Miracle-dz/UniFAR-FTUs huggingface dataset:
Extended Self-Renewal and Accelerated Reprogramming in the Absence of Kdm5b

ABSTRACT Embryonic stem (ES) cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in induced pluripotent stem (iPS) cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with the epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process.
Tracking 3D Moving Objects Based on GPS/IMU Navigation Solution, Laser Scanner Point Cloud and GIS Data

Monitoring vehicular road traffic is a key component of any autonomous driving platform. Detecting moving objects, and tracking them, is crucial to navigating around objects and predicting their locations and trajectories. Laser sensors provide an excellent observation of the area around vehicles, but the point cloud of objects may be noisy, occluded, and prone to different errors. Consequently, object tracking is an open problem, especially for low-quality point clouds. This paper describes a pipeline to integrate various sensor data and prior information, such as a Geospatial Information System (GIS) map, to segment and track moving objects in a scene. We show that even a low-quality GIS map, such as OpenStreetMap (OSM), can improve the tracking accuracy, as well as decrease processing time. A bank of Kalman filters is used to track moving objects in a scene. In addition, we apply non-holonomic constraint to provide a better orientation estimation of moving objects. The results show that moving objects can be correctly detected, and accurately tracked, over time, based on modest quality Light Detection And Ranging (LiDAR) data, a coarse GIS map, and a fairly accurate Global Positioning System (GPS) and Inertial Measurement Unit (IMU) navigation solution.
Anxiety Reduction through Detachment: Subjective, Physiological, and Neural Effects

The ability to volitionally regulate emotions helps to adapt behavior to changing environmental demands and can alleviate subjective distress. We show that a cognitive strategy of detachment attenuates subjective and physiological measures of anticipatory anxiety for pain and reduces reactivity to receipt of pain itself. Using functional magnetic resonance imaging, we locate the potentialsite andsourceof this modulation of anticipatory anxiety in the medial prefrontal/anterior cingulate and anterolateral prefrontal cortex, respectively.
Nonmyopic View Planning for Active Object Detection

One of the central problems in computer vision is the detection of semantically important objects and the estimation of their pose. Most of the work in object detection has been based on single image processing and its performance is limited by occlusions and ambiguity in appearance and geometry. This paper proposes an active approach to object detection by controlling the point of view of a mobile depth camera. When an initial static detection phase identifies an object of interest, several hypotheses are made about its class and orientation. The sensor then plans a sequence of views, which balances the amount of energy used to move with the chance of identifying the correct hypothesis. We formulate an active hypothesis testing problem, which includes sensor mobility, and solve it using a point-based approximate POMDP algorithm. The validity of our approach is verified through simulation and real-world experiments with the PR2 robot. The results suggest that our approach outperforms the widely-used greedy view point selection and provides a significant improvement over static object detection.
Increasing TLB reach using superpages backed by shadow memory

The amount of memory that can be accessed without causing a translation lookaside buffer (TLB) fault, the reach of a TLB, is failing to keep pace with the increasingly large working sets of applications. We propose to extend TLB reach via a novel Memory Controller TLB (MTLB) that lets us aggressively create superpages from non-contiguous, unaligned regions of physical memory. This flexibility increases the OS's ability to use superpages on arbitrary application data. The MTLB supports shadow pages, regions of physical address space for which the MTLB remaps accesses to "real" physical pages. The MTLB preserves per-base-page referenced and dirty bits, which enables the OS to swap shadow-backed superpages a page at a time, unlike conventional superpages. Simulation of five applications, including two SPECint95 benchmarks, demonstrated that a modest-sized MTLB improves performance of applications with moderate-to-high TLB miss rates by 5-20%. Simulation also showed that this mechanism can more than double the effective reach of a processor TLB with no modification to the processor MMU.
Estimation on Scale Error of SSC Retrieval Model Based on Scale Expansion Method

Although the variance of suspended sediment concentration (SSC) distribution is an important parameter for estimating scale error of SSC retrieval results, in the past it has not been possible to use this parameter because the requisite comprehensive oceanic optical data sets have not been available. In this study, the approaches of scale expansion, correlation analysis, and regression analysis were used to reveal the relationship between the variance of SSC distribution and the SSC of central pixel, average SSC, and pixel size in a moving window. According to the study results, it was found that the variance of SSC distribution was highly correlated to the SSC of central pixel and average SSC in a given scale window, while less correlated to pixel size. Additionally, the relationship model between the variance of SSC distribution and average SSC in a given scale window was used to correct the scale errors in retrieval results combined with a scale error model. The results showed that the greatest scale error of SSC retrieval results was up to 30%.
Coexpression of Spectrally Distinct Rhodopsins in Aedes aegypti R7 Photoreceptors

The retina of the mosquito Aedes aegypti can be divided into four regions based on the non-overlapping expression of a UV sensitive Aaop8 rhodopsin and a long wavelength sensitive Aaop2 type rhodopsin in the R7 photoreceptors. We show here that another rhodopsin, Aaop9, is expressed in all R7 photoreceptors and a subset of R8 photoreceptors. In the dorsal region, Aaop9 is expressed in both the cell body and rhabdomere of R7 and R8 cells. In other retinal regions Aaop9 is expressed only in R7 cells, being localized to the R7 rhabdomere in the central and ventral regions and in both the cell body and rhabdomere within the ventral stripe. Within the dorsal-central transition area ommatidia do not show a strict pairing of R7–R8 cell types. Thus, Aaop9 is coexpressed in the two classes of R7 photoreceptors previously distinguished by the non-overlapping expression of Aaop8 and Aaop2 rhodopsins. Electroretinogram analysis of transgenic Drosophila shows that Aaop9 is a short wavelength rhodopsin with an optimal response to 400–450 nm light. The coexpressed Aaop2 rhodopsin has dual wavelength sensitivity of 500–550 nm and near 350 nm in the UV region. As predicted by the spectral properties of each rhodopsin, Drosophila photoreceptors expressing both Aaop9 and Aaop2 rhodopsins exhibit a uniform sensitivity across the broad 350–550 nm light range. We propose that rhodopsin coexpression is an adaptation within the R7 cells to improve visual function in the low-light environments in which Ae. aegypti is active.
Perturbative degrees of freedom in loop quantum gravity: anisotropies

The relation between an isotropic model and an anisotropic model in loop quantum cosmology is discussed in detail, comparing the strict symmetry reduction with a perturbative implementation of symmetry. While the latter cannot be done in a canonical manner, it allows one to consider the dynamics including the role of small non-symmetric degrees of freedom for the symmetric evolution. This serves as a model for the general situation of perturbative degrees of freedom in a background-independent quantization such as loop quantum gravity, and for the more complicated addition of perturbative inhomogeneities. While being crucial for cosmological phenomenology, it is shown that perturbative non-symmetric degrees of freedom do not allow definitive conclusions for the singularity issue and in such a situation could even lead to wrong claims.
Visualization of hepatic uptake transporter function in healthy subjects by using gadoxetic acid-enhanced MR imaging.

PURPOSE To determine if genetic polymorphisms of liver-specific human organic anion transporting polypeptide (OATP) 1B1 and OATP1B3 influence cellular uptake of gadoxetic acid in vitro and if functionally relevant polymorphisms are confounders for liver enhancement by gadoxetic acid in healthy subjects. MATERIALS AND METHODS This study received ethics approval, and all subjects provided written informed consent. Cellular uptake of gadoxetic acid by OATP1B1 and OATP1B3 and their frequent genetic variants was measured by using stable transfected embryonic kidney HEK293 cells. Liver signal intensity at gadoxetic acid-enhanced MR imaging and pharmacokinetics of gadoxetic acid were evaluated in 36 healthy carriers of SLCO1B1/1B3 wild-type alleles (n = 10), SLCO1B1*1b/*1b (n = 8), SLCO1B1*15/*15 (n = 7), SLCO1B1*5/*15 (n = 1), SLCO1B1*1a/*5 (n = 6), and SLCO1B3*4/*4 (n = 4) by using T1-weighted MR imaging and liquid chromatography tandem mass spectrometry. RESULTS Transport activity for gadoxetic acid was increased in cells transfected with SLCO1B1c.388A>G (12.8 pmol/[mg·min]6 3.53, P = .001) but decreased in cells with SLCO1B1c.388A>G/521T>C (3.11 pmol/[mg·min] ± 0.918, P = .004) compared with cells with nonvariant transporter (6.32 pmol/[mg·min] ± 2.73). Compared with activity of cells transfected with the nonvariant SLCO1B3 (7.43 pmol/[mg·min] ± 2.43), SLCO1B3c.699G>A was a gain-of-function variant (15.1 pmol/[mg·min] ± 5.52, P = .002), whereas SLCO1B3c.334T>G (0.364 pmol/[mg·min] ± 0.125, P = .0001) and SLCO1B3c.1564G>T (0.295 pmol/[mg·min] ± 0.247, P = .0001) were variants with lower function. Liver enhancement with gadoxetic acid was reduced in subjects with OATP1B1*1a/*5 compared with wild-type subjects and those with OATP1B1*1b/*1b (area under enhancement curve, 3-480 minutes in arbitrary units [au]; 20.7 au ± 6.85 vs 36.5 au ± 8.08 [P = .006] vs 34.6 au ± 8.92 [P = .026]). The OATP1B3*4 polymorphism was not of functional relevance. No pharmacokinetic characteristics of gadoxetic acid were influenced by genetic polymorphisms of OATP1B1 and OATP1B3. CONCLUSION Liver-specific OATP1B1 and OATP1B3 are uptake carriers for gadoxetic acid in subjects. Genetic polymorphisms of OATP1B1 are signal confounders in gadoxetic acid-enhanced liver MR imaging.
Cognitive Constraints on How Economic Rewards Affect Cooperation

Cooperation often fails to spread in proportion to its potential benefits. This phenomenon is captured by prisoner's dilemma games, in which cooperation rates appear to be determined by the distinctive structure of economic incentives (e.g., $3 for mutual cooperation vs. $5 for unilateral defection). Rather than comparing economic values of cooperating versus not ($3 vs. $5), we tested the hypothesis that players simply compare numeric values (3 vs. 5), such that subjective numbers (mental magnitudes) are logarithmically scaled. Supporting our hypothesis, increasing only numeric values of rewards (from $3 to 300¢) increased cooperation (Study 1), whereas increasing economic values increased cooperation only when there were also numeric increases (Study 2). Thus, changing rewards from 3¢ to 300¢ increased cooperation rates, but an economically identical change from 3¢ to $3 elicited no gains. Finally, logarithmically scaled reward values predicted 97% of variation in cooperation, whereas the face value of economic rewards predicted none. We conclude that representations of numeric value constrain how economic rewards affect cooperation.
LETTER TO THE EDITOR: On quantum matrix algebras satisfying the Cayley - Hamilton - Newton identities

The Cayley - Hamilton - Newton identities which generalize both the characteristic identity and the Newton relations have been recently obtained for the algebras of the RTT-type. We extend this result to a wider class of algebras defined by a pair of compatible solutions of the Yang - Baxter equation. This class includes the RTT algebras as well as the reflection equation algebras.
Object detection via receptive field co-occurrence and spatial cloud-point data

The use of image and spatial information together in mobile robots systems it is a promising field, due to the enhanced level of discrimination and efficiency that can be gained. In this paper we employ an RGB-D camera for object detection and clustering and develop methods that combine the two strands of information: first we cluster potential objects by means of their spatial position and then link geometry and co-occurrence histograms to enable reliable object detection. Experiments and design parameters are presented for example scenarios of object detection under clutter.
[Neoadjuvant chemotherapy for recurrent colorectal cancer].

BACKGROUND The prognosis after surgical resection of recurrent colorectal cancer is still poor, even if it is diagnosed as "resectable" before operation. Neoadjuvant chemotherapy (NAC) may reduce the recurrence rate after resection of recurrent lesions by ensuring the surgical margin and controlling micro-metastases. This report presents the treatment regimen and outcome of NAC for recurrent colorectal cancer at this institution. PATIENTS AND METHODS Nineteen patients with recurrent colorectal cancer, excluding hepatic and pulmonary metastases, received NAC before laparotomy between April 2005 and November 2011. The FOLFIRI3 regimen combined with molecular targeting agents was used for NAC, and 4 to 8 courses were administered. Laparotomy was performed during the 4-to 6-week period after the last NAC administration, and 12 courses of mFOLFOX6 were recommended as adjuvant chemotherapy after the operation. RESULTS Complete remission was observed in 1 patient and partial remission in 7 patients according to Response Evaluation Criteria in Solid Tumors ver. 3, and no progressive disease was observed. Curative resection was achieved in 13 patients. The 3-year overall survival rate was 83.6%, and the 3-year relapse-free survival rate was 50.3%. CONCLUSION This retrospective study using a small number of subjects suggested that NAC for recurrent colorectal cancer may increase the curative resection rate while reducing the recurrence rate.
Identifikasi Daerah Jelajah Beruk (Macaca Nemestrina Linnaeus, 1766) Menggunakan Aplikasi Sistem Informasi Geografis Di Kawasan Hutan Universitas Riau

Macaca nemestrina is one including appendix II containing list of endangered species. The research aims to understand home range to know daily behavior and mapping range of Macaca nemestrina in the area of Riau University forest and surrounding areas. This research using a method of direct observation by way of follow, noticed as well as record every activity performed by groups of Macaca nemestrina. The determination of the regional daily range in overlay using software arcgis 10.1. Daily activity were analysed by counting average time daily activity and percentage number of daily activity fauna. Home range Macaca nemestrina were analysed using kernel density estimation (KDE) located on program Geospatial Modelling Environment (GME) and ArcGis 10.1. Home range outermost Macaca nemestrina were analysed by the method of Minimum Convex Polygon (MCP). The result showed that Macaca nemestrina in the area of Riau University forest having broad areas of 176.553 m². Maps of the home range Macaca nemestrina having range regions core level very high density area of 7.916 m², high area of 11.344 m², mid 41.468 m², low area of 83.28 m² and level of density is very 32.542 m². The activity of Macaca nemestrina is eat, break, migrates, grooming and social interaction. The highest activity is break activity 36,68%, the lowest activity is grooming 4,10%. The percentage of eating 25,33%, social interaction 29,69% and devolve activity 4,20%. To scatter cruiser regions Macaca nemestrina in forest area of Riau University were on the point coordinates 101°22'44,565'BT–101°23'8,918'BT and 0°28'56,122'LU–0°28' 32,798'LU.
Segmental Semi-Markov Models for Endpoint Detection in Plasma Etching

We investigate two statistical-detection problems, change-point detection and pattern matching in plasma etch endpoint detection. Our approach is based on a segmental semi-Markov model framework. In the change-point detection problem, the changepoint corresponds to state switching in the model. For pattern matching, the pattern is approximated as a sequence of linear segments which are then modeled as segments (states) in the model. The segmental semi-Markov model is an extension of the standard hidden Markov model (HMM), from which learning and inference algorithms are extended to solve the problems of change-point detection and pattern matching in a principled manner. Results on both simulated and real data from semiconductor manufacturing illustrate the flexibility and accuracy of the proposed framework.
Practical and Theoretical Aspects of a Parallel Twig Join Algorithm for XML Processing using a GPGPU

With an increasing amount of data and demand for fast query processing, the efﬁciency of database operations continues to be a challenging task. A common approach is to leverage parallel hardware platforms. With the introduction of general-purpose GPU (Graphics Processing Unit) computing, massively parallel hardware has become available within commodity hardware. XML is based on a tree-structured data model. Naturally, the most popular XML querying language (XPath) uses patterns of selection predicates on multiple elements, related by a tree structure. These are often abstracted by twig patterns . Finding all occurrences of such a (XML query) twig pattern in an XML document is a core operation for XML query processing. We present a new algorithm, GPU-Twig, for matching twig patterns in large XML documents, using a GPU. Our algorithm uses the data and task parallelism of the GPU to perform memory-intensive tasks whereas the CPU is used to perform I/O and resource management. We therefore efﬁciently exploit both the high-bandwidth GPU memory interface and the lower-bandwidth CPU main memory.
A quantitative analysis of the effect of flexible loads on reserve markets

We propose and analyze a day-ahead reserve market model that handles bids from flexible loads. This pool market model takes into account the fact that a load modulation in one. Direction must usually be compensated later by a modulation of the same magnitude in the opposite direction. Our analysis takes into account the gaming possibilities of producers and retailers, controlling load flexibility, in the day-ahead energy and reserve I markets, and in imbalance settlement. This analysis is carried out by an agent-based approach where, for every round, each actor uses linear programs to maximize its profit according to forecasts of the prices. The procurement of a reserve is assumed to be determined, for each period, as a fixed percentage of the total consumption cleared in the energy market for the same period. The results show that the provision of reserves by flexible loads has a negligible impact on the energy market prices but, markedly decreases the cost of reserve procurement. However, as the rate of flexible loads increases, the system operator has to rely more and more on non-contracted reserves, which may cancel out the benefits made in the procurement of reserves.
Stability of Velocity in the Group of Seven Countries: A Kalman Filter Approach

This paper estimates forecasting models using annual data for the income velocity of money in the G-7 countries. The predictions are conditional upon the realized value of the long-term domestic government bond rate. Such conditional forecasts did not deteriorate over the period 1980-1988 as compared with the earlier postwar period. Velocity of M1 is found to be very interest-elastic in almost all countries; velocity of M2 less so. The specifications (based on Kalman filters and smoothers) point to a non-constant (stochastic) trend in velocity, hence questioning the assumptions required for the cointegration techniques used in other research on the demand for money.
Whole Grain Pasta: A Physicochemical and Sensory Study

WHOLE GRAIN PASTA: A PHYSICOCHEMICAL AND SENSORY STUDY Ryan West University of Guelph, 2012 Co-advisors: Professor Lisa Duizer Professor Koushik Seetharaman Whole grain is associated with rougher texture and off-flavours which has decreased consumer acceptance. Pasta drying is also critical during production because of influence on texture and quality. The effects of drying type and whole grain content (WGC) on physicochemical and qualitative properties of pasta were investigated. Increasing WGC lowered paste viscosity and increased cooking loss while low temperature drying improved quality. The impact of these effects on pasta texture and flavour was further explored. While bitterness, branniness, and surface roughness positively correlated with WGC, drying type only affected firmness. Phenolic content, headspace, and textural analysis corroborated this data. Change in pasta flavour upon addition of sodium-reduced cheese sauce was also examined. Sodium not only enhances flavour of dishes, it also suppresses bitterness. While flavours were uniquely affected upon sauce addition, sodium content did not affect bitterness. Headspace analysis showed volatile concentration to reduce, likely caused by a barrier created from the sauce.