Miracle-dz/UniFAR-FTUs huggingface dataset:
Preimplantation Genetic Diagnosis for Aneuploidy and Translocations Using Array Comparative Genomic Hybridization

At least 50% of human embryos are abnormal, and that increases to 80% in women 40 years or older. These abnormalities result in low implantation rates in embryos transferred during in vitro fertilization procedures, from 30% in women <35 years to 6% in women 40 years or older. Thus selecting normal embryos for transfer should improve pregnancy results. The genetic analysis of embryos is called Preimplantation Genetic Diagnosis (PGD) and for chromosome analysis it was first performed using FISH with up to 12 probes analyzed simultaneously on single cells. However, suboptimal utilization of the technique and the complexity of fixing single cells produced conflicting results. PGD has been invigorated by the introduction of microarray testing which allows for the analysis of all 24 chromosome types in one test, without the need of cell fixation, and with staggering redundancy, making the test much more robust and reliable. Recent data published and presented at scientific meetings has been suggestive of increased implantation rates and pregnancy rates following microarray testing, improvements in outcome that have been predicted for quite some time. By using markers that cover most of the genome, not only aneuploidy can be detected in single cells but also translocations. Our validation results indicate that array CGH has a 6Mb resolution in single cells, and thus the majority of translocations can be analyzed since this is also the limit of karyotyping. Even for translocations with smaller exchanged fragments, provided that three out of the four fragments are above 6Mb, the translocation can be detected.
Fast tree-trellis list Viterbi decoding

A list Viterbi algorithm (LVA) finds the n most likely paths in a trellis diagram of a convolutional code. One of the most efficient LVAs is the tree-trellis algorithm of Soong and Huang. We propose a new implementation of this algorithm. Instead of storing the candidate paths in a single list sorted according to the metrics of the paths, we show that it is computationally more efficient to use several unsorted lists, where all paths of the same list have the same metric. For an arbitrary integer bit metric, both the time and space complexity of our implementation are linear in n. Experimental results for a binary symmetric channel and an additive white Gaussian noise channel show that our implementation is much faster than all previous LVAs.
A Complexity-Effective Decoding Architecture Based on Instruction Streams

A complex decoding logic is a performance bottleneck for those high-frequency microprocessors that implement variable length instruction set architectures. The need of removing this complexity from the critical execution path has lead to the design of alternative techniques, like the trace cache fetch architecture. The trace cache stores decoded instructions, and thus the instructions fetched from it do not require to be decoded again. However, this is achieved at the cost of increasing the complexity of the fetch engine. This paper presents a first glance at a complexityeffective decoding architecture. Our proposal does not use a special-purpose storage like the trace cache. Instead, our architecture stores frequently executed instructions in the memory hierarchy. The already decoded instructions can be fetched from memory, removing the complex instruction decoder from the critical path. Our final objective is to provide all the benefits of fetching already decoded instructions, but without increasing the implementation cost and complexity of the fetch architecture.
Visual Tuning Properties of Genetically Identified Layer 2/3 Neuronal Types in the Primary Visual Cortex of Cre-Transgenic Mice

The putative excitatory and inhibitory cell classes within the mouse primary visual cortex V1 have different functional properties as studied using recording microelectrode. Excitatory neurons show high selectivity for the orientation angle of moving gratings while the putative inhibitory neurons show poor selectivity. However, the study of selectivity of the genetically identified interneurons and their subtypes remain controversial. Here we use novel Cre-driver and reporter mice to identify genetic subpopulations in vivo for two-photon calcium dye imaging: Wfs1(+)/Gad1(−) mice that labels layer 2/3 excitatory cell population and Pvalb(+)/Gad1(+) mice that labels a genetic subpopulation of inhibitory neurons. The cells in both mice were identically labeled with a tdTomato protein, visible in vivo, using a Cre-reporter line. We found that the Wfs1(+) cells exhibited visual tuning properties comparable to the excitatory population, i.e., high selectivity and tuning to the angle, direction, and spatial frequency of oriented moving gratings. The functional tuning of Pvalb(+) neurons was consistent with previously reported narrow-spiking interneurons in microelectrode studies, exhibiting poorer selectivity than the excitatory neurons. This study demonstrates the utility of Cre-transgenic mouse technology in selective targeting of subpopulations of neurons and makes them amenable to structural, functional, and connectivity studies.
Differential Impact of Science Policy on Subfields of Human Embryonic Stem Cell Research

In this research, we examine how restrictive policy influenced performance in human embryonic stem cell research (hESC) between 1998 and 2008. In previous research, researchers argued whether restrictive policy decreased the performance of stem cell research in some nations, especially in the US. Here, we hypothesize that this policy influenced specific subfields of the hESC research. To investigate the selective policy effects, we categorize hESC research publications into three subfields—derivation, differentiation, and medical application research. Our analysis shows that restrictive policy had different effects on different subfields. In general, the US outperformed in overall hESC research throughout these periods. In the derivation of hESC, however, the US almost lost its competence under restrictive policy. Interestingly, the US scientific community showed prominent resilience in hESC research through international collaboration. We concluded that the US resilience and performance stemmed from the wide breadth of research portfolio of US scientists across the hESC subfields, combined with their strategic efforts to collaborate internationally on derivation research.
EigenRep: Reputation Management in P2P Networks

Peer-to-peer file-sharing networks are currently receiving much attention as a means of sharing and distributing information. However, as recent experience with P2P networks such as Gnutella shows, the anonymous, open nature of these networks offers an almost ideal environment for the spread of self-replicating inauthentic files. We describe an algorithm to decrease the number of downloads of inauthentic files in a peer-to-peer file-sharing network that assigns each peer a unique global reputation value, based on the peer’s history of uploads. We present a distributed and secure method to compute global reputation values, based on Power iteration. By having peers use these global reputation values to choose the peers from whom they download, the network effectively identifies malicious peers and isolates them from the network. In simulations, this reputation system has been shown to significantly decrease the number of inauthentic files on the network, even under a variety of conditions where malicious peers cooperate in an attempt to deliberately subvert the system.
Analysis of timing jitter in inverters induced by power-supply noise

This paper describes the transformation process of power-supply noise (PSN) to timing jitter of inverters. The focus is on the inverters used in multiphase clock-generator circuits (CGCs) commonly needed for switched-capacitor (SC) sigma-delta (SigmaDelta) analog-to-digital converters (ADCs). Closed form expressions relating timing jitter and PSN are presented and the results are compared with Monte-Carlo simulations performed in Spectre at BSIM3v3 transistor model level using the processes AMS 0.35mum and UMC 0.18mum. The PSN is assumed to have a white frequency distribution with independent power and ground noise. The results show that the transformation process is approximately linear and that the jitter impact decreases as transistors move deeper into the submicron domain. Furthermore, the transformation process is not symmetrical and is dependent on switching direction, even if the PMOS and NMOS sizings are such that the effects due to difference in hole and electron mobility are mitigated
Naringenin suppresses K562 human leukemia cell proliferation and ameliorates Adriamycin-induced oxidative damage in polymorphonuclear leukocytes

Treatments for leukemia remain unsatisfactory. Conventional chemotherapy agents that aim to kill tumor cells may also damage normal cells and thus result in severe side-effects. Naringenin, a natural polyphenolic compound with antioxidant effects, has been revealed to have significant antitumor effects with low toxicity in preliminary studies. Thus, it is considered as one of the most promising flavonoids in the treatment of leukemia. In the present study, the effects of naringenin on the K562 human leukemia cell line and the underlying mechanisms were explored in vitro. In addition, human peripheral blood polymorphonuclear leukocytes (PMNs) were used as a normal control in order to evaluate the effects of naringenin on normal granulocytes and in the mediation of Adriamycin (ADM)-induced oxidative damage. The results revealed that K562 proliferation was significantly inhibited by naringenin in a time- and concentration-dependent manner; however, minimal cytotoxic effects were observed in PMNs when naringenin was used at concentrations <400 μmol/l. Morphological changes indicative of apoptosis were observed in naringenin-treated K562 cells. Flow cytometric analysis indicated that the K562 cells were arrested in the G0/G1 phase of the cell cycle with a significantly upregulated rate of apoptosis. Furthermore, in the naringenin-treated K562 cells, the labeling index of proliferating cell nuclear antigen was observed to be increased by immunochemical staining, the mRNA and protein expression levels of p21/WAF1 were strongly upregulated in reverse transcription-polymerase chain reaction and western blot analyses, whereas p53 gene expression was not significantly changed. In PMNs to which naringenin (50~80 μmol/l) was added 1 h subsequent to ADM, the cell damage induced by ADM was significantly reduced, coincident with reductions in the levels of reactive oxygen species (ROS) and malondialdehyde (MDA) and increases in the activity of superoxide dismutase and glutathione peroxidase. However, the cytotoxic effect of ADM in K562 cells was not significantly altered by naringenin, and the oxidative stress indices in K562 cells remained stable. In conclusion, the present study revealed the promising value of naringenin in leukemia treatment. Naringenin demonstrated a significant inhibitory effect on the growth of K562 cells but not on normal PMNs. Furthermore, naringenin protected PMNs from ADM-induced oxidative damage at low concentrations. Cell cycle arrest and apoptosis-inducing effects, achieved through p53-independent p21/WAF1 upregulation, are likely to be the mechanism of the antileukemic effects of naringenin, and the protective effect against ADM chemotherapy-induced damage in PMNs may be due to the antioxidant capability of this agent at low concentrations.
Operational analysis of timed Petri nets and application to the computation of performance bounds

Operational analysis techniques are used to partially characterize the behavior of timed Petri nets under very weak assumptions on their timing semantics. New operational inequalities are derived that are typical of the presence of synchronization and that were therefore not considered in queuing network models. An interesting application of the operational laws to the statement and the efficient solution of problems related to the estimation of performance bounds insensitive to the timing probability distributions is shown. The results obtained generalize and improve in a clear setting results that were derived in the last few years for several different subclasses of timed Petri nets. In particular, the extension to well-formed colored nets appears straightforward and allows an efficient exploitation of model symmetries. <<ETX>>
Changes in REIT Liquidity 1990-94 : The Role of “ New REITs

Bhasin, Cole, and Kiely (1997) document significant increases in REIT liquidity from 1990-94 as measured by a narrowing of the percentage bid-ask spread. However, they measure the average spread in each year across all firms in the industry. In this article, we demonstrate that, when the comparison is restricted to the panel of REITs operating in both time periods, percentage spreads widened rather than narrowed. We reconcile these seemingly contradictory results by showing that the narrowing of industry-wide spreads previously reported was driven by the spreads of “new REITs” that went public during 1991-94. Hence, this manuscript contribute to the growing number of papers that differentiate the more recently established REITs from their predecessors.
Relationship between Maximal Oxygen Consumption () and Home Range Area in Mammals

Home range is defined as the area traversed during normal daily activities, such as foraging, avoiding predators, and social or antagonistic behaviors. All else being equal, larger home ranges should be associated with longer daily movement distances and/or higher average movement speeds. The maximal rate of oxygen consumption () generally sets an upper limit to the intensity of work (e.g., speed of locomotion) that an animal can sustain without fatigue. Therefore, home range area and are predicted to evolve in concert (coadapt). We gathered literature data on home range and for 55 species of mammals. We computed residuals from log-log (allometric) regressions on body mass with two different regression models: ordinary least squares (OLS) and phylogenetic generalized least squares (PGLS). Residuals were weakly positively related for both the OLS (r = 0.278, one-tailed P < 0.05) and PGLS (r = 0.210, P > 0.05) regressions. For , the PGLS regression model had a slightly higher likelihood than the OLS model, but the situation was reversed for home range area. In addition, for both home range area and , models that fit better than either OLS or PGLS were obtained by modeling residual variation with the Ornstein-Uhlenbeck process to mimic stabilizing selection (RegOU), indicating that phylogenetic signal is present in both size-adjusted traits, consistent with findings of previous studies. (However, residuals from the RegOU models cannot be tested for correlation due to mathematical complexities.) We conclude that the best estimate of the residual correlation is probably somewhere between these two values reported above. Possible reasons for the low correlation between residual home range area and are discussed.
TRAFFIC FLOW FORECASTING USING APPROXIMATE NEAREST NEIGHBOR NONPARAMETRIC REGRESSION

The purpose of this research is to enhance nonparametric regression (NPR) for use in real-time systems by first reducing execution time using advanced data structures and imprecise computations and then developing a methodology for applying NPR. Due to the nature of the enhancements to nonparametric regression, each application of NPR will be specific for each system. This research, therefore, provides general guidelines for deploying nonparametric regression, similar to how Box and Jenkins (1970) provided a methodology for conducting time series analysis
Self-adjoint extensions by additive perturbations

Let AN be the symmetric operator given by the restriction of A to N , where A is a self-adjoint operator on the Hilbert space H and N is a linear dense set which is closed with respect to the graph norm on D(A), the operator domain of A. We show that any self-adjoint extension Aof AN such that D(A� )∩ D(A) = N can be additively decomposed by the sum A� = ¯ A+T� , where both the operators ¯ A and Ttake values in the strong dual of D(A). The operator ¯ A is the closed extension of A to the whole H whereas Tis explicitly written in terms of a (abstract) boundary condition depending on N and on the extension parameter � ,a self-adjoint operator on an auxiliary Hilbert space isomorphic (as a set) to the deficiency spaces of AN . The explicit connection with both Kre˘in's resolvent formula and von Neumann's theory of self-adjoint extensions is given.
Replication Independent Formation of Extrachromosomal Circular DNA in Mammalian Cell-Free System

Extrachromosomal circular DNA (eccDNA) is a pool of circular double stranded DNA molecules found in all eukaryotic cells and composed of repeated chromosomal sequences. It was proposed to be involved in genomic instability, aging and alternative telomere lengthening. Our study presents novel mammalian cell-free system for eccDNA generation. Using purified protein extract we show that eccDNA formation does not involve de-novo DNA synthesis suggesting that eccDNA is generated through excision of chromosomal sequences. This process is carried out by sequence- independent enzymes as human protein extract can produce mouse- specific eccDNA from high molecular weight mouse DNA, and vice versa. EccDNA production does not depend on ATP, requires residual amounts of Mg2+ and is enhanced by double strand DNA breaks.
Stochastic Uncertainty Models for the Luminance Consistency Assumption

In this paper, a stochastic formulation of the brightness consistency used in many computer vision problems involving dynamic scenes (for instance, motion estimation or point tracking) is proposed. Usually, this model, which assumes that the luminance of a point is constant along its trajectory, is expressed in a differential form through the total derivative of the luminance function. This differential equation linearly links the point velocity to the spatial and temporal gradients of the luminance function. However, when dealing with images, the available information only holds at discrete time and on a discrete grid. In this paper, we formalize the image luminance as a continuous function transported by a flow known only up to some uncertainties related to such a discretization process. Relying on stochastic calculus, we define a formulation of the luminance function preservation in which these uncertainties are taken into account. From such a framework, it can be shown that the usual deterministic optical flow constraint equation corresponds to our stochastic evolution under some strong constraints. These constraints can be relaxed by imposing a weaker temporal assumption on the luminance function and also in introducing anisotropic intensity-based uncertainties. We also show that these uncertainties can be computed at each point of the image grid from the image data and hence provide meaningful information on the reliability of the motion estimates. To demonstrate the benefit of such a stochastic formulation of the brightness consistency assumption, we have considered a local least-squares motion estimator relying on this new constraint. This new motion estimator significantly improves the quality of the results.
Concussion in sports: postconcussive activity levels, symptoms, and neurocognitive performance.

CONTEXT Evidence suggests that athletes engaging in high-intensity activities after concussion have more difficulties with cognitive recovery. OBJECTIVE To examine the role postinjury activity level plays in postconcussive symptoms and performance on neurocognitive tests in a population of student-athletes. DESIGN Retrospective cohort study with repeated measures of neurocognitive performance and symptom reporting. SETTING University-based sports concussion clinic. PATIENTS OR OTHER PARTICIPANTS Ninety-five student-athletes (80 males, 15 females: age = 15.88 +/- 1.35 years) were retrospectively assigned to 1 of 5 groups based on a postinjury activity intensity scale. MAIN OUTCOME MEASURE(S) We employed a regression analysis for repeated measures to evaluate the relationship of activity intensity to symptoms and neurocognitive outcome up to 33 days after concussion. Postconcussion symptom scores and neurocognitive (verbal memory, visual memory, visual motor speed, and reaction time) scores served as the primary outcome measures. RESULTS Level of exertion was significantly related to all outcome variables (P < .02 for all comparisons). With multivariate analysis, activity intensity remained significant with respect to visual memory (P = .003) and reaction time (P < .001). CONCLUSIONS Activity level after concussion affected symptoms and neurocognitive recovery. Athletes engaging in high levels of activity after concussion demonstrated worse neurocognitive performance. For these tasks, those engaging in moderate levels of activity demonstrated the best performance.
Study of Prediction Models Compared with the measurement Results of Rainfall Rate and Ku-Band Attenuation at Indonesia

Statistic shows that the tropical regions experienced intense rainfall throughout the year. Thus the study of rainfall rate for tropical countries is very important due to the significant effect of rain rate of the satellite communication. Prior to this work, several rain attenuation models have been tested to be used in Bandung since the implementation of ITU-R model is overestimated for Bandung. In this work, three different rain attenuation prediction models have been used to determine the best rain attenuation model to be adopted in Bandung, Indonesia. Two years of measured rain rate data for Bandung shows that the measured rain rate is 120mm/hour with 17 dB of measured rain attenuation. Comparison between the predicted models and the measured value of rain attenuation are presented and the results show that the best model to be utilized at Bandung is Brazil model with R0.01 is 16.94dB.
From action intentions to action effects: how does the sense of agency come about?

Sense of agency refers to the feeling of controlling an external event through one’s own action. On one influential view, agency depends on how predictable the consequences of one’s action are, getting stronger as the match between predicted and actual effect of an action gets closer. Thus, sense of agency arises when external events that follow our action are consistent with predictions of action effects made by the motor system while we perform or simply intend to perform an action. According to this view, agency is inferred retrospectively, after an action has been performed and its consequences are known. In contrast, little is known about whether and how internal processes involved in the selection of actions may influence subjective sense of control, in advance of the action itself, and irrespective of effect predictability. In this article, we review several classes of behavioral and neuroimaging data suggesting that earlier processes, linked to fluency of action selection, prospectively contribute to sense of agency. These findings have important implications for better understanding human volition and abnormalities of action experience.
Measuring the Value of a Public Good: An Empirical Comparison of Elicitation Procedures

The problems associated with accurately measuring the value of a public good in an applied setting are considered. The values obtained from hypothetical elicitation procedures are compared and contrasted with those obtained in a marketplace. When hypothetical measurements are elicited in the field, buying-selling discrepancies similar to those predicted by psychological models of behavior are observed. However, when the market-like elicitation process is repeated, values are more consistent with diminishing marginal utility. The authors cannot reject the hypothesis that these individuals exhibit loss- aversion behavior. The marketplace, however, is a strong disciplinarian of limiting this type of behavior. Copyright 1987 by American Economic Association.