Miracle-dz/UniFAR-FTUs huggingface dataset:
Freshwater Fish Gill Ion Transport: August Krogh to morpholinos and microprobes

August Krogh proposed that freshwater fishes (and other freshwater animals) maintain body NaCl homoeostasis by extracting these ions from the environment via separate Na+/NH4+ and Cl−/HCO3− exchangers in the gill epithelium. Subsequent data from other laboratories suggested that Na+ uptake was more probably coupled to H+ secretion via a vesicular proton pump (V‐ATPase) electrically coupled to a Na+ channel. However, despite uncertainty about electrochemical gradients, evidence has accrued that epithelial Na+/H+ exchange indeed may be an alternative pathway for Na+ uptake. The specific pathways for Na+ uptake may be species and environment specific. An apical Cl−/HCO3− exchanger is generally accepted for most species (some species do not extract Cl− from freshwater), but the relative roles of anion exchanger‐like (SLC4A1) vs. pendrin‐like (SLC26Z4) exchangers are unknown, and also may be species specific. Most recently, data have supported the presence of an apical Na+ + Cl− cotransporter (NCC‐type), despite thermodynamic uncertainty. Ammonia extrusion may be via NH3 diffusing through the paracellular junctions or NH4+ substitution on both basolateral and apical ionic exchangers (Na+ + K+‐ATPase; Na+ + K+ + Cl− ‐ cotransporter; and Na+/H+ exchanger), but recent evidence suggests that Rhesus‐glycoproteins mediate both basolateral and apical movement of ammonia.
Isocitrate dehydrogenase mutations: new opportunities for translational research

Over the last decade, comprehensive genome-wide sequencing studies have enabled us to find out unexpected genetic alterations of metabolism in cancer. An example is the identification of arginine missense mutations of isocitrate dehydrogenases-1 and -2 (IDH1/2) in glioma, acute myeloid leukemia (AML), chondrosarcomas, and cholangiocarcinoma. These alterations are closely associated with the production of a new stereospecific metabolite, (R)-2-hydroxyglutarate (R-2HG). A large number of follow-up studies have been performed to address the molecular mechanisms of IDH1/2 mutations underlying how these events contribute to malignant transformation. In the meanwhile, the development of selective mutant IDH1/2 chemical inhibitors is being actively pursued in the scientific community and pharmaceutical industry. The present review article briefly discusses the important findings that highlight the molecular mechanisms of IDH1/2 mutations in cancer and provides a current status for development of selective mutant IDH1/2 chemical inhibitors. [BMB Reports 2015; 48(5): 266-270]
Comparison of depth-based features for lipreading

We examine the effect of depth information captured by Microsoft Kinect on the task of visual speech recognition. We propose depth-based active appearance model (AAM) features and show improved results over discrete cosine transform (DCT). The visual and depth features are evaluated on a database of 54 speakers each uttering 50 isolated words. In order to exploit the speech dynamics, the features are enhanced by a simplified one-stage variant of hierarchical linear discriminant analysis (Hi-LDA). In the experiments, we consider feature fusion via combined video-depth active appearance model as a form of early integration, and compare it to traditional multi-stream hidden Markov Model as a form of decision fusion. We also perform experiments on audio-visual recognition in noisy environments and show improved results of incorporating depth information over both traditional audio-video fusion and utilization of speech enhancement algorithms.
A simple and effective greedy multilayer router for MCMs

We present a very fast area router for MCM design. Given a set of nets and a routing area, it repeatedly routes as many nets as possible in two layers selected from top to bottom until all the nets are routed. The router uses a line sweep technique and a simple net selection algorithm. By using e cient data structures and a novel priority scheme, the routing can be nished in time almost proportional to the routing area. For the benchmark circuits, the proposed router generates comparable routing results faster by over an order of magnitude (18 times on the average) than the previously reported best router.
Impact of Schistosoma japonicum Infection on Collagen-Induced Arthritis in DBA/1 Mice: A Murine Model of Human Rheumatoid Arthritis

Background The hygiene hypothesis suggests that helminth infections prevent a range of autoimmune diseases. Methodology/Principal Findings To investigate the effects of S. japonicum infection on collagen-induced arthritis (CIA), male DBA/1 mice were challenged with unisexual or bisexual S. japonicum cercariae two weeks prior to bovine type II collagen (CII) immunization or at the onset of CIA. S. japonicum infection prior to CII immunization significantly reduced the severity of CIA. ELISA (enzyme linked immunosorbent assay) showed that the levels of anti-CII IgG and IgG2a were reduced in prior schistosome-infected mice, while anti-CII IgG1 was elevated. Splenocyte proliferation against both polyclonal and antigen-specific stimuli was reduced by prior schistosome infection as measured by tritiated thymidine incorporation (3H-TdR). Cytokine profiles and CD4+ T cells subpopulation analysis by ELISA and flow cytometry (FCM) demonstrated that prior schistosome infection resulted in a significant down-regulation of pro-inflammatory cytokines (IFN-γ, TNF-α, IL-1β and IL-6) and Th1 cells, together with up-regulation of the anti-inflammatory cytokine IL-10 and Th2 cells. Interestingly, the expansion of Treg cells and the reduction of Th17 cells were only observed in bisexually infected mice. In addition, prior schistosome infection notably reduced the expression of pro-inflammatory cytokines and receptor activator of NF-κB ligand (RANKL) in the inflamed joint. However, the disease was exacerbated at one week after infection when established CIA mice were challenged with bisexual cercariae. Conclusion/Significance Our data provide direct evidence that the Th2 response evoked by prior S. japonicum infection can suppress the Th1 response and pro-inflammatory mediator and that bisexual infection with egg-laying up-regulates the Treg response and down-regulates the Th17 response, resulting in an amelioration of autoimmune arthritis. The beneficial effects might depend on the establishment of a Th2-dominant response rather than the presence of the eggs. Our results suggest that anti-inflammatory molecules from the parasite could treat autoimmune diseases.
Code comprehension problems as learning events

Code comprehension problems have been shown to be effective assessment items in computer science education. In this paper we present qualitative and quantitative results of a study evaluating the effectiveness of code comprehension questions with feedback as learning events. Students taking an introductory programming course that satisfies a university requirement interacted with an online tutoring system using code comprehension problems about simple array algorithms as a part of a homework assignment. Students answered the problems in their own words first, before selecting a multiple choice option from the system. Both the open-ended and multiple-choice responses were collected and analyzed. Results indicate that code comprehension questions with appropriate feedback can be learning events. The use of open-ended and multiple choice responses to the same question is also shown to be useful in refining distracter items for future assessment. Recommendations from this study can be applied not only to tutoring systems, but also to the type of interactions used in worked examples in class lecture and textbook production.
Native mode functional test generation for processors with applications to self test and design validation

New methodologies based on functional testing and built-in self-test can narrow the gap between necessary solutions and existing techniques for processor validation and testing. We present a versatile automatic functional test generation methodology for microprocessors. The generated assembly instruction sequences can be applied to both design validation and manufacturing test, especially in high speed "native" mode. All the functional capabilities of complex processors can be exercised, leading to high quality validation sequences and manufacturing tests with high fault coverage. The tests can also be applied in a built-in self-test fashion. Experimental results on two microprocessors show that this method is very effective in generating high quality manufacturing tests as well as in functional design validation.
Sparse Wide-Baseline Virtual View Generation

Given a number of images of a scene, Virtual View Generation (VVG) is the process of generating the images that would have been seen from viewpoints other than the one of the input images. As shown in Fig. 1, the movie industry already uses VVG for visual effect generation in films such as “The Matrix. ” It could also allow a director to modify a scene by changing the viewpoint without the trouble and expense of reshooting it. Similarly, it is a necessary component of free viewpoint tv, which would allow a spectator to watch a show from any desired viewpoint. In many of today’s VVG systems, the approach is to shoot the scene using very many cameras and generate the video with a predefined trajectory that cannot depart much from the input camera array positions. Image synthesis mostly involves interpolation or re-sampling [7, 5]. In this thesis, we will develop an approach to VVG using a more limited number of cameras than what is the norm today. This will make VVG much more practical and flexible since it will require less effort to synchronize and calibrate and it will become possible to apply VVG to a more set of applications like surveillance systems where it is impractical and expensive to install a large number of cameras. However, achieving this will involve solving a number of severe difficulties. Since we do not have a dense sampling of the imaging space, interpolation and resampling based methods are not suitable. Therefore, additional cues like depth must be included to the formulation. Once the depth is known, it is not very difficult to synthesize new images. However, our case involves dense wide-baseline matching and handling of large occlusions resulting from the regions where only one camera is able to capture. These are problematic issues because:
Nucleotide Diversity in Gorillas

Comparison of the levels of nucleotide diversity in humans and apes may provide valuable information for inferring the demographic history of these species, the effect of social structure on genetic diversity, patterns of past migration, and signatures of past selection events. Previous DNA sequence data from both the mitochondrial and the nuclear genomes suggested a much higher level of nucleotide diversity in the African apes than in humans. Noting that the nuclear DNA data from the apes were very limited, we previously conducted a DNA polymorphism study in humans and another in chimpanzees and bonobos, using 50 DNA segments randomly chosen from the noncoding, nonrepetitive parts of the human genome. The data revealed that the nucleotide diversity (π) in bonobos (0.077%) is actually lower than that in humans (0.087%) and that π in chimpanzees (0.134%) is only 50% higher than that in humans. In the present study we sequenced the same 50 segments in 15 western lowland gorillas and estimated π to be 0.158%. This is the highest value among the African apes but is only about two times higher than that in humans. Interestingly, available mtDNA sequence data also suggest a twofold higher nucleotide diversity in gorillas than in humans, but suggest a threefold higher nucleotide diversity in chimpanzees than in humans. The higher mtDNA diversity in chimpanzees might be due to the unique pattern in the evolution of chimpanzee mtDNA. From the nuclear DNA π values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200.
Theory and Practice of Econometric Modelling Using PcGive 10

This review offers a guided tour to PcGive 10 modules for econometrics analysis of time series (PcGive), limited dependent variable (LogitJD) and static and dynamic panel data analyses (DPD), financial econometric (GARCH) and time series (ARFIMA) modelling. Several empirical applications are reported to illustrate the package.
Relation Between Alkaline Phosphatase, Serum Phosphate, and All-Cause or Cardiovascular Mortality

Background— Higher levels of serum alkaline phosphatase (AlkP) are associated with excess mortality in dialysis patients, but whether AlkP is associated with adverse outcomes among people without kidney failure is unknown. Methods and Results— We first analyzed the association between AlkP and cardiovascular outcomes among 4115 participants with a previous myocardial infarction (the Cholesterol And Recurrent Events [CARE] study). Results were validated by analyzing the association between AlkP and mortality in an independent sample of 14 716 adults from the general US population (the Third National Health and Nutrition Examination Survey). A graded, independent association was noted between baseline tertile of AlkP and the adjusted hazard ratio of all-cause mortality in CARE participants (Ptrend=0.02). After adjustment for serum phosphate, hepatic enzymes, and other potential confounders, participants with AlkP in the highest tertile had an adjusted hazard ratio of 1.43 (95% confidence interval 1.08 to 1.89) compared with those in the lowest tertile. Multivariable-adjusted associations between higher AlkP and all-cause and cardiovascular mortality were present in the Third National Health and Nutrition Examination Survey (Ptrend across tertiles of AlkP=0.006 and 0.038, respectively). Findings from both CARE and the Third National Health and Nutrition Examination Survey were similar among individuals with and without evidence of kidney disease, defined by estimated glomerular filtration rate <60 mL · min−1 · 1.73 m−2. Conclusions— We found an independent relation between higher levels of AlkP and adverse outcomes among survivors of myocardial infarction and in a general population sample. The excess risk of death was present in people without evidence of kidney disease and was particularly high among people with higher levels of both AlkP and serum phosphate.
Neurogenomic mechanisms of social plasticity

Group-living animals must adjust the expression of their social behaviour to changes in their social environment and to transitions between life-history stages, and this social plasticity can be seen as an adaptive trait that can be under positive selection when changes in the environment outpace the rate of genetic evolutionary change. Here, we propose a conceptual framework for understanding the neuromolecular mechanisms of social plasticity. According to this framework, social plasticity is achieved by rewiring or by biochemically switching nodes of a neural network underlying social behaviour in response to perceived social information. Therefore, at the molecular level, it depends on the social regulation of gene expression, so that different genomic and epigenetic states of this brain network correspond to different behavioural states, and the switches between states are orchestrated by signalling pathways that interface the social environment and the genotype. Different types of social plasticity can be recognized based on the observed patterns of inter- versus intra-individual occurrence, time scale and reversibility. It is proposed that these different types of social plasticity rely on different proximate mechanisms at the physiological, neural and genomic level.
Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1

Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs – MUS81 and Yen1/GEN1– uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions.
HIDDEN TOPIC DISCOVERY TOWARD CLASSIFICATION AND CLUSTERING IN VIETNAMESE WEB DOCUMENTS

Acknowledgements My deepest thank must first go to my research advisor, Prof. Dr. Ha Quang Thuy, who offers me an endless inspiration in scientific research, leading me to this research area. I particularly appreciate his unconditional support and advice in both academic environment and daily life during the last four years. Many thanks go to Dr. Phan Xuan Hieu who has given me many advices and comments. This work can not be possible without his support. Also, I would like to thank him for being my friend, my older brother who has brought me a lot of lessons in both scientific research and daily life. My thanks also go to all members of seminar group " data mining ". Especially, I would like to thank Bsc. Nguyen Thu Trang for helping me a lot in collecting data and doing experiments. I highly acknowledge the invaluable support and advice in both technical and daily life of my teachers, my colleagues in " Developing content filter systems to support management and implementation public security – ensure policy " Finally, from bottom of my heart, I would specially like to say thanks to all members in my family, all my friends. They are really an endless encouragement in my life. ii Assurance I certify that the achievements in this thesis belong to my personal, and are not copied from any other's results. Throughout the dissertation, all the mentions are either my proposal, or summarized from many sources. All the references have clear origins, and properly quoted. I am responsible for this statement. Figure 1.1. Graphical model representation of the aspect model in the asymmetric (a) and symmetric (b) parameterization. Figure 1.2. Sketch of the probability sub-simplex spanned by the aspect model ([55]). 10 Figure 1.3. Graphical model representation of LDA-The boxes is " plates " representing replicates. The outer plate represents documents, while the inner plate represents the repeated choice of topics and words within a document [20] .
The Orientation Selectivity of Color-Responsive Neurons in Macaque V1

Form has a strong influence on color perception. We investigated the neural basis of the form–color link in macaque primary visual cortex (V1) by studying orientation selectivity of single V1 cells for pure color patterns. Neurons that responded to color were classified, based on cone inputs and spatial selectivity, into chromatically single-opponent and double-opponent groups. Single-opponent cells responded well to color but weakly to luminance contrast; they were not orientation selective for color patterns. Most double-opponent cells were orientation selective to pure color stimuli as well as to achromatic patterns. We also found non-opponent cells that responded weakly or not at all to pure color; most were orientation selective for luminance patterns. Double-opponent and non-opponent cells' orientation selectivities were not contrast invariant; selectivity usually increased with contrast. Double-opponent cells were approximately equally orientation selective for luminance and equiluminant color stimuli when stimuli were matched in average cone contrast. V1 double-opponent cells could be the neural basis of the influence of form on color perception. The combined activities of single- and double-opponent cells in V1 are needed for the full repertoire of color perception.
A time-dependent radiative model of HD 209458b

We present a time-dependent radiative model of the atmosphere of HD 209458b and investigate its thermal structure and chemical composition. In a first step, the stellar heating profile and radiative timescales were calculated under planet-averaged insolation conditions. We find that 99.99% of the incoming stellar flux has been absorbed before reaching the 7 bar level. Stellar photons cannot therefore penetrate deeply enough to explain the large radius of the planet. We derive a radiative time constant which increases with depth and reaches about 8 h at 0.1 bar and 2.3 days at 1 bar. Time-dependent temperature profiles were also calculated, in the limit of a zonal wind that is independent of height (i.e. solid-body rotation) and constant absorption coefficients. We predict day-night variations of the effective temperature of ~600 K, for an equatorial rotation rate of 1 km s -1 , in good agreement with the predictions by Showmann & Guillot (2002). This rotation rate yields day-to-night temperature variations in excess of 600 K above the 0.1-bar level. These variations rapidly decrease with depth below the 1-bar level and become negligible below the ~5-bar level for rotation rates of at least 0.5 km s -1 . At high altitudes (mbar pressures or less), the night temperatures are low enough to allow sodium to condense into Na 2 S. Synthetic transit spectra of the visible Na doublet show a much weaker sodium absorption on the morning limb than on the evening limb. The calculated dimming of the sodium feature during planetary transites agrees with the value reported by Charbonneau et al. (2002).
MATRIX MODEL FOR POLYAKOV LOOPS, STRING FIELD THEORY IN THE TEMPORAL GAUGE AND WINDING STRING CONDENSATIONS IN ANTI-DE SITTER SPACE

Closed string field theory is constructed by stochastically quantizing a matrix model for Polyakov loops that describes phases of a large N gauge theory at finite temperature. Coherent states in this string field theory describes winding string condensation which has been expected to cause topology change from thermal AdS geometry to AdS-Schwarzschild black hole geometry. D-branes in this closed string field theory is also discussed. Based on a talk given at CosPA 2007, Taipei.
Reachability analysis using partitioned-ROBDDs

We address the problem of finite state machine (FSM) traversal, a key step in most sequential verification and synthesis algorithms. We propose the use of partitioned ROBDDs to reduce the memory explosion problem associated with symbolic state space exploration techniques. In our technique, the reachable state set is represented as a partitioned ROBDD (A. Narayan et al., 1996). Different partitions of the Boolean space are allowed to have different variable orderings and only one partition needs to be in memory at any given time. We show the effectiveness of our approach on a set of ISCAS89 benchmark circuits. Our techniques result in a significant reduction in total memory utilization. For a given memory limit, partitioned ROBDD based method can complete traversal for many circuits for which monolithic ROBDDs fail. For circuits where both partitioned ROBDDs as well as monolithic ROBDDs cannot complete traversal, partitioned ROBDDs can reach a significantly larger set of states.