gebhart/patrepeval huggingface dataset:
Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data (2016)

Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up to large, ultra-high dimensional biological data. More specifically, we scale up the novel Hilbert-Schmidt Independence Criterion Lasso (HSIC Lasso) to handle millions of features with tens of thousand samples. The proposed method is guaranteed to find an optimal subset of maximally predictive features with minimal redundancy, yielding higher predictive power and improved interpretability. Its effectiveness is demonstrated through applications to classify phenotypes based on module expression in human prostate cancer patients and to detect enzymes among protein structures. We achieve high accuracy with as few as 20 out of one million features --- a dimensionality reduction of 99.998%. Our algorithm can be implemented on commodity cloud computing platforms. The dramatic reduction of features may lead to the ubiquitous deployment of sophisticated prediction models in mobile health care applications.
Visual marker detection and decoding in AR systems: a comparative study (2002)

Visual markers are widely used in existing augmented reality (AR) applications [7,12,11,19 ]. In most of such applications, the performance of an AR system depends highly on the tracking system for visual marker detection, tracking,and pose estimation. Currently, there are more than one marker based tracking/calibration systems available. It is thus desirable for the user to know which marker tracking system is likely to perform the best for a specific AR application. To this purpose, we compare several marker systems all using planar square coded visual markers. We present the evaluation results, both qualitatively and quantitatively, for the following properties: the usability, efficiency, accuracy, and reliability. For a particular AR application, there are different marker detection and tracking requirements. Therefore, the purpose of this work is not to rank the existing marker systems; instead, we try to analyze the strength and weakness of various aspects of the marker tracking systems and provide the AR application developers with this information.
Effect of off-axis illumination on stepper overlay (1995)

Modified illumination schemes for wafer steppers, such as oblique and low partial coherence illumination, can improve the imaging performance for some types of microlithography patterns. Implementation of these methods by simple insertion of apertures into a stepper illuminator, without reoptimization of the illuminator, can lead to deterioration in illumination power and uniformity. The different apertures may also affect lens aberrations, lens distortion and illumination telecentricity and require adjustments for the effective control of dose, focus and reduction ratio. This study has examined the set-up of a modified illumination system, the effects of four different illuminator apertures on several lens parameters and the consequent effect on overlay between layers printed with different apertures. It is found that the lens performance is either not significantly changed or can be compensated adequately in the case of off-axis illumination apertures but deteriorates when using low partial coherence illumination. However, preliminary overlay tests between fields printed using different apertures show acceptable performance in all cases.
Image Description using Visual Dependency Representations (2013)

Describing the main event of an image involves identifying the objects depicted and predicting the relationships between them.Previous approaches have represented images as unstructured bags of regions, which makes it difficult to accurately predict meaningful relationships between regions.In this paper, we introduce visual dependency representations to capture the relationships between the objects in an image, and hypothesize that this representation can improve image description.We test this hypothesis using a new data set of region-annotated images, associated with visual dependency representations and gold-standard descriptions.We describe two template-based description generation models that operate over visual dependency representations.In an image description task, we find that these models outperform approaches that rely on object proximity or corpus information to generate descriptions on both automatic measures and on human judgements.
Controllable Monoaddition of Carbon Nucleophiles to 1,2,3,4-Diepoxybutane: Two-directional Chain Extension of a C2 Symmetric Four Carbon Diepoxide as a Route to Differentiated Syn 1,2-Diols (2002)

A strategy for the construction of unsymmetrically protected isolated syn 1,2-diols bearing various unsaturated appendages is described. Reaction conditions are described for selective monoaddition to C2 symmetric 1,2,3,4-diepoxybutane which permits both differential protection of the intermediate epoxy alcohols and a second chain elongation. This sequence provides access to unsymmetrical mono-protected diols bearing unsaturated appendages not readily accessible by asymmetric dihydroxylation.
Uses of plant lectins in bioscience and biomedicine (2007)

New research directions in the last decade have led to major developments in the uses of plant lectins in bioscience and biomedicine. Major advances have been made in our understanding how lectins in the diet can act on the gastrointestinal tract and the physiological consequences of their actions, and how they can modulate body- and organ metabolism, the immune system and the gut microflora. Particularly striking progress has been made in unravelling the effects, often beneficial, of both orally- and parenterally administered lectins, including lectins of Viscum album-, Phaseolus vulgaris-, Robinia pseudoacacia, Agaricus bisporus, etc on tumours and in cancer therapy. Results have also made it possible to devise and try out other beneficial applications of plant lectins as gut-, metabolic- and hormonal regulators, immune reagents, probiotic/prebiotic oral supplements and to develop methods based on the oral application of lectins to protect the intestines against the often lethally harmful effects of chemo- and radiotherapy. With the development of genetically modified (GM) plants by transferring the genes of some of the natural insecticidal lectins such as the various Bacillus thuringiensis lectin-Cry toxins or some insecticidal plant lectins to major crop plants, a possible new avenue in plant protection may have opened up.
Quantitative Colocalization Analysis of Multicolor Confocal Immunofluorescence Microscopy Images: Pushing Pixels to Explore Biological Phenomena (2007)

Quantitative colocalization analysis is an advanced digital imaging tool to examine antigens of interest in immunofluorescence images obtained using confocal microscopes. It employs specialized algorithms to estimate the degree of overlap of fluorescence signals and thus enables acquiring important new information not otherwise obtainable using qualitative approaches alone. As raw confocal images have high levels of background, they should be prepared to become suitable for reliable calculation of colocalization coefficients by correcting it. We provide concise theoretical basis of quantitative colocalization analysis, discuss its limitations, and describe proper use of the technique. The use of quantitative colocalization analysis is demonstrated by studying bile salt export pump and multidrug resistance associated protein 2 in the liver and major basic protein and platelet activating factor receptor antigens in conjunctiva. The review is focused on the applicability and correct interpretation of the results of colocalization coefficients calculations.
Civil GPS from a future perspective (1983)

After a review of the present GPS program status and its announced schedule, a change of perspective to the future is attempted. Well before the year 2000, widespread civil use is predicted, spurred by the availability of simple and reliable $500 equipment for applications including hiking and automobile driving. The purpose is to focus on today's system issues of L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> access, user charge policy, differential GPS standards, global mapping standards, and how to obtain a fair return on the American GPS investment, from the future perspective. The challenge is clear; the questions are: "Who is concerned?" and "Where does the civil planning responsibility lie?"
Oligothiophene Derivatives Functionalized with a Diketopyrrolopyrrolo Core for Solution-Processed Field Effect Transistors: Effect of Alkyl Substituents and Thermal Annealing (2008)

Two new oligothiophene derivatives bearing a diketopyrrolopyrrole core, 2,5-di-n-hexyl-3,6-bis(5′′-n-hexyl[2,2′;5′,2′′]terthiophen-5-yl)pyrrolo[3,4-c]pyrrole-1,4-dione (DHT6DPPC6) and 2,5-di-n-dodecyl-3,6-bis(5′′-n-hexyl[2,2′;5′,2′′]terthiophen-5-yl)pyrrolo[3,4-c]pyrrole-1,4-dione (DHT6DPPC12), and their use in solution-processed organic field effect transistors are reported. Depending on the type of alkyl substituent and film annealing temperature, the crystal grain sizes and interlayer spacing vary as observed using atomic force microscopy and X-ray diffractometry, respectively. These changes in film morphology and interlayer spacing lead to an order of magnitude difference in the field effect mobilities. The field effect mobilities for annealed DHT6DPPC6 and DHT6DPPC12 films are 0.02 and 0.01 cm2/V s, respectively.
The effects of seaweed extract inclusion on gut morphology, selected intestinal microbiota, nutrient digestibility, volatile fatty acid concentrations and the immune status of the weaned pig (2008)

An experiment (complete randomised design) was conducted to investigate the effects of Laminaria hyperborea and Laminaria digitata seaweed extract inclusion on gut morphology, selected intestinal microbiota populations, volatile fatty acid concentrations and the immune status of the weaned pig. Twenty-eight piglets (24 days of age, 6.5 ± 1.4 kg live weight) were assigned to one of four dietary treatments for 7 days and then sacrificed: (T1) basal diet (control); (T2) basal diet and 1.5 g/kg L. hyperborea seaweed extract; (T3) basal diet and 1.5 g/kg L. digitata seaweed extract; and (T4) basal diet and 1.5 g/kg of a combination of L. hyperborea and L. digitata seaweed extract. The seaweed extract contained both laminarin and fucoidan. Digesta samples were taken from the caecum and colon to measure the enterobacteria, bifidobacteria and lactobacilli populations and for volatile fatty acid analysis. Tissue samples were taken from the duodenum, jejunum and ileum for morphological examination. Blood samples were taken to determine the cytokine gene expression profile and to measure the phagocytotic capacity of the blood. Pigs offered diets containing L. hyperborea seaweed extract had less bifidobacteria in the colon (P < 0.05) and lactobacilli in the caecum (P < 0.05) and colon (P < 0.001). The inclusion of L. digitata seaweed extract resulted in lower populations of enterobacteria in the caecum and colon (P < 0.01), bifidobacteria in the caecum (P < 0.05), and lactobacilli in the caecum (P < 0.05) and colon (P < 0.001). Pigs offered the combination of L. hyperborea and L. digitata seaweed extracts had less enterobacteria (P < 0.05) and lactobacilli (P < 0.01) in the caecum and colon. Pigs offered the L. digitata-supplemented diet had a reduced villous height in the duodenum and jejunum (P < 0.05). The inclusion of the L. digitata seaweed extract increased the molar proportion of butyric acid in the colon (P < 0.05). There was a significant reduction in the ammonia concentration in the colon with the inclusion of L. hyperborea (P < 0.01) and L. digitata (P < 0.05) seaweed extracts. An increase in the expression of the Interleukin-8 mRNA was observed on day 6 with the supplementation of the combination of L. hyperborea and L. digitata seaweed extract (P < 0.05). The inclusion of L. hyperborea seaweed extract resulted in an increase in total monocyte number (P < 0.05). In conclusion, the supplementation of L. hyperborea and L. digitata seaweed extract alone and in combination reduced the enterobacteria, bifidobacteria and lactobacilli populations in the caecum and colon, while only marginal effects on the immune response was observed.
Optimization of V/sub DD/ and V/sub TH/ for low-power and high-speed applications (2002)

Closed-form formulas are presented for optimum supply voltage (V/sub DD/) and threshold voltage (V/sub TH/) that minimize power dissipation when technology parameters and required speed are given. The formulas take into account short-channel effects and the variation of V/sub TH/ and temperature. Using typical device parameters, it is shown that a simple guideline to optimize the power consumption is to set the ratio of maximum leakage power to total power about 30%. Extending the analysis, the future VLSI design trend is discussed. The optimum V/sub DD/ coincides with the SIA roadmap and the optimum V/sub TH/ for logic blocks at the highest temperature and at the lowest process variation corner is in the range of 0 V-0.1 V over generations.
Machine learning a probabilistic perspective (2012)

Today's Web-enabled deluge of electronic data calls for automated methods of data analysis. Machine learning provides these, developing methods that can automatically detect patterns in data and then use the uncovered patterns to predict future data. This textbook offers a comprehensive and self-contained introduction to the field of machine learning, based on a unified, probabilistic approach. The coverage combines breadth and depth, offering necessary background material on such topics as probability, optimization, and linear algebra as well as discussion of recent developments in the field, including conditional random fields, L1 regularization, and deep learning. The book is written in an informal, accessible style, complete with pseudo-code for the most important algorithms. All topics are copiously illustrated with color images and worked examples drawn from such application domains as biology, text processing, computer vision, and robotics. Rather than providing a cookbook of different heuristic methods, the book stresses a principled model-based approach, often using the language of graphical models to specify models in a concise and intuitive way. Almost all the models described have been implemented in a MATLAB software package--PMTK (probabilistic modeling toolkit)--that is freely available online. The book is suitable for upper-level undergraduates with an introductory-level college math background and beginning graduate students.
Extracellular Signal-Regulated Kinase Induces the Megakaryocyte GPIIb/CD41 Gene through MafB/Kreisler (2004)

Extracellular signal-regulated kinase (ERK) facilitates cell cycle progression in most mammalian cells, but in certain cell types prolonged signaling through this pathway promotes differentiation and lineage-specific gene expression through mechanisms that are poorly understood. Here, we characterize the transcriptional regulation of platelet GPIIb integrin (CD41) by ERK during megakaryocyte differentiation. ERK-dependent transactivation involves the proximal promoter of GPIIb within 114 bp upstream of the transcriptional start site. GATA, Ets, and Sp1 consensus sequences within this region are each necessary and function combinatorially in ERK-activated transcription. MafB/Kreisler is induced in response to ERK and synergizes with GATA and Ets to enhance transcription from the proximal promoter. The requirement for MafB in promoter regulation is demonstrated by inhibition of transactivation following dominant-negative or antisense suppression of MafB function. Thus, ERK promotes megakaryocyte differentiation by coordinate regulation of nuclear factors that synergize in GPIIb promoter regulation. These results establish a novel role for MafB as a regulator of ERK-induced gene expression.
Insight into the Structure of Amyloid Fibrils from the Analysis of Globular Proteins (2006)

The conversion from soluble states into cross-beta fibrillar aggregates is a property shared by many different proteins and peptides and was hence conjectured to be a generic feature of polypeptide chains. Increasing evidence is now accumulating that such fibrillar assemblies are generally characterized by a parallel in-register alignment of beta-strands contributed by distinct protein molecules. Here we assume a universal mechanism is responsible for beta-structure formation and deduce sequence-specific interaction energies between pairs of protein fragments from a statistical analysis of the native folds of globular proteins. The derived fragment-fragment interaction was implemented within a novel algorithm, prediction of amyloid structure aggregation (PASTA), to investigate the role of sequence heterogeneity in driving specific aggregation into ordered self-propagating cross-beta structures. The algorithm predicts that the parallel in-register arrangement of sequence portions that participate in the fibril cross-beta core is favoured in most cases. However, the antiparallel arrangement is correctly discriminated when present in fibrils formed by short peptides. The predictions of the most aggregation-prone portions of initially unfolded polypeptide chains are also in excellent agreement with available experimental observations. These results corroborate the recent hypothesis that the amyloid structure is stabilised by the same physicochemical determinants as those operating in folded proteins. They also suggest that side chain-side chain interaction across neighbouring beta-strands is a key determinant of amyloid fibril formation and of their self-propagating ability.
The application of lattice-reduction to the K-Best algorithm for near-optimal MIMO detection (2008)

An efficient lattice-reduction (LR) aided implementation of the K-best algorithm is proposed for the general infinite lattice detection problem, which is realized with about 80% less complexity than currently reported architectures. The saving in complexity is achieved by the introduction of an on-demand candidate generation scheme along with a distributed sorting scheme. The proposed scheme does not require any a priori knowledge of the candidate displacement as it expands the candidates using the Schnorr-Euchner method. It is scalable in terms of the number of transmit antennas and its complexity grows sub-linearly with the constellation order. The parallelism intrinsic to the algorithm makes it suitable for the pipelined VLSI implementation.
Programmed Death 1 Expression on HIV-Specific CD4+ T Cells Is Driven by Viral Replication and Associated with T Cell Dysfunction (2007)

Functional impairment of HIV-specific CD4(+) T cells during chronic HIV infection is closely linked to viral replication and thought to be due to T cell exhaustion. Programmed death 1 (PD-1) has been linked to T cell dysfunction in chronic viral infections, and blockade of the PD-1 pathway restores HIV-specific CD4(+) and CD8(+) T cell function in HIV infection. This study extends those findings by directly examining PD-1 expression on virus-specific CD4(+) T cells. To investigate the role of PD-1 in HIV-associated CD4(+) T cell dysfunction, we measured PD-1 expression on blood and lymph node T cells from HIV-infected subjects with chronic disease. PD-1 expression was significantly higher on IFN-gamma-producing HIV-specific CD4(+) T cells compared with total or CMV-specific CD4(+) T cells in untreated HIV-infected subjects (p = 0.0001 and p < 0.0001, respectively). PD-1 expression on HIV-specific CD4(+) T cells from subjects receiving antiretroviral therapy was significantly reduced (p = 0.007), and there was a direct correlation between PD-1 expression on HIV-specific CD4(+) T cells and plasma viral load (r = 0.71; p = 0.005). PD-1 expression was significantly higher on HIV-specific T cells in the lymph node, the main site of HIV replication, compared with those in the blood (p = 0.0078). Thus, PD-1 expression on HIV-specific CD4(+) T cells is driven by persistent HIV replication, providing a potential target for enhancing the functional capacity of HIV-specific CD4(+) T cells.
Algorithms for accelerated convergence of adaptive PCA (2000)

We derive and discuss new adaptive algorithms for principal component analysis (PCA) that are shown to converge faster than the traditional PCA algorithms due to Oja, Sanger, and Xu. It is well known that traditional PCA algorithms that are derived by using gradient descent on an objective function are slow to converge. Furthermore, the convergence of these algorithms depends on appropriate choices of the gain sequences. Since online applications demand faster convergence and an automatic selection of gains, we present new adaptive algorithms to solve these problems. We first present an unconstrained objective function, which can be minimized to obtain the principal components. We derive adaptive algorithms from this objective function by using: 1) gradient descent; 2) steepest descent; 3) conjugate direction; and 4) Newton-Raphson methods. Although gradient descent produces Xu's LMSER algorithm, the steepest descent, conjugate direction, and Newton-Raphson methods produce new adaptive algorithms for PCA. We also provide a discussion on the landscape of the objective function, and present a global convergence proof of the adaptive gradient descent PCA algorithm using stochastic approximation theory. Extensive experiments with stationary and nonstationary multidimensional Gaussian sequences show faster convergence of the new algorithms over the traditional gradient descent methods.We also compare the steepest descent adaptive algorithm with state-of-the-art methods on stationary and nonstationary sequences.
PREMENSTRUAL SYNDROMES (1997)

The recent inclusion of research criteria for premenstrual dysphoric disorder in the fourth edition of the Diagnostic and Statistical Manual of Mental Disorders should help physicians recognize women with symptoms of irritability, tension, dysphoria, and lability of mood that seriously interfere with their lifestyle. Premenstrual dysphoric disorder can be differentiated from premenstrual syndrome, which is primarily reserved for milder physical symptoms and minor mood changes. The use of criteria from the Diagnostic and Statistical Manual in conjunction with prospective daily charting for at least two menstrual cycles is now accepted as common practice in confirming the diagnosis. Treatment options range from the conservative (lifestyle and stress management) to treatment with psychotropic medications and hormonal or surgical interventions to eliminate ovulation for the more extreme cases. Results from several randomized, placebo-controlled trials have clearly demonstrated that selective serotonin reuptake inhibitors, as well as medical or surgical oophorectomy, are effective in treating premenstrual dysphoric disorder. Taken together, these data indicate that treatment may be accomplished by either eliminating the hormonal trigger or by reversing the sensitivity of the serotonergic system.