Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model. The purpose of this paper is to develop the hierarchical model of Lonnstedt and Speed (2002) into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples. The model is reset in the context of general linear models with arbitrary coefficients and contrasts of interest. The approach applies equally well to both single channel and two color microarray experiments. Consistent, closed form estimators are derived for the hyperparameters in the model. The estimators proposed have robust behavior even for small numbers of arrays and allow for incomplete data arising from spot filtering or spot quality weights. The posterior odds statistic is reformulated in terms of a moderated t-statistic in which posterior residual standard deviations are used in place of ordinary standard deviations. The empirical Bayes approach is equivalent to shrinkage of the estimated sample variances towards a pooled estimate, resulting in far more stable inference when the number of arrays is small. The use of moderated t-statistics has the advantage over the posterior odds that the number of hyperparameters which need to estimated is reduced; in particular, knowledge of the non-null prior for the fold changes are not required. The moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom. The moderated t inferential approach extends to accommodate tests of composite null hypotheses through the use of moderated F-statistics. The performance of the methods is demonstrated in a simulation study. Results are presented for two publicly available data sets.
Large measles epidemic in the Netherlands, May 2013 to March 2014: changing epidemiology

Since the early 1990s, the Netherlands has experienced several large measles epidemics, in 1992–94, 1999–2000 and in 2013–14. These outbreaks mainly affected orthodox Protestants, a geographically clustered population with overall lower measles-mumps-rubella first dose (MMR-1) vaccination coverage (60%) than the rest of the country (> 95%). In the 2013–14 epidemic described here, which occurred between 27 May 2013 and 12 March 2014, 2,700 cases were reported. Several control measures were implemented including MMR vaccination for 6–14-month-olds and recommendations to reduce the risk in healthcare workers. The vast majority of reported cases were unvaccinated (94%, n = 2,539), mostly for religious reasons (84%, n = 2,135). The median age in the epidemic was 10 years, 4 years older than in the previous epidemic in 1999–2000. A likely explanation is that the inter-epidemic interval before the 2013–2014 epidemic was longer than the interval before the 1999–2000 epidemic. The size of the unvaccinated orthodox Protestant community is insufficient to allow endemic transmission of measles in the Netherlands. However, large epidemics are expected in the future, which is likely to interfere with measles elimination in the Netherlands and elsewhere.
Lossless abstraction of imperfect information games

Finding an equilibrium of an extensive form game of imperfect information is a fundamental problem in computational game theory, but current techniques do not scale to large games. To address this, we introduce the ordered game isomorphism and the related ordered game isomorphic abstraction transformation. For a multi-player sequential game of imperfect information with observable actions and an ordered signal space, we prove that any Nash equilibrium in an abstracted smaller game, obtained by one or more applications of the transformation, can be easily converted into a Nash equilibrium in the original game. We present an algorithm, GameShrink, for abstracting the game using our isomorphism exhaustively. Its complexity is õ(n2), where n is the number of nodes in a structure we call the signal tree. It is no larger than the game tree, and on nontrivial games it is drastically smaller, so GameShrink has time and space complexity sublinear in the size of the game tree. Using GameShrink, we find an equilibrium to a poker game with 3.1 billion nodes—over four orders of magnitude more than in the largest poker game solved previously. To address even larger games, we introduce approximation methods that do not preserve equilibrium, but nevertheless yield (ex post) provably close-to-optimal strategies.
Face Adaptation Effects: Reviewing the Impact of Adapting Information, Time, and Transfer

The ability to adapt is essential to live and survive in an ever-changing environment such as the human ecosystem. Here we review the literature on adaptation effects of face stimuli to give an overview of existing findings in this area, highlight gaps in its research literature, initiate new directions in face adaptation research, and help to design future adaptation studies. Furthermore, this review should lead to better understanding of the processing characteristics as well as the mental representations of face-relevant information. The review systematizes studies at a behavioral level in respect of a framework which includes three dimensions representing the major characteristics of studies in this field of research. These dimensions comprise (1) the specificity of adapting face information, e.g., identity, gender, or age aspects of the material to be adapted to (2) aspects of timing (e.g., the sustainability of adaptation effects) and (3) transfer relations between face images presented during adaptation and adaptation tests (e.g., images of the same or different identities). The review concludes with options for how to combine findings across different dimensions to demonstrate the relevance of our framework for future studies.
Prediction of the age at onset in spinocerebellar ataxia type 1, 2, 3 and 6

Background The most common spinocerebellar ataxias (SCA)—SCA1, SCA2, SCA3, and SCA6—are caused by (CAG)n repeat expansion. While the number of repeats of the coding (CAG)n expansions is correlated with the age at onset, there are no appropriate models that include both affected and preclinical carriers allowing for the prediction of age at onset. Methods We combined data from two major European cohorts of SCA1, SCA2, SCA3, and SCA6 mutation carriers: 1187 affected individuals from the EUROSCA registry and 123 preclinical individuals from the RISCA cohort. For each SCA genotype, a regression model was fitted using a log-normal distribution for age at onset with the repeat length of the alleles as covariates. From these models, we calculated expected age at onset from birth and conditionally that this age is greater than the current age. Results For SCA2 and SCA3 genotypes, the expanded allele was a significant predictor of age at onset (−0.105±0.005 and −0.056±0.003) while for SCA1 and SCA6 genotypes both the size of the expanded and normal alleles were significant (expanded: −0.049±0.002 and −0.090±0.009, respectively; normal: +0.013±0.005 and −0.029±0.010, respectively). According to the model, we indicated the median values (90% critical region) and the expectancy (SD) of the predicted age at onset for each SCA genotype according to the CAG repeat size and current age. Conclusions These estimations can be valuable in clinical and research. However, results need to be confirmed in other independent cohorts and in future longitudinal studies. ClinicalTrials.gov, number NCT01037777 and NCT00136630 for the French patients.
Capacity of Non-Malleable Codes

Non-malleable codes, introduced by Dziembowski et al., encode messages s in a manner, so that tampering the codeword causes the decoder to either output s or a message that is independent of s. While this is an impossible goal to achieve against unrestricted tampering functions, rather surprisingly non-malleable coding becomes possible against every fixed family P of tampering functions that is not too large (for instance, when I≤I 22αn for some α <; 1, where n is the number of bits in a codeword). In this paper, we study the capacity of non-malleable codes, and establish optimal bounds on the achievable rate as a function of the family size, answering an open problem from Dziembowski et al. Specifically, We prove that for every family P with IFI I≤I 22αn, there exist non-malleable codes against P with rate arbitrarily close to 1-α [this is achieved with high probability (w.h.p.) by a randomized construction]. We show the existence of families of size exp(nO(1)2αn) against which there is no non-malleable code of rate 1 - α (in fact this is the case w.h.p for a random family of this size). We also show that 1 - α is the best achievable rate for the family of functions, which are only allowed to tamper the first αn bits of the codeword, which is of special interest. As a corollary, this implies that the capacity of non-malleable coding in the split-state model (where the tampering function acts independently but arbitrarily on the two halves of the codeword, a model which has received some attention recently) equals 1/2. We also give an efficient Monte Carlo construction of codes of rate close to 1 with polynomial time encoding and decoding that is non-malleable against any fixed c > 0 and family P of size 2nc, in particular tampering functions with, say, cubic size circuits.
Lentes intraoculares fácicas de câmara posterior

O objetivo deste artigo foi reunir estudos que reportam resultados disponíveis na literatura científica, considerando a previsibilidade, segurança, eficácia, e estabilidade das lentes intraoculares fácicas de câmara posterior. E relatar as complicações documentadas para estas lentes. A revisão criteriosa dos estudos publicados na literatura ate o momento revelam resultado satisfatórios quanto à eficácia, elevada previsibilidade, estabilidade e segurança do implante de lente intraocular de câmara posterior, para correção das miopia, hipermetropia e astigmatismo. Descritores: Lentes intraoculares; Lentes intraoculares fácicas; Erros de refração; Cristalino: Procedimentos cirúrgicos refrativos; Complicações pós operatórias AbstrAct
Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity

We describe snap-to-it probes, a novel probe technology to enhance the hybridization specificity of natural and unnatural nucleic acid oligomers using a simple and readily introduced structural motif. Snap-to-it probes were prepared from peptide nucleic acid (PNA) oligomers by modifying each terminus with a coordinating ligand. The two coordinating ligands constrain the probe into a macrocyclic configuration through formation of an intramolecular chelate with a divalent transition metal ion. On hybridization with a DNA target, the intramolecular chelate in the snap-to-it probe dissociates, resulting in the probe ‘snapping-to’ and binding the target nucleic acid. Thermal transition analysis of snap-to-it probes with complementary and single-mismatch DNA targets revealed that the transition between free and target-bound probe conformations was a reversible equilibrium, and the intramolecular chelate provided a thermodynamic barrier to target binding that resulted in a significant increase in mismatch discrimination. A 4–6°C increase in specificity (ΔTm) was observed from snap-to-it probes bearing either terminal iminodiacetic acid ligands coordinated with Ni2+, or terminal dihistidine and nitrilotriacetic acid ligands coordinated with Cu2+. The difference in specificity of the PNA oligomer relative to DNA was more than doubled in snap-to-it probes. Snap-to-it probes labeled with a fluorophore-quencher pair exhibited target-dependent fluorescence enhancement upon binding with target DNA.
Estimating Drivable Collision-Free Space from Monocular Video

In this paper we propose a novel algorithm for estimating the drivable collision-free space for autonomous navigation of on-road and on-water vehicles. In contrast to previous approaches that use stereo cameras or LIDAR, we show a method to solve this problem using a single camera. Inspired by the success of many vision algorithms that employ dynamic programming for efficient inference, we reduce the free space estimation task to an inference problem on a 1D graph, where each node represents a column in the image and its label denotes a position that separates the free space from the obstacles. Our algorithm exploits several image and geometric features based on edges, color, and homography to define potential functions on the 1D graph, whose parameters are learned through structured SVM. We show promising results on the challenging KITTI dataset as well as video collected from boats.
Prognostic Value of p53 Expression in Stage IB1 Cervical Carcinoma

The purpose of this retrospective study was to evaluate the patterns of p53 expression in stage IB1 squamous cell carcinoma of the uterine cervix, to compare p53 expression with clinicopathological findings, and to assess its prognostic value. 27 patients with stage IB1 squamous cell carcinoma of the uterine cervix underwent abdominal radical hysterectomy and pelvic lymph node dissection. Expression of p53 was studied immunohistochemically. Overexpression of p53 was detected in 33.3% of the tumors, low expression was seen in 11.1%, and negative expression was found in 55.6%. Deep cervical stromal invasion (≧1/2) was found to be associated with the increased risk of lymph node metastases (odds ratio = 17.5). A significantly lower percentage of patients survived when p53 overexpression was observed (p = 0.0315). Univariate analysis revealed that tumor size (2–3.9 cm), lymph node metastasis, tumor invasion into parametria, tumor invasion into blood/lymph vessels, squamous cell carcinoma antigen (≧2 ng/ml), and p53 overexpression had a significantly lower recurrence-free survival rate. None of these above factors obtained significance in the multivariate analysis. This study suggests that expression of p53 may be indicative of an unfavorable prognosis in patients with stage IB1 squamous cell carcinoma of the uterine cervix.
A statistical approach to packet loss concealment for video

We have developed a statistical prediction technique to compensate for lost pixel blocks during real time transmission of video over packet-switched networks. The approach could as well be used for standard inter-frame coding. The method is based on the joint modeling of pixel statistics by Gaussian mixtures. Different EM variants for decreasing computational complexity and storage space are proposed. In the case of 4/spl times/4 luminance blocks, our method increases performance by 2.3 dB when augmenting the number of mixture components from 1 to 64. We show that these results are statistically significant.
Order of Magnitude Smaller Limit on the Electric Dipole Moment of the Electron

Stubbornly Spherical The shape of the electron's charge distribution reflects the degree to which switching the direction of time impacts the basic ingredients of the universe. The Standard Model (SM) of particle physics predicts a very slight asphericity of the charge distribution, whereas SM extensions such as supersymmetry posit bigger and potentially measurable, but still tiny, deviations from a perfect sphere. Polar molecules have been identified as ideal settings for measuring this asymmetry, which should be reflected in a finite electric dipole moment (EDM) because of the extremely large effective electric fields that act on an electron inside such molecules. Using electron spin precession in the molecule ThO, Baron et al. (p. 269, published online 19 December; see the cover; see the Perspective by Brown) measured the EDM of the electron as consistent with zero. This excludes some of the extensions to the SM and sets a bound to the search for a nonzero EDM in other facilities, such as the Large Hadron Collider. Spin precession measurements in the polar molecule thorium monoxide indicate a nearly spherical charge distribution of an electron. [Also see Perspective by Brown] The Standard Model of particle physics is known to be incomplete. Extensions to the Standard Model, such as weak-scale supersymmetry, posit the existence of new particles and interactions that are asymmetric under time reversal (T) and nearly always predict a small yet potentially measurable electron electric dipole moment (EDM), de, in the range of 10−27 to 10−30 e·cm. The EDM is an asymmetric charge distribution along the electron spin (S→) that is also asymmetric under T. Using the polar molecule thorium monoxide, we measured de = (–2.1 ± 3.7stat ± 2.5syst) × 10−29 e·cm. This corresponds to an upper limit of | de | < 8.7 × 10−29 e·cm with 90% confidence, an order of magnitude improvement in sensitivity relative to the previous best limit. Our result constrains T-violating physics at the TeV energy scale.
Evolutionary Function Approximation for Reinforcement Learning

Temporal difference methods are theoretically grounded and empirically effective methods for addressing reinforcement learning problems. In most real-world reinforcement learning tasks, TD methods require a function approximator to represent the value function. However, using function approximators requires manually making crucial representational decisions. This paper investigates evolutionary function approximation, a novel approach to automatically selecting function approximator representations that enable efficient individual learning. This method evolves individuals that are better able to learn. We present a fully implemented instantiation of evolutionary function approximation which combines NEAT, a neuroevolutionary optimization technique, with Q-learning, a popular TD method. The resulting NEAT+Q algorithm automatically discovers effective representations for neural network function approximators. This paper also presents on-line evolutionary computation, which improves the on-line performance of evolutionary computation by borrowing selection mechanisms used in TD methods to choose individual actions and using them in evolutionary computation to select policies for evaluation. We evaluate these contributions with extended empirical studies in two domains: 1) the mountain car task, a standard reinforcement learning benchmark on which neural network function approximators have previously performed poorly and 2) server job scheduling, a large probabilistic domain drawn from the field of autonomic computing. The results demonstrate that evolutionary function approximation can significantly improve the performance of TD methods and on-line evolutionary computation can significantly improve evolutionary methods. This paper also presents additional tests that offer insight into what factors can make neural network function approximation difficult in practice.
The Persistent Effect of Geographic Distance in Acquisition Target Selection

Valuable resources often exist at distant points from a firm's current locations, with the result that strategic decisions such as growth have a spatial dimension in which firms seek information and choose between geographically distributed alternatives. Studies show that geographic proximity facilitates the flow of resources, but there is limited understanding of factors that exacerbate or ease the impact of geographic distance when firms seek new resources. This paper argues that the difficulty of search increases with distance, particularly when search involves greater information processing, but that firms can partially overcome the constraints of distance with direct, contextual, and vicarious learning. We study 2,070 domestic acquisition announcements by U.S. chemical manufacturers founded after 1979. The results demonstrate the persistent effect of spatial geography on organizational search processes.
Kiwifruit under plastic covering: impact on fruit quality and on orchard microclimate

Italy has a preeminent rank in kiwifruit industry, being the first exporter and the second largest producer after China. However, in the last few years kiwifruit yields and the total cultivated area considerably decreased, due to the disease spread of the bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa). Bacterial canker has affected significantly orchards productivity and consequently has caused severe economic losses in all major areas of kiwifruit cultivation, including Italy,and considerable damage to the international kiwifruit industry.Several climatic conditions and cultural practices affect the development of the bacterial canker.Orchard hygiene, restrictions on the movement of nursery plants, orchard management and cultural practices, chemical and biological controls and breeding programs are being employed to limit the diffusion of the disease and help kiwifruit orchards to survive and produce. A possible way seems to be the modification of environmental conditions and it is being explored through the building of plastic covers over the orchards. This research work is focused on the impact of plastic cover on fruit quality, microclimate conditions and incidence of Psa. To evaluate the impact of plastic cover on microclimate, quality of fruits and disease incidence the following parameters were evaluated: climatic parameters (temperature, PAR), quality parameters (color, fruit firmness, titratable acidity, °Brix, vitamin C), disease incidence (%). The use of a permanenttunnel modify light intensity and microclimate without any negative consequences on kiwifruits quality. Covering a kiwifruit orchard with a protective canopy reduces the spread of Psa throughout the orchard when covers are constructed over vines with low levels of infection.The use of plastic covers ensure the production of the current and future kiwifruit without compromising the quality of the fruit, but future trials will provide further information clarifying the effectiveness of the actual crop covers.
Relationship between fractal dimension and power-law exponent of heart rate variability in normal and heart failure subjects

Among the plethora of indices that can describe the fractal-like behaviour of heart rate variability (HRV), the fractal dimension (FD) and the power-law exponent (β) have gained wide acceptance. Since HRV is generally modelled with fractional Brownian motion (fBm), the linear scaling relationship between β and FD, valid for fBm, is often applied to HRV series to derive one index from the other. In this paper the relationship between β and FD is calculated in normal (NR) and heart failure (HF) HRV series. Results revealed that a linear dependence between β and FD can be found only when the slope of the spectral density is calculated over the whole spectrum instead of considering more widespread very low frequency ranges. Moreover, the relationship is slightly different from that characterizing fBm and is not unique for the two categories of subjects. The common practice of estimating β from FD for HRV applying the theoretical relationship should be reconsidered.