence finite) proof.
Microcultures and informal learning: a heuristic guiding analysis of conditions for informal learning in local higher education workplaces

This article contributes to knowledge about learning in workgroups, so called microcultures in higher education. It argues that socially constructed and institutionalised traditions, recurrent practices, and tacit assumptions in the various microcultures influence academic teachers towards certain behaviour. In line with this perspective, we present a heuristic with the potential to differentiate various types of microcultures: the commons, the market, the club, and the square. The heuristic is based on a socio-cultural perspective and research on collective action. Its purpose is to assist academic developers to fine-tune their approaches while engaging with colleagues, but also to aid further inquiry into how institutionalised norms and traditions influence academic teaching and student learning.
A Deadlock Prevention Approach based on Atomic Transaction for Resource Co-allocation

Grid is a distributed platform that makes the utilization of distributed and powerful sharing resources for those submitted applications more conveniently. Applications designed to execute on grid frequently require the simultaneous co-allocation of multiple resources to meet performance requirement. In particular, the problem of co-allocating grid resources that span multiple administrative domains is complicated by the possibility of deadlock and the lack of means for changing information between the independent applications. Motivated by this, this paper develops a new method for fast co-allocation of grid resources. The proposed method is based on Atomic Transaction and is free from deadlock. Experimental results demonstrate that the proposed method yields a significant performance improvement over other existing deadlock prevention methods.
Conductance-based computational model of basal ganglia

The basal ganglia play an important role in motor control and their malfunction is implicated in several disorders including Parkinson's disease (PD), in which dopamine concentration is greatly reduced. This is associated with changes in their firing patterns, evidenced by increase in firing rate of output nuclei of basal ganglia and synchronization between neurons of different micro-circuitry of basal ganglia. The most effective way to alleviate the symptoms of PD is to take Levodopa which replenishes dopamine storage in the brain. However, long-term use of Levodopa results in motor fluctuations and dyskinesia. Here, we developed a conductance-based computational model of basal ganglia which considers modulatory effects of dopamine on its target nucleus, that is on striatum. This model can be used to investigate the effect of variations of the dopamine levels on motor fluctuation. Moreover, the effect of applying deep brain electrical stimulation on different nuclei of basal ganglia can be investigated through the proposed model.
The Effect of Explaining on Learning: a Case Study with a Data Normalization Tutor

Several studies have shown that explaining actions increases students' knowledge. In this paper, we discuss how NORMIT supports self-explanation. NORMIT is a constraint-based tutor that teaches data normalization. We present the system first, and then discuss how it supports self-explanation. We hypothesized the self-explanation support in NORMIT would result in increased problem solving skills and better conceptual knowledge. An evaluation study of the system was performed, the results of which confirmed our hypothesis. Students who self-explained learnt constraints significantly faster, and acquired more domain knowledge.
Epigenetic Determinants of CYP1A1 Induction by the Aryl Hydrocarbon Receptor Agonist 3,3',4,4',5-Pentachlorobiphenyl (PCB 126)

Many enzymes involved in xenobiotic metabolism, including cytochrome P450 (CYP) 1A1, are regulated by the aryl hydrocarbon receptor (AhR). 3,3',4,4',5-Pentachlorobiphenyl (PCB 126) is a potent ligand for AhR and can thus induce the expression of CYP1A1. Interestingly, we observed that human carcinoma cell lines derived from different types of epithelial cells displayed divergent degrees of CYP1A1 induction after exposure to PCB 126. Since epigenetic mechanisms are known to be involved in cell type-specific gene expression, we sought to assess the epigenetic determinants of CYP1A1 induction in these carcinoma cell lines. In contrast to HepG2 hepatocarcinoma cells, HeLa cervical carcinoma cells showed significantly lower levels of CYP1A1 mRNA expression following PCB 126 exposure. Our results show that the two cell lines maintained differences in the chromatin architecture along the CYP1A1 promoter region. Furthermore, treatment with the epigenetic modifiers, trichostatin A (TSA) and 5-aza-2'-deoxycytidine (5-Aza-dC), significantly increased the expression of CYP1A1 after PCB 126 treatment in HeLa cells. However, we did not observe apparent differences in methylation levels or specific location of CpG DNA methylation between the two cell lines in the analyzed CYP1A1 promoter region. Taken together, our findings suggest that the differences in CYP1A1 expression between HepG2 and HeLa cells are due to differences in the chromatin architecture of the CYP1A1 promoter and thus establish a role of epigenetic regulation in cell-specific CYP1A1 expression.
An Ultraviolet to Mid-Infrared Study of the Physical and Wind Properties of HD 164270 (WC9) and Comparison to BD +30 3639 ([WC9])

We present new Spitzer IRS observations of HD 164270 (WC9, WR103). A quantitative analysis of the UV, optical, near-, and mid-IR spectra of HD 164270 is presented, allowing for line blanketing and wind clumping, revealing T* ~ 48 kK, log L/L☉ ~ 4.9, and ~ 10-5 M☉ yr-1 for a volume filling factor of f ~ 0.1. Our models predict that He is partially recombined in the outer stellar wind, such that recent radio-derived mass-loss rates of WC9 stars have been underestimated. We obtain C/He ~ 0.2 and O/He ~ 0.01 by number from optical diagnostics. Mid-IR fine-structure lines of [Ne II] 12.8 μm and [S III] 18.7 μm are observed, with [Ne III] 15.5 μm and [S IV] 10.5 μm absent. From these we obtain Ne/He ~ Ne+/He = 2.2 × 10-3 by number, 7 times higher than the solar value (as recently derived by Asplund et al.), and S/He ~ S2+/He = 5.1 × 10-5 by number. From a comparison with similar results for other WC subtypes we conclude that WC9 stars are as chemically advanced as earlier subtypes. We consider why late WC stars are exclusively observed in high-metallicity environments. In addition, we compare the UV/optical/mid-IR spectroscopic morphology of HD 164270 with the planetary nebula central star BD +30 3639 ([WC9]). Their UV and optical signatures are remarkably similar, such that our quantitative comparisons confirm similarities in stellar temperature, wind densities, and chemistry first proposed by Smith & Aller, in spite of completely different evolutionary histories, with HD 164270 presently a factor of 10 more massive than BD +30 3639. At mid-IR wavelengths, the dust from the dense young nebula of BD +30 3639 completely dominates its appearance, in contrast with HD 164270.
I/O-Efficient Algorithms on Triangle Listing and Counting

This article studies I/O-efficient algorithms for the triangle listing problem and the triangle counting problem, whose solutions are basic operators in dealing with many other graph problems. In the former problem, given an undirected graph G, the objective is to find all the cliques involving 3 vertices in G. In the latter problem, the objective is to report just the number of such cliques without having to enumerate them. Both problems have been well studied in internal memory, but still remain as difficult challenges when G does not fit in memory, thus making it crucial to minimize the number of disk I/Os performed. Although previous research has attempted to tackle these challenges, the state-of-the-art solutions rely on a set of crippling assumptions to guarantee good performance. Motivated by this, we develop a new algorithm that is provably I/O and CPU efficient at the same time, without making any assumption on the input G at all. The algorithm uses ideas drastically different from all the previous approaches, and outperforms the existing competitors by a factor of over an order of magnitude in our extensive experimentation.
Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai

The marine mollusk Aplysia is a useful model organism for studying the cellular bases of behavior and plasticity. However, molecular studies of Aplysia have been limited by the lack of genomic information. Recently, a large scale characterization of neuronal transcripts was performed in A. californica. Here, we report the analysis of a parallel set of neuronal transcripts from a closely related species A. kurodai found in the northwestern Pacific. We collected 4,859 nonredundant sequences from the nervous system tissue of A. kurodai. By performing microarray and real-time PCR analyses, we found that ApC/EBP, matrilin, antistasin, and eIF3e clones were significantly up-regulated and a BAT1 homologous clone was significantly down-regulated by 5-HT treatment. Among these, we further demonstrated that the Ap-eIF3e plays a key role in 5-HT-induced long-term facilitation (LTF) as a positive regulator.
Effects of Action Video Game Experience on Change Detection

Monitoring digital displays for changes will be an increasing part of a soldier's duties as the U.S. Army transforms to a networked system of systems; however, it is well established that humans often fail to detect such changes in contexts with competing demands on attention. Interventions that enhance visual attention might also enhance change detection, because focused attention has been identified as a requirement for change detection. Given current claims that habitual experience with action video games can increase attentional resources, we investigated whether such experience would lessen the incidence of change blindness in two change detection tasks. Although we replicated a previously demonstrated difference between players and nonplayers on the flanker-compatibility test (Green & Bavelier, 2003), we failed to find evidence that habitual action video game players were superior to nonplayers when it came to change detection.
Oxygen in the Southern Ocean From Argo Floats: Determination of Processes Driving Air‐Sea Fluxes

The Southern Ocean is of outsized significance to the global oxygen and carbon cycles with relatively poor measurement coverage due to harsh winters and seasonal ice cover. In this study, we use recent advances in the parameterization of air-sea oxygen fluxes to analyze nine years of oxygen data from a recalibrated Argo oxygen dataset and from air-calibrated oxygen floats deployed as part of the Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) project. From this combined dataset of 150 floats, we find a total Southern Ocean oxygen sink of -183 ± 80 Tmol yr−1 (positive to the atmosphere), greater than prior estimates. The uptake occurs primarily in the Polar-Frontal Antarctic Zone (PAZ, -94 ± 30 Tmol O2 yr−1) and Seasonal Ice Zone (SIZ, -111 ± 9.3 Tmol O2 yr−1). This flux is driven by wintertime ventilation, with a large portion of the flux in the SIZ passing through regions with fractional sea ice. The Subtropical Zone (STZ) is seasonally driven by thermal fluxes and exhibits a net outgassing of 47 ± 29 Tmol O2 yr−1 that is likely driven by biological production. The Subantarctic Zone (SAZ) uptake is -25 ± 12 Tmol O2 yr−1. Total oxygen fluxes were separated into a thermal and non-thermal component. The non-thermal flux is correlated with net primary production and mixed layer depth in the STZ, SAZ, and PAZ, but not in the SIZ where seasonal sea ice slows the air-sea gas flux response to the entrainment of deep, low oxygen waters.
International collaboration in packaging education: hands-on system-on-package (SOP) graduate level courses at Indian Institute of Science and Georgia Tech PRC

System-on-package (SOP) continues to revolutionize the realization of convergent systems in microelectronics packaging. The SOP concept which began at the Packaging Research Center (PRC) at Georgia Tech has benefited its international collaborative partners in education including the Indian Institute of Science (IISc). The academic program for electronics packaging currently in the Centre for Electronics Design and Technology (CEDT) at IISc is aimed at educating a new breed of globally-competitive engineers in the new SOP technology to meet the next generation workforce need of global as well as the Indian electronics industry. This has been possible with the hands-on electronics packaging course being taught at IISc. The first-ever fundamental systems packaging textbook from the PRC, and in which IISc has been a partner has brought awareness among the engineering students as to the need for better packaging in electronic products and systems. This paper will highlight the electronics packaging scenario in India, the first-of-its-kind electronics packaging course curriculum in CEDT at the IISc, explain the benefits of research integration with education and look at how SOP technology and packaging education has helped to enrich the engineering students at the graduate level.
Similarity in form and function of the hippocampus in rodents, monkeys, and humans

We begin by describing an historical scientific debate in which the fundamental idea that species are related by evolutionary descent was challenged. The challenge was based on supposed neuroanatomical differences between humans and other primates with respect to a structure known then as the hippocampus minor. The debate took place in the early 1860s, just after the publication of Darwin’s famous book. We then recount the difficult road that was traveled to develop an animal model of human memory impairment, a matter that also turned on questions about similarities and differences between humans and other primates. We then describe how the insight that there are multiple memory systems helped to secure the animal model and how the animal model was ultimately used to identify the neuroanatomy of long-term declarative memory (sometimes termed explicit memory). Finally, we describe a challenge to the animal model and to cross-species comparisons by considering the case of the concurrent discrimination task, drawing on findings from humans and monkeys. We suggest that analysis of such cases, based on the understanding that there are multiple memory systems with different properties, has served to emphasize the similarities in memory function across mammalian species.
Azooxanthellate? Most Hawaiian black corals contain Symbiodinium

The ecological success of shallow-water reef-building corals (Hexacorallia: Scleractinia) is framed by their intimate endosymbiosis with photosynthetic dinoflagellates in the genus Symbiodinium (zooxanthellae). In contrast, the closely related black corals (Hexacorallia: Anthipatharia) are described as azooxanthellate (lacking Symbiodinium), a trait thought to reflect their preference for low-light environments that do not support photosynthesis. We examined 14 antipatharian species collected between 10 and 396 m from Hawai'i and Johnston Atoll for the presence of Symbiodinium using molecular typing and histology. Symbiodinium internal transcribed spacer-2 (ITS-2) region sequences were retrieved from 43 per cent of the antipatharian samples and 71 per cent of the examined species, and across the entire depth range. The ITS-2 sequences were identical or very similar to those commonly found in shallow-water scleractinian corals throughout the Pacific. Histological analyses revealed low densities of Symbiodinium cells inside antipatharian gastrodermal tissues (0–92 cells mm−3), suggesting that the Symbiodinium are endosymbiotic. These findings confirm that the capacity to engage in endosymbiosis with Symbiodinium is evolutionarily conserved across the cnidarian subclass Hexacorallia, and that antipatharians associate with Symbiodinium types found in shallow-water scleractinians. This study represents the deepest record for Symbiodinium to date, and suggests that some members of this dinoflagellate genus have extremely diverse habitat preferences and broad environmental ranges.
Protein kinase C epsilon mediation of CRF- and ethanol-induced GABA release in central amygdala

In the central amygdala (CeA), ethanol acts via corticotrophin-releasing factor (CRF) type 1 receptors to enhance GABA release. Amygdala CRF mediates anxiety associated with stress and drug dependence, and it regulates ethanol intake. Because mutant mice that lack PKCε exhibit reduced anxiety-like behavior and alcohol consumption, we investigated whether PKCε lies downstream of CRF1 receptors in the CeA. Compared with PKCε+/+ CeA neurons, PKCε−/− neurons showed increased GABAergic tone due to enhanced GABA release. CRF and ethanol stimulated GABA release in the PKCε+/+ CeA, but not in the PKCε−/− CeA. A PKCε-specific inhibitor blocked both CRF- and ethanol-induced GABA release in the PKCε+/+ CeA, confirming findings in the PKCε−/− CeA. These results identify a PKCε signaling pathway in the CeA that is activated by CRF1 receptor stimulation, mediates GABA release at nerve terminals, and regulates anxiety and alcohol consumption.
Constructions of Permutation Arrays for Certain Scheduling Cost Measures

Constructions of permutation arrays are presented that are optimal or nearly‐optimal with respect to two cost measures: the so‐called longest‐jump measure and the longest‐monotone‐greedy‐subsequence measure. These measures arise in the context of scheduling problems in asynchronous, shared memory, multiprocessor machines. © 1995 Wiley Periodicals, Inc.
Placing cybereducation in the UK classroom

The use of the Internet in the classroom has often been characterized as a practice that disconnects the teacher from traditional forms of externally imposed influence. This paper examines this assertion by mapping the emerging field of cybereducation and considering how endemic knowledge is contextualized by national curricular authorities. The field theories of Pierre Bourdieu and Basil Bernstein are employed in order to demonstrate the relationship between expert discourse and classroom pedagogy, using the National Grid for Learning (NGfL) as a case study. This attempt to capture the dynamics of cybereducation ultimately suggests how this emergent intellectual field’s fragmentation and decoupling from State education forces offers policymakers the capacity to influence use. Progress of the UK government in integrating knowledge from an emergent educational field with its incumbent priorities is gauged, demonstrating the way in which national education officials have attempted to constrain potential departures from unregulated, officially mandated curriculum.
Cognitive function in elderly can be ameliorated by training in temporal information processing.

PURPOSES The study offers a promising direction for rehabilitation, as for the first time cognitive benefits of training in temporal information processing (TIP) using Fast ForWord were identified in elderly adults. As TIP creates a fundamental basis for human cognition, we focussed on two questions: (1) can TIP be improved by Fast ForWord training? (2) can a transfer of the trained skill from the time domain to the untrained cognitive domain be observed after the training? METHODS 30 healthy seniors were classified according to three groups which underwent either temporal Fast ForWord training (Group A) or non-temporal control training (Group B). Group C was comprised of non-active controls. Various cognitive functions, i.e., TIP, as well as some aspects of attention and short-term memory, were compared before and after the training. RESULTS Only for Group A was the improved TIP accompanied by amelioration of both attentional and memory resources. The observed improvements were maintained for up to 18 months. Although in Group B some improvements in TIP were also evidenced after the training, significant improvements were observed neither in Group B nor C. CONCLUSIONS Temporal training is effective for amelioration of cognitive function in seniors. Its application may foster improved life quality in increasingly aging societies.
Automatic orthographic alignment of speech

The objective of the research is to develop a procedure for automatically aligning an orthographic transcription with the speech waveform. The alignment process was performed at the phonetic level. The words were converted into a sequence of phonemes using an on-line dictionary and a network of phones was created using phonological rules. The phonetic alignment was accomplished using a microsegment-based approach which utilized a probabilistic framework. Acoustic boundaries were proposed at points of maximal spectral change, and were aligned with the phone network using a timewarping algorithm incorporating both acoustic and durational weights to the score. This approach was then compared to the traditional frame-based technique, which can be interpreted as proposing boundaries at every frame before the process of aligning with the network. The acoustic as well as the durational models were trained on the TIMIT corpus, and the algorithm was tested on a different subset of the corpus. To investigate the robustness of the procedure, the resulting algorithm was trained and evaluated on the same subsets, respectively, of the NTIMIT corpus, which is the telephone version of the TIMIT utterances. A word overlap ratio of 93.2 % and a word absolute error of 20.4 ms were achieved on the TIMIT corpus. This corresponds to a phone overlap ratio of 81.7 % and a phone absolute error of 12.9 ms. Thesis Supervisor: James R. Glass Title: Research Scientist