Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppression of effects of gradient imperfections on imaging with alternate ascending/descending directional navigation

Alternate ascending/descending directional navigation (ALADDIN) is a new imaging technique that provides interslice perfusion‐weighted and magnetization transfer (MT) asymmetry images. In this article, we investigated the effects of gradient imperfections on ALADDIN MT asymmetry (MTA) signals. Subtraction artifacts increasing with readout offsets were detectable in ALADDIN MTA images from an agarose phantom but not from a water phantom. Slice‐select offsets had no significant effect on the artifacts in MTA. The artifacts were suppressed by averaging signals over the readout gradient polarities independent of scan parameters. All these results suggested that the subtraction artifacts were induced by readout eddy currents. With suppression of the artifacts, ALADDIN signals in human brain and skeletal muscle varied less with scan conditions. Percent signal changes of MTA in human skeletal muscle (0.51 ± 0.11%, N = 3) were about 30% of those in white matter. The new averaging scheme will allow for more accurate MTA imaging with ALADDIN, especially at off‐center positions. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Concurrent mental activities affect ERPs and impair performance of ERP-spellers

Being one of the most popular and extensively studied ERP-BCI paradigm, ERP-spellers are commonly built and tested in ideal lab settings. However, in practical applications, users may encounter complex situations and various mental processing that have been believed to affect ERP signals. This kind of effect will probably induce a deteriorated performance of ERP-spellers. In the current study, a working memory task was interleaved within an RC ERP-speller paradigm to examine the effect of concurrent mental processing both on ERPs evoked by the stimuli of speller and its performance, especially when a speller is built under pure lab setting but used under complex mental activities in real life. The results show that the amplitude of N200, P360 and N550 were significantly affected by the working memory task. Moreover, the performance of ERP-spellers was significantly deteriorated by concurrently performing a working memory task, not only when a speller is trained and used in different settings, but also when a speller is both built and used in the same complex setting. These findings introduce a challenge for ERP-spellers to be used outside lab-settings and in daily work, especially when users are undergoing complex mental processing and experiencing heavy mental workload.
Analytical modeling of read stability metric of SRAM cell in nanoscale era

In this paper, we propose an analytical model for read stability metric (read margin) of sub-45nm SRAM cells. First, analytical expressions for Vread and Vtrip of the cell are derived. The expressions are obtained using a simple model for the I–V characteristics of the transistors valid for sub-45nm technologies. The I–V model, which is based on the n-th power model, has integer powers of voltage. The accuracy of the analytical model is verified by comparing its results with those of HSPICE simulations. The results show a very good accuracy for the proposed model for a wide range of transistor sizes. The accuracy of the models is also verified in the presence of threshold voltage fluctuations.
A Bayesian approach to estimation of a statistical change-point in the mean parameter for high dimensional non-linear time series

We propose a semiparametric approach to infer the existence of and estimate the location of a statistical change-point to a nonlinear high dimensional time series contaminated with an additive noise component. In particular, we consider a p―dimensional stochastic process of independent multivariate normal observations where the mean function varies smoothly except at a single change-point. Our approach first involves a dimension reduction of the original time series through a random matrix multiplication. Next, we conduct a Bayesian analysis on the empirical detail coefficients of this dimensionally reduced time series after a wavelet transform. We also present a means to associate confidence bounds to the conclusions of our results. Aside from being computationally efficient and straight forward to implement, the primary advantage of our methods is seen in how these methods apply to a much larger class of time series whose mean functions are subject to only general smoothness conditions.
Evaluation of consistency of jumping technique in horses between the ages of 6 months and 4 years.

OBJECTIVE To determine whether differences in jumping technique among horses are consistent at various ages. ANIMALS 12 Dutch Warmblood horses. PROCEDURE Kinematics were recorded during free jumps of horses when they were 6 months old (ie, no jumping experience) and 4 years old (ie, the horses had started their training period to become show jumpers). Mean +/- SD height of the horses was 1.40 +/- 0.04 m at 6 months of age and 1.70 +/- 0.05 m at 4 years of age. RESULTS Strong correlations were found between values from 6-month-old foals and 4-year-old horses for variables such as peak vertical acceleration generated by the hind limbs (r, 0.91), peak rate of change of effective energy generated by the hind limbs (r, 0.71), vertical velocity at takeoff (r, 0.65), vertical displacement of the center of gravity during the airborne phase (r, 0.81), and duration of the airborne phase (r, 0.70). CONCLUSIONS AND CLINICAL RELEVANCE Although there are substantial anatomic and behavioral changes during the growing period, certain characteristics of jumping technique observed in naïve 4-year-olds are already detectable when those horses are foals.
DDS-driven PLL frequency synthesizer for X-band radar signal simulation

A DDS-driven PLL frequency synthesizer architecture is given in this paper. The AD9854 DDS device is used to generate low frequency reference signal and to drive the PLL and VCO to generate RF signal. Experiments and measurement results showed that this frequency synthesizer had wider bandwidth and low phase noise level, and can be used to generate X-band continuous wave signal, FM chirp signal and frequency agile signal for radar signal simulation
Field Validation of Aedes aegypti (Diptera: Culicidae) Age Estimation by Analysis of Cuticular Hydrocarbons

Abstract In previous studies, we developed linear regression models to age-grade female Aedes aegypti L. reared and maintained under controlled laboratory conditions. The models were based on temporal differences between two cuticular hydrocarbons, pentacosane (C25H52) and nonacosane (C29H60), which were extracted from Ae. aegypti legs and analyzed by gas-liquid chromatography. These initial models predicted adult female age up to 165 DD (12–15 calendar d at 28°C). The age of older mosquitoes, however, could not be accurately predicted. In this study, our original regression models were tested using age data obtained from mosquitoes maintained in a field laboratory and those that were marked, released, and recaptured in northwestern Thailand. Our field data led to the development of two new regression models: one for the cool-dry season (February–March) and one for the rainy season (July–August). Both models resulted in better estimates of age than the original model and thus improved our ability to predict the age of Ae. aegypti to 15 calendar d. Females older than 15 d can be identified as such, but their exact age cannot yet be estimated. The new models will be useful for epidemiological studies and evaluating the impact of Ae. aegypti control interventions for disease prevention.
Creating User-Input Driven Cinemagraphs

Cinemagraphs are a relatively recent media which turns a video clip into a still photograph with an area of repeated animation. Originally created through manual manipulation with photo editing software, automated tools are now being developed to assist in the creation of cinemagraphs. However, a number of the tools available today are either entirely automatic or does not sufficiently focus on the area of animation. This project aims to create an automated tool to create photorealistic cinemagraphs while still allowing the user to assert creative control over the final product.
Distortion of allele frequency distributions provides a test for recent population bottlenecks.

We use population genetics theory and computer simulations to demonstrate that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci. Bottlenecks cause alleles at low frequency (< 0.1) to become less abundant than alleles in one or more intermediate allele frequency class (e.g., 0.1-0.2). This distortion is transient and likely to be detectable for only a few dozen generations. Consequently only recent bottlenecks are likely to be detected by tests for distortions in distributions of allele frequencies. We illustrate and evaluate a qualitative graphical method for detecting a bottleneck-induced distortion of allele frequency distributions. The simple novel method requires no information on historical population sizes or levels of genetic variation; it requires only samples of 5 to 20 polymorphic loci and approximately 30 individuals. The graphical method often differentiates between empirical datasets from bottlenecked and nonbottlenecked natural populations. Computer simulations show that the graphical method is likely (P > .80) to detect an allele frequency distortion after a bottleneck of < or = 20 breeding individuals when 8 to 10 polymorphic microsatellite loci are analyzed.
Genetics of mitochondrial biogenesis.

INTR OD UCTION . 249 THE GENETIC FUNCTION OF M ITOCH ONDRIAL DNA . 250 OR GAN IZATION OF M IT OCH ONDRIAL DNA . 256 Structure of Mammalian mtDNA . 256 Transcription and Prucessing of RNA in Animal Mitochundria . 256 Structure of Yeast mtDNA . 258 Transcription and Processing of Mitochondrial RNA in yeast 259 Mitochondrial RNA Splicing 261 D EPENDEN CE OF M ITOCH OND RIAL BIOGENESIS ON NUCLEAR GEN ES . 264 PET Genes and pet Mutants . 265 Characterization of PET Genes . 268 N UCLEAR -MIT OCHONDR IAL INT ERACT IONS . 269 Do Mitochondria Affect the Expression of Nuclear DNA? 270 Requirement of Nuclear Gene Products for Expression of mtDNA 270 TRANS PORT OF PR OTEINS IN TO MITOCH ON DR IA . 273 Posttranslational versus Cotranslational Transport. 274 Primary Translation Products . 274 Mitochondrial Receptors 276 Transport Routes . 277 ASSEMBLY OF M ITOCHONDRIAL ENZyMES . 278
ACCELERATED STABILITY STUDIES OF A POLYHERBAL PREPARATION (EAZMOVR) CAPSULE

The stability of Eazmov capsule in accelerated condition ie by exposing it to the temperature at 45°C and 40°C with 75% relative humidity was studied. The samples were periodically anallysed upto six months for their organoleptic characteristics, assay of active plant ingredients and the DPTLC finger printing and their peak area analysis, which were found to be stable/ consistent during the period of study. The change in quantifiable components was within 90% of the initial amount, indicating e stability of product for more than three years at room temperature.
Mg 3pns and 3pnd (J=1) autoionizing series.

The Mg 3{ital pns} ({ital n}=10--18) and 3{ital pnd} ({ital n}=9--40) doubly excited {ital J}=1 autoionizing states have been observed experimentally using an isolated-core excitation method with stepwise laser excitation. Linearly polarized laser light excites the 3{ital pnd} {ital J}=1 and {ital J}=3 states, as well as the 3{ital pns} {ital J}=1 states. Our previous study of the {ital J}=3 states enables the {ital J}=1 states in the 3{ital pnd} spectra to be identified. We have also calculated the spectra from a reaction matrix, and the agreement between theory and experiment is generally excellent. Differences between the {ital J}=1 and {ital J}=3 features are discussed and qualitatively explained in terms of semiclassical arguments. Additionally, energies of the 3{ital sns} {sup 1}{ital S}{sub 0} ({ital n}=11--22) Rydberg levels are reported.
Competition between Decapping Complex Formation and Ubiquitin-Mediated Proteasomal Degradation Controls Human Dcp2 Decapping Activity

ABSTRACT mRNA decapping is a central step in eukaryotic mRNA decay that simultaneously shuts down translation initiation and activates mRNA degradation. A major complex responsible for decapping consists of the decapping enzyme Dcp2 in association with decapping enhancers. An important question is how the activity and accumulation of Dcp2 are regulated at the cellular level to ensure the specificity and fidelity of the Dcp2 decapping complex. Here, we show that human Dcp2 levels and activity are controlled by a competition between decapping complex assembly and Dcp2 degradation. This is mediated by a regulatory domain in the Dcp2 C terminus, which, on the one hand, promotes Dcp2 activation via decapping complex formation mediated by the decapping enhancer Hedls and, on the other hand, targets Dcp2 for ubiquitin-mediated proteasomal degradation in the absence of Hedls association. This competition between Dcp2 activation and degradation restricts the accumulation and activity of uncomplexed Dcp2, which may be important for preventing uncontrolled decapping or for regulating Dcp2 levels and activity according to cellular needs.
Platelet‐like particle formation in the human megakaryoblastic leukaemia cell lines, MEG‐01 and MEG‐01s

The platelet‐sized particle formation in the human megakaryoblastic leukaemia cell line MEG‐01 and its subline MEG‐01s was examined. MEG‐01 and MEG‐01s cells spontaneously released platelet‐sized particles into the culture medium, in which the cells occasionally extended cytoplasmic processes similar to those of megakaryocyte proplatelets. Scanning electron microscopic images showed cytoplasmic processes elongated from blebs on the MEG‐01 and MEG‐01s cell surface and were constricted between segments of platelet size. Immunofluorescence staining with anti‐tubulin antibody showed that the cytoplasmic processes contained microtubules that were organized into a ring, which is a characteristic of circulating platelets. Some platelet‐sized particles, probably released by ruptures at the sites of the process constriction, were metabolically active in an MTT assay (about 50%). Some particles also expressed the platelet‐specific glycoproteins GPIIb, IIIa and GMP‐140. Rarely, in response to thrombin, particles underwent a shape change from spherical to a shape with irregular membrane protrusions and fine filopodia, and aggregating with one another. The particles also had increased GMP‐140 (P‐selectin) expression with the addition of thrombin. These results show the usefulness of the MEG‐01 and MEG‐01s cell lines for the study of thrombopoiesis.
Logistic Markov Decision Processes

User modeling in advertising and recommendation has typically focused on myopic predictors of user responses. In this work, we consider the long-term decision problem associated with user interaction. We propose a concise specification of long-term interaction dynamics by combining factored dynamic Bayesian networks with logistic predictors of user responses, allowing state-of-the-art prediction models to be seamlessly extended. We show how to solve such models at scale by providing a constraint generation approach for approximate linear programming that overcomes the variable coupling and non-linearity induced by the logistic regression predictor. The efficacy of the approach is demonstrated on advertising domains with up to 2^54 states and 2^39 actions.
Auto-Tuning of Multivariable PID Controllers Using Iterative Feedback Tuning

Abstract A new auto-tuning approach for centralized MIMO PID controllers and unknown process models is presented. Classical multivariable PID controller tuning methods are combined with iterative feedback tuning (IFT) to develop an auto-tuning method with a bounded number of tuning parameters. The method is demonstrated and validated with a steam generator example. Very good simulation results are obtained. Abstract
Altered gene expression in mice with lupus treated with edratide, a peptide that ameliorates the disease manifestations.

OBJECTIVE To identify genes that are differently expressed in (NZB x NZW)F(1) mice with established lupus compared with healthy controls, and to determine how gene expression is affected by treatment with hCDR1 (Edratide), a peptide synthesized on the basis of the sequence of the first complementarity-determining region (CDR1) of an autoantibody. METHODS RNA was extracted from spleen cells of young, disease-free mice and of older mice with systemic lupus erythematosus (SLE) that were treated with hCDR1 or with vehicle alone. Gene expression was assessed using the DNA microarray technique and verified by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS In mice with SLE, numerous genes showed increased or decreased expression relative to that in the disease-free controls. Treatment with hCDR1 restored the expression of many of these genes to control levels. Real-time RT-PCR verified that in diseased mice RNA transcripts of Tnfsf4, Il5ra, Zbtb20, and Nid1 were up-regulated, while transcripts of Tfpi and S100a8 were down-regulated, and confirmed the effects of hCDR1 on the expression of those genes. Kidney immunostaining demonstrated that the up-regulated expression of OX40 ligand, which is a protein product of the gene tumor necrosis factor (ligand) superfamily member 4, in diseased mice was reduced by hCDR1. CONCLUSION Expression of numerous genes in mice with SLE differs from that in young, disease-free control mice. Treatment with hCDR1 restores the expression of 22% of these genes to levels similar to those in controls. Thus, one of the mechanisms by which hCDR1 exerts its beneficial effects on the clinical symptoms of SLE is through regulation of gene expression.
Genetic reprogramming of lactate dehydrogenase, citrate synthase, and phosphofructokinase mRNA in bovine nuclear transfer embryos produced using bovine fibroblast cell nuclei

Adult animal cloning has progressed to allow the production of offspring cloned from adult cells, however many cloned calves die prenatally or shortly after birth. This study examined the expression of three important metabolic enzymes, lactate dehydrogenase (LDH), citrate synthase, and phosphofructokinase (PFK), to determine if their detection in nuclear transfer (NT) embryos mimics that determined for in vitro produced embryos. A day 40 nuclear transfer produced fetus derived from an adult cell line was collected and fetal fibroblast cultures were established and maintained. Reconstructed NT embryos were then produced from this cell line, and RT‐PCR was used to evaluate mRNA reprogramming. All three mRNAs encoding these enzymes were detected in the regenerated fetal fibroblast cell line. Detection patterns were first determined for IVF produced embryos (1‐cell, 2‐cell, 6–8 cell, morula, and blastocyst stages) to compare with their detection in NT embryos. PFK has three subunits: PFK‐L, PFK‐M, and PFK‐P. PFK‐L and PFK‐P were not detected in bovine oocytes. PFK subunits were not detected in 6–8 cell embryos but were detected in blastocysts. Results from NT embryo RT‐PCR demonstrated that PFK was not detected in 8‐cell NT embryos but was detected in NT blastocysts indicating that proper nuclear reprogramming had occurred. Citrate synthase was detected in oocytes and throughout development to the blastocyst stage in both bovine IVF and NT embryos. LDH‐A and LDH‐B were detected in bovine oocytes and in all stages of IVF and NT embryos examined up to the blastocyst stage. A third subunit, LDH‐C was not detected at the blastocyst stage in IVF or NT embryos but was detected in all earlier stages and in mature oocytes. In addition, LDH‐C mRNA was detected in gonad isolated from the NT and an in vivo produced control fetus. These results indicate that the three metabolic enzymes maintain normal expression patterns and therefore must be properly reprogrammed following nuclear transfer. Mol. Reprod. Dev. 56:458–464, 2000. © 2000 Wiley‐Liss, Inc.
The energy cost of growth

Energy requirements for growth can be separated into two components. One is the requirement for substrates from which to form the components of the new tissue, the other is the extra energy needed to meet the metabolic cost of growth. The first requirement is, of courae, absolute in so far as I g of new tissue containing, say, 25% fat and 15% protein cannot be deposited without a dietary supply of about 13.4 kJ of appropriate energy. This is in fact the average energy content of tissue deposited in the rapidly growing malnourished child recovering on an energy-rich milk diet (Spady, Payne, Picou & Waterlow, 1976). The requirement will be variable as the composition of the new tissue varies. Thus, weight gain in older animals tends to involve the deposition of more energy because of the higher fat content. Similarly, in the malnourished child, measurements of muscle mass by Jackson, Picou & Reeds (1976) have clearly shown that new tissue can contain from as little as 5 to as much as 30 kJ/g according to the fat content. However, this paper will be concerned with the second component of the energy cost of growth, the metabolic cost observed as heat production associated with growth.
Concerted evolution: molecular mechanism and biological implications.

A surprisingly large fraction of the eukaryotic genome is repetitive. More than one third of the human genome consists of interspersed repetitive DNA, and tandemly repeated DNA sequences may occupy as much as 10% of the human genome. The majority of the repetitive sequences are nongenic; the rest encode multigene families. The genomic organization of repetitive DNA sequences takes different forms: these repetitive sequences either disperse throughout the genome, as with short interspersed sequences (SINEs), long interspersed sequences (LINEs), and transposable elements, or, like tRNA genes and human histone genes, they may cluster in one or a few chromosomal regions.
Robust Optimization and Data Approximation in Machine Learning

Modern learning problems in nature language processing, computer vision, computational biology, etc. often involve large-scale datasets with millions of samples and/or millions of features, thus are challenging to solve. Simply replacing the original data with a simpler approximation such as a sparse matrix or a low-rank matrix does allow a dramatic reduction in the computational effort required to solve the problem, however some information of the original data will be lost during the approximation process. In some cases, the solution obtained by directly solving the learning problem with approximated data might be infeasible for the original problem or might have undesired properties. In this thesis, we present a new approach that utilizes data approximation techniques and takes into account, via robust optimization the error made during the approximation process in order to obtain learning algorithms that could solve large-scale learning problems efficiently while preserving the learning quality.In the first part of this thesis, we give a brief review of robust optimization and its appearance in machine learning literature. In the second part of this thesis, we examine two data approximation techniques, namely data thresholding and low-rank approximation, and then discuss their connection to robust optimization.