Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease

The tripartite DENN module, comprised of a N-terminal longin domain, followed by DENN, and d-DENN domains, is a GDP-GTP exchange factor (GEFs) for Rab GTPases, which are regulators of practically all membrane trafficking events in eukaryotes. Using sequence and structure analysis we identify multiple novel homologs of the DENN module, many of which can be traced back to the ancestral eukaryote. These findings provide unexpected leads regarding key cellular processes such as autophagy, vesicle-vacuole interactions, chromosome segregation, and human disease. Of these, SMCR8, the folliculin interacting protein-1 and 2 (FNIP1 and FNIP2), nitrogen permease regulator 2 (NPR2), and NPR3 are proposed to function in recruiting Rab GTPases during different steps of autophagy, fusion of autophagosomes with the vacuole and regulation of cellular metabolism. Another novel DENN protein identified in this study is C9ORF72; expansions of the hexanucleotide GGGGCC in its first intron have been recently implicated in amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD). While this mutation is proposed to cause a RNA-level defect, the identification of C9ORF72 as a potential DENN-type GEF raises the possibility that at least part of the pathology might relate to a specific Rab-dependent vesicular trafficking process, as has been observed in the case of some other neurological conditions with similar phenotypes. We present evidence that the longin domain, such as those found in the DENN module, are likely to have been ultimately derived from the related domains found in prokaryotic GTPase-activating proteins of MglA-like GTPases. Thus, the origin of the longin domains from this ancient GTPase-interacting domain, concomitant with the radiation of GTPases, especially of the Rab clade, played an important role in the dynamics of eukaryotic intracellular membrane systems.
The Fragility of Overshooting

Using VAR, a large literature claims to find evidence of some form of Dornbuschovershooting. But the evidence is fragile in the sense of Leamer. The literature uses the wrong test for overshooting, unusually narrow confidence intervals and questionable shocks. In addition, it is difficult to reconcile overshooting with the fact that daily and weekly exchangerates are approximately martingales.
Novel scheme for infrared image enhancement based on Contourlet transform

Low contrast and large noise are two main characteristics of infrared image, considering this characteristics, a novel scheme for infrared image enhancement based on Contourlet transform is proposed. Firstly, Contourlet transform is performed on the original infrared image, we can obtain lowpass subband and bandpass subband at different scales and directions. At lowpass subband, the linear transformation based on the maximal and minimal coefficient of subband is applied to enhance the global contrast. At bandpass subband, the fuzzy nonlinear enhancement operator is used to enhance the high frequency subband coefficient, the objective characteristics of the texture is enhanced, but the background is suppressed. Finally, the inverse transform of Contourlet is applied to produce enhanced infrared image. Through simulation, the results show that the proposed scheme could enhance contrast and highlight the edge of the image texture information and details effectively.
Prostate Stromal Cells Express the Progesterone Receptor to Control Cancer Cell Mobility

Background Reciprocal interactions between epithelium and stroma play vital roles for prostate cancer development and progression. Enhanced secretions of cytokines and growth factors by cancer associated fibroblasts in prostate tumors create a favorable microenvironment for cancer cells to grow and metastasize. Our previous work showed that the progesterone receptor (PR) was expressed specifically in prostate stromal fibroblasts and smooth muscle cells. However, the expression levels of PR and its impact to tumor microenvironment in prostate tumors are poorly understood. Methods Immunohistochemistry assays are applied to human prostate tissue biopsies. Cell migration, invasion and proliferation assays are performed using human prostate cells. Real-time PCR and ELISA are applied to measure gene expression at molecular levels. Results Immunohistochemistry assays showed that PR protein levels were decreased in cancer associated stroma when compared with paired normal prostate stroma. Using in vitro prostate stromal cell models, we showed that conditioned media collected from PR positive stromal cells inhibited prostate cancer cell migration and invasion, but had minor suppressive impacts on cancer cell proliferation. PR suppressed the secretion of stromal derived factor-1 (SDF-1) and interlukin-6 (IL-6) by stromal cells independent to PR ligands. Blocking PR expression by siRNA or supplementation of exogenous SDF-1 or IL-6 to conditioned media from PR positive stromal cells counteracted the inhibitory effects of PR to cancer cell migration and invasion. Conclusions Decreased expression of the PR in cancer associated stroma may contribute to the elevated SDF-1 and IL-6 levels in prostate tumors and enhance prostate tumor progression.
Text-mining approach for verifying alignment of information systems curriculum with industry skills

Managing and developing competencies or skills are vital to professional development of an individual. Many tertiary education institutions are therefore focused on developing curriculum that will help the graduating students acquire skills that are aligned with industry practice. Industry skills frameworks such as Skills Framework for the Information Age (SFIA) define the professionals required for an IT professional. Therefore, mapping the curriculum competencies to the industry skills framework has a dual purpose of aiding the educationists to improve the curriculum, and the students to plan the courses according to their career plan. Existing mapping methods are manual and painstaking processes. In this paper, we present an automated solution based on text analytics techniques to map the curriculum to industry framework and provide a visual based analysis to discover the strengths and weakness of the curriculum. We evaluated our solution model on an undergraduate core curriculum; Bachelor of Science (Information Systems Management) degree program BSc (ISM), offered by the School of Information Systems (SIS), Singapore Management University (SMU) and Skills Framework for the Information Age (SFIA).
Efficacy Of Back Propagation Neural Network Based On Various Statistical Measures For Pd Pattern Classification Task

Partial Discharge is the breakdown confined to the localized regions of the insulating medium. The analysis and classification of Partial Discharge based on its site of occurrence is a complex process notwithstanding the intricacies involved in the digital computer acquisition system, since partial discharge is inherently a stochastic and a non-Markovian process in which there can be significant statistical variability. Since each defect has a particular deterioration mechanism, it is imperative to discern the correlation between the discharge patterns and the nature of defect in order to ascertain the quality of insulation. Neural Network which is a non-parametric method has been a recent innovative technique suitable for partial discharge pattern classification. The Back Propagation Algorithm Neural Network is verified and validated for the various inputs based on established validation techniques. As against the conventional technique of using mathematical descriptors adopted by previous researchers, unique characteristic input feature vectors have been devised in this work in order to provide a possible solution to a simple yet an effective preprocessing methodology. The efficacy of the classification of the standard partial discharge defect sources has been evaluated and analyzed
The Legislative Upheaval in Public-Sector Labor Law: A Search for Common Elements

The 2010 elections lead to major changes in the law governing public employee collective bargaining in numerous states. Most visible were the changes in Wisconsin, which led to the largest demonstrations in Madison since the Vietnam War, and in Ohio which were repealed by an overwhelming vote in a public referendum. Less noticed were repeals of collective bargaining laws in Oklahoma and Tennessee and significant changes to the laws in Idaho, Illinois, Indiana, Massachusetts, Michigan, Nebraska, Nevada and New Jersey. This article examines the legislative upheavals in these states, searching for common elements. It finds the following trends among the enactments: eliminating collective bargaining rights for all or some employees, limiting the scope of bargaining, changes to impasse resolution processes in ways that advantage employers, and providing for amending or revoking collective bargaining agreements during period of fiscal distress. It places these changes in historical context, observing that the 1990s saw a similar upheaval that limited public employee collective bargaining rights in various states while the 2000s saw the pendulum swing in the opposite direction as many states expanded public employee collective bargaining. It suggests that future swings of the pendulum will depend on the outcomes in future elections.
Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks

The extent to which convergent adaptation to similar ecological niches occurs by a predictable genetic basis remains a fundamental question in biology. Threespine stickleback fish have undergone an adaptive radiation in which ancestral oceanic populations repeatedly colonized and adapted to freshwater habitats. In multiple lakes in British Columbia, two different freshwater ecotypes have evolved: a deep‐bodied benthic form adapted to forage near the lake substrate, and a narrow‐bodied limnetic form adapted to forage in open water. Here, we use genome‐wide linkage mapping in marine × benthic F2 genetic crosses to test the extent of shared genomic regions underlying benthic adaptation in three benthic populations. We identify at least 100 Quantitative Trait Loci (QTL) harboring genes influencing skeletal morphology. The majority of QTL (57%) are unique to one cross. However, four genomic regions affecting eight craniofacial and armor phenotypes are found in all three benthic populations. We find that QTL are clustered in the genome and overlapping QTL regions are enriched for genomic signatures of natural selection. These findings suggest that benthic adaptation has occurred via both parallel and nonparallel genetic changes.
Special education public management and formalism in inclusive public policies - the case of Brazil

The idea of inclusive education has gained prominence in the ideological context of modern Western democracies. Thus, this analysis focuses on the understanding of how the Brazilian inclusive education has been managed from the Decree-Law n° 6.571/2008, which was repealed on November 17, 2011, considering the formalism perspective. Formalism is taken as a perspective of analysis of the inclusive public policies, which allows us to question the apparent stability and uniformity of institutional practices and discourse of the national administration. The works approach is largely qualitative, and uses multiple methods. Two steps were taken, starting with all the Brazilian State Boards of Education (survey research), and concluding with the Rio Grande do Norte State Board of Education and one of its school (case study). Data was collected through documental research and interviews with key actors, and analyzed by content analysis. It was found that, despite the legal pressure on the environment to an isomorphism of practices among State Boards, there are peculiarities among them, justified by the contextual and cultural aspects that are shared by actors and organizations. In the specific case study of the Rio Grande do Norte State Board of Education, it was concluded that the formalistic practice allows questioning the effectiveness of the official knowledge policies and its other form of narrative that regards not only the special education, but the very plurality of logical and social experiences. From a theoretical point of view, the study has called attention to the presence of formalism in special education administration.
Energy efficiency in cooperative cognitive wireless networks

In this work, we analyze the energy efficiency of a wireless link, while considering spectrum sharing, and cooperation. Insightful results are obtained using a simple network model, with two source-destination pairs. We assume that one source-destination pair has higher priority to use the spectrum, while the other pair is allowed to access the channel under power constraints. The proposed cooperative scheme, named Cooperative Underlay, allows simultaneous transmissions of both high- and low-priority users, and the low-priority user may be requested to act as a relay. We investigate the trade-off between energy efficiency and throughput for the high-priority user, with and without cooperation, and demonstrate the improvement in energy efficiency due to the use of cooperation. Additionally, we study the case that the relay node can transmit and receive simultaneously, and discuss the effect of self-interference in the energy efficiency, for different degrees of accuracy in interference cancellation.
Event-Handling Based Smart Video Surveillance System

Smart video surveillance is well suited for a broad range of applications. Moving object classification in the field of video surveillance is a key component of smart surveillance software. In this paper, we have proposed reliable software with its large features for people and object classification which works well in challenging real-world constraints, including the presence of shadows, low resolution imagery, occlusion, perspective distortions, arbitrary camera viewpoints, and groups of people. We have discussed a generic model of smart video surveillance systems that can meet requirements of strong commercial applications and also shown the implication of the software for the security purposes which made the whole system as a smart video surveillance. Smart surveillance systems use automatic image understanding techniques to extract information from the surveillance data and handling events and stored data efficiently.
Efficient acclimation of the chloroplast antioxidant defence of Arabidopsis thaliana leaves in response to a 10- or 100-fold light increment and the possible involvement of retrograde signals

Chloroplasts are equipped with a nuclear-encoded antioxidant defence system the components of which are usually expressed at high transcript and activity levels. To significantly challenge the chloroplast antioxidant system, Arabidopsis thaliana plants, acclimated to extremely low light slightly above the light compensation point or to normal growth chamber light, were moved to high light corresponding to a 100- and 10-fold light jump, for 6 h and 24 h in order to observe the responses of the water-water cycle at the transcript, protein, enzyme activity, and metabolite levels. The plants coped efficiently with the high light regime and the photoinhibition was fully reversible. Reactive oxygen species (ROS), glutathione and ascorbate levels as well as redox states, respectively, revealed no particular oxidative stress in low-light-acclimated plants transferred to 100-fold excess light. Strong regulation of the water-water cycle enzymes at the transcript level was only partly reflected at the protein and activity levels. In general, low light plants had higher stromal (sAPX) and thylakoid ascorbate peroxidase (tAPX), dehydroascorbate reductase (DHAR), and CuZn superoxide dismutase (CuZnSOD) protein contents than normal light-grown plants. Mutants defective in components relevant for retrograde signalling, namely stn7, ex1, tpt1, and a mutant expressing E . coli catalase in the chloroplast showed unaltered transcriptional responses of water-water cycle enzymes. These findings, together with the response of marker transcripts, indicate that abscisic acid is not involved and that the plastoquinone redox state and reactive oxygen species do not play a major role in regulating the transcriptional response at t=6 h, while other marker transcripts suggest a major role for reductive power, metabolites, and lipids as signals for the response of the water-water cycle.
Crevicular Alkaline Phosphatase Activity and Rate of Tooth Movement of Female Orthodontic Subjects under Different Continuous Force Applications

Purpose. This study is aimed to compare the effects of two different orthodontic forces on crevicular alkaline phosphatase activity, rate of tooth movement, and root resorption. Materials and Methods. Twelve female subjects of class II division 1 malocclusion participated. Maxillary canines with bonded fixed appliances acted as the tested teeth, while their antagonists with no appliances acted as the controls. Canine retraction was performed using nickel titanium coil spring that delivered forces of 100 gm or 150 gm to either side. Crevicular fluid was analyzed for ALP activity, and study models were casted to measure tooth movements. Root resorption was assessed using periapical radiographs before and after the force application. Results. ALP activity at the mesial sites peaked at week 1 for 150 gm group with significant differences when compared with the 100 gm group. Cumulative canine movements were significantly greater in the 150 gm force (2.10 ± 0.50 mm) than in the 100 gm force (1.57 ± 0.44 mm). No root resorption was in the maxillary canines after retraction. Conclusions. A force of 150 gm produced faster tooth movements and higher ALP activity compared with the 100 gm group and had no detrimental effects such as root resorption.
Noise reduction in PET sinograms using non-local total variation regularization

Positron Emission Tomography is a technique of molecular imaging and provides information about biochemical process within the body of a patient, it is employed for diagnosis, staggering, and treatment planning. However, the resulting images have high noise levels that may cause difficulties for reading and interpreting the images by medical staff. For this reason, it is necessary to perform a denoising step to achieve better signal to noise ratio. In this paper, an approach is presented to denoise Positron Emission Tomography sinogram images using non-local total variation in the sinogram domain. The images are modeled in the sinogram domain using a Poisson noise model, it is proposed to adapt the SPIRAL algorithm to approximate the objective function to be minimized with separable quadratic functions to include the nonlocal total variation as a regularization term.
In Vivo Competence of Murine Cytomegalovirus under the Control of the Human Cytomegalovirus Major Immediate-Early Enhancer in the Establishment of Latency and Reactivation

ABSTRACT The human cytomegalovirus (HCMV) major immediate-early enhancer has been postulated to play a pivotal role in the control of latency and reactivation. However, the absence of an animal model has obstructed a direct test of this hypothesis. Here we report on the establishment of an in vivo, experimentally tractable system for quantitatively investigating physiological functions of the HCMV enhancer. Using a neonate BALB/c mouse model, we show that a chimeric murine CMV under the control of the HCMV enhancer is competent in vivo, replicating in key organs of mice with acute CMV infection and exhibiting latency/reactivation features comparable for the most part to those of the parental and revertant viruses.
Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird

Phylogeographical studies of Nearctic songbirds conducted to date have yielded unexpectedly low levels of genetic differentiation and weak phylogeographical structure in mitochondrial DNA lineages as compared with species studied in Neotropical areas. Factors leading to this pattern may include (i) gene flow, (ii) population expansions from bottlenecked populations, and (iii) selective sweeps. Here we provide evidence for the role played by Pleistocene postglacial population expansions on the phylogeography of MacGillivray's warbler (Oporornis tolmiei), a long–distance migratory bird. Samples from 12 breeding localities in the temperate USA were compared with those from two localities in north–astern Mexico. The former showed evidence of a Late Pleistocene population expansion as indicated by low haplotype and nucleotide diversity, a star–like phylogeny of alleles, and a mismatch distribution indicating a sudden increase in effective population size. By contrast, the Mexican population showed high levels of genetic diversity and a mismatch distribution as expected for a population unaffected by sudden demographic change. Haplotypes from the two regions formed two distinct phylogroups which separated roughly one million years ago according to a conventional molecular clock for songbirds. This study provides support for the Pleistocene expansion hypothesis in MacGillivray's warbler and suggests that postglacial expansion of bottlenecked populations is responsible for the lack of variation and structure reported for most North American songbird species.
Real-time Video over the Internet : A Big Picture

Real-time video over the Internet is becoming an important component of many multimedia applications. Due to both the requirements from video applications and the nature of the current Internet (e.g., delay, loss, and heterogeneity), there are many challenging issues for transporting real-time video over the Internet. This paper takes a holistic approach to address key challenges from both transport and compression perspectives. In particular, we outline a framework for real-time video over the Internet, which includes the following four components: congestion control, error control, error-resilient mechanisms and packetization. For each of the four components, we discuss existing proposed solutions. We point out that there is a need of synergy from both transport and compression perspectives in designing protocols and algorithms for real-time video over the Internet.
Amplification of compressional MHD waves in systems with forced entropy oscillations

The propagation of compressional MHD waves is studied for an externally driven system. It is assumed that the combined action of the external sources and sinks of the entropy results in the harmonic oscillation of the entropy (and temperature) in the system. It is found that with the appropriate resonant conditions fast and slow waves get amplified due to the phenomenon of parametric resonance. Besides, it is shown that the considered waves are mutually coupled as a consequence of the nonequilibrium state of the background medium. The coupling is strongest when the plasma β ≈ 1. The proposed formalism is sufficiently general and can be applied for many dynamical systems, both under terrestrial and astrophysical conditions. PACS numbers: 52.35. -g, 52.35. Bj, 52.35. Mw, 47.70. Nd
A self-balancing striping scheme for NAND-flash storage systems

To use multiple memory banks in parallel is a nature approach to boost the performance of flash-memory storage systems. However, realistic data-access localities unevenly load each memory bank and thus the benefits of parallelism is severely limited. In this work, we propose to encode popular data with redundancy by means of erasure codes. Load balancing is thus achieved by accessing only lightly loaded banks, because to retrieve a subset of data blocks and code blocks sufficiently reconstructs the requested data. The technical issues pertain to redundancy allocation, redundancy placement, and request scheduling. By experiments, we found that, by offering 10% extra redundant space, the read response time is largely improved by 30%.