gebhart/patrepeval huggingface dataset:
Unsupervised texture segmentation in a deterministic annealing framework (1998)

We present a novel optimization framework for unsupervised texture segmentation that relies on statistical tests as a measure of homogeneity. Texture segmentation is formulated as a data clustering problem based on sparse proximity data. Dissimilarities of pairs of textured regions are computed from a multiscale Gabor filter image representation. We discuss and compare a class of clustering objective functions which is systematically derived from invariance principles. As a general optimization framework, we propose deterministic annealing based on a mean-field approximation. The canonical way to derive clustering algorithms within this framework as well as an efficient implementation of mean-field annealing and the closely related Gibbs sampler are presented. We apply both annealing variants to Brodatz-like microtexture mixtures and real-word images.
창작, 토론, 비평을 활용한 에어로빅 가르치기: 반성적 수업모형(the ORDER approach)을 적용한 대학 교양 수업 사례연구 (2013)

대학 교양체육수업은 각 분야의 예비전문인으로서 대학생들이 신체적, 인지적, 정의적 측면의 기본적인 소양을 함양할 수 있도록 구성되어야 한다(최의창, 2010). 본 연구는 단순한 기능중심 교양체육수업을 지양하고신체활동에 대한 폭넓은 이해와 실천, 무용소양의 함양을 위해 Lavender(1996)의 반성적 수업모형(the ORDER approach)을 적용한 대학 교양 에어로빅 수업의 사례를 소개한다. 매 학기 반성적 수업모형을 적용한 수업의 구성 및 운영, 학생 관찰 및 면담, 수정 및 보완 단계를 거듭하여 기능연습 및 분석, 창작, 비평 활동이 통합된 에어로빅 수업을 개발하였다. 2011년 3월부터 2011년 12월까지 총 5개의 에어로빅 수업에서 점진적으로 반성적 수업모형을 적용하였다. 매 수업의 주요 장면을 사진, 동영상으로 촬영하여 관찰하고, 이상적 사례 선택(Goets & LeCompte, 1984)으로 선정한 총 10명의 학생들을 면담하였다. 반성적 에어로빅 수업을 운영한 결과, 학생들이 인식한 에어로빅 수업의 변화는 다섯 가지로 나타났다. 첫째, “기능 숙달 및 체력증진 중심”에서 “움직임 이해 및 실천 중심”으로의 목표 변화이다. 둘째, “동작 배열 및 연습 중심”에서 “동작구성 및 창작 중심”으로의 내용 변화이다. 셋째, “지시 및 연습형”에서 “토론 및 반성형”으로의 방법 변화이다. 넷째, “주1회 맛보기”에서 “한 학기 습관화”로의 참여 변화이다. 다섯째, “졸업 필수 1학점”에서 “생활 필수 1종목”으로의 인식 변화이다. 또한 학생들이 발견한 에어로빅의 교육적 가치는 운동적 가치, 심미적 가치, 조화로운 삶의 가치로 나타났다. 이를 바탕으로 학생들의 적극적인 참여와 움직임 및 창작활동을 장려할 수 있는 다양한 형태의 수업 개발과 교양체육 교수자의 반성적 성찰 및 실천적 지식의 함양을 제안한다.
A CRISPR-based approach for targeted DNA demethylation (2016)

In mammalian cells, DNA methylation critically regulates gene expression and thus has pivotal roles in myriad of physiological and pathological processes. Here we report a novel method for targeted DNA demethylation using the widely used clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system. Initially, modified single guide RNAs (sgRNAs) (sgRNA2.0) were constructed by inserting two copies of bacteriophage MS2 RNA elements into the conventional sgRNAs, which would facilitate the tethering of the Tet1 catalytic domain (Tet-CD), in fusion with dCas9 or MS2 coat proteins, to the targeted gene loci. Subsequently, such system was shown to significantly upregulate transcription of the target genes, including RANKL, MAGEB2 or MMP2, which was in close correlation to DNA demethylation of their neighboring CpGs in the promoters. In addition, the dCas9/sgRNA2.0-directed demethylation system appeared to afford efficient demethylation of the target genes with tenuous off-target effects. Applications of this system would not only help us understand mechanistically how DNA methylation might regulate gene expression in specific contexts, but also enable control of gene expression and functionality with potential clinical benefits.
BCL-2 FAMILY: Regulators of Cell Death (1998)

An expanding family of BCL-2 related proteins share homology, clustered within four conserved regions, namely BCL-2 homology (BH1-4) domains, which control the ability of these proteins to dimerize and function as regulators of apoptosis. Moreover, BCL-XL, BCL-2, and BAX can form ion-conductive pores in artificial membranes. The BCL-2 family, comprised of both pro-apoptotic and anti-apoptotic members, acts as a checkpoint upstream of CASPASES and mitochondrial dysfunction. BID and BAD possess the minimal death domain BH3, and the phosphorylation of BAD connects proximal survival signals to the BCL-2 family. BCL-2 and BCL-XL display a reciprocal pattern of expression during lymphocyte development. Gain- and loss-of-function models revealed stage-specific roles for BCL-2 and BCL-XL. BCL-2 can rescue maturation at several points of lymphocyte development. The BCL-2 family also reveals evidence for a cell-autonomous coordination between the opposing pathways of proliferation and cell death.
Rapid emergence of novel antigenic and genetic variants of equine infectious anemia virus during persistent infection (1986)

Previous results from our laboratory have demonstrated that equine infectious anemia virus displays structural variations in its surface glycoproteins and RNA genome during passage and chronic infections in experimentally infected Shetland ponies (Montelaro et al., J. Biol. Chem. 259:10539-10544, 1984; Payne et al., J. Gen. Virol. 65:1395-1399, 1984). The present study was undertaken to obtain an antigenic and biochemical characterization of equine infectious anemia virus isolates recovered from an experimentally infected pony during sequential disease episodes, each separated by intervals of only 4 to 8 weeks. The virus isolates could be distinguished antigenically by neutralization assays with serum from the infected pony and by Western blot analysis with a monoclonal antibody against the major surface glycoprotein gp90, thus demonstrating that novel antigenic variants of equine infectious anemia virus predominate during each clinical episode. The respective virion glycoproteins displayed different electrophoretic mobilities on sodium dodecyl sulfate-polyacrylamide gels, indicating structural variation. Tryptic peptide and glycopeptide maps of the viral proteins of each virus isolate revealed biochemical alterations involving amino acid sequence and glycosylation patterns in the virion surface glycoproteins gp90 and gp45. In contrast, no structural variation was observed in the internal viral proteins pp15, p26, and p9 from any of the four virus isolates. Oligonucleotide mapping experiments revealed similar but unique RNase T1-resistant oligonucleotide fingerprints of the RNA genomes of each of the virus isolates. Localization of altered oligonucleotides for one virus isolate placed two of three unique oligonucleotides within the predicted env gene region of the genome, perhaps correlating with the structural variation observed in the envelope glycoproteins. Thus these results support the concept that equine infectious anemia virus is indeed capable of relatively rapid genomic variations during replication, some of which result in altered glycoprotein structures and antigenic variants which are responsible for the unique periodic disease nature observed in persistently infected animals. The findings of envelope specific differences in isolates of visna virus and of human T-cell lymphotropic virus III (acquired immune deficiency syndrome-related virus) suggest that this variation may be a common characteristic of the subfamily Lentivirinae.
Rbm15-Mkl1 Interacts with the Setd1b Histone H3-Lys4 Methyltransferase via a SPOC Domain That Is Required for Cytokine-Independent Proliferation (2012)

The Rbm15-Mkl1 fusion protein is associated with acute megakaryoblastic leukemia (AMKL), although little is known regarding the molecular mechanism(s) whereby this fusion protein contributes to leukemogenesis. Here, we show that both Rbm15 and the leukemogenic Rbm15-Mkl1 fusion protein interact with the Setd1b histone H3-Lys4 methyltransferase (also known as KMT2G). This interaction is direct and requires the Rbm15 SPOC domain and the Setd1b LSD motif. Over-expression of Rbm15-Mkl1 in the 6133 megakaryoblastic leukemia cell line, previously established by expression of the Rbm15-Mkl1 fusion protein in mice (Mercher et al., [2009] J. Clin. Invest. 119, 852-864), leads to decreased levels of endogenous Rbm15 and increased levels of endogenous Mkl1. These cells exhibit enhanced proliferation and cytokine-independent cell growth, which requires an intact Rbm15 SPOC domain that mediates interaction between the Rbm15-Mkl1 fusion protein and the Setd1b methyltransferase. These results reveal altered Setd1b complex function and consequent altered epigenetic regulation as a possible molecular mechanism that mediates the leukemogenic activity of the Rbm15-Mkl1 fusion protein in AMKL.
Sphingosine 1-Phosphate Receptor Signaling (2009)

The sphingosine 1-phosphate (S1P) receptor signaling system is a productive model system. A hydrophobic zwitterionic lysophospholipid ligand with difficult physical properties interacts with five high-affinity G protein-coupled receptors to generate multiple downstream signals. These signals modulate homeostasis and pathology on a steep agonist concentration-response curve. Ligand presence is essential for vascular development and endothelial integrity, while acute increases in ligand concentrations result in cardiac death. Understanding this integrated biochemical system has exemplified the impact of both genetics and chemistry. Developing specific tools with defined biochemical properties for the reversible modulation of signals in real time has been essential to complement insights gained from genetic approaches that may be irreversible and compensated. Despite its knife-edge between life and death, this system, based in part on receptor subtype-selectivity and in part on differential attenuation of deleterious signals, now appears to be on the cusp of meaningful therapy for multiple sclerosis.
On the mechanism of energy transduction in myosin subfragment 1. (1984)

It is proposed that the myosin subfragment 1 moiety of the muscle contractile apparatus is a self-contained "engine" whose operational plan is based on the interactive nature of ATP (or degradation intermediate) binding and actin binding, made possible by an intersite communication system. It is suggested that the spatial information required for examining this engine can, at least provisionally, be derived from fluorescence resonance energy transfer measurements interpreted by the Förster equation and that the existence of an intersite communication system can be deduced from piece-wise detection of interacting pairs of points.
Expanding the Genetic Code of Escherichia coli (2001)

A unique transfer RNA (tRNA)/aminoacyl-tRNA synthetase pair has been generated that expands the number of genetically encoded amino acids in Escherichia coli. When introduced into E. coli, this pair leads to the in vivo incorporation of the synthetic amino acid O-methyl-l-tyrosine into protein in response to an amber nonsense codon. The fidelity of translation is greater than 99%, as determined by analysis of dihydrofolate reductase containing the unnatural amino acid. This approach should provide a general method for increasing the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the common 20 amino acids.
Antibody expression in protease-deficient strains of the methylotrophic yeastOgataea minuta (2007)

When human antibody genes were expressed in the methylotrophic yeast Ogataea minuta, the secreted antibody became partially degraded. To suppress the degradation, a vacuolar protease-deficient strain was constructed and its antibody production was evaluated. Although antibody productivity was improved in the vacuolar protease-deficient strain, the secreted antibody still became partially degraded. Peptide sequencing revealed that the cleavage occurred in the CH1 region of the heavy chain, implying that the cleavage was caused by an aspartic protease, Yps1p. To inhibit this cleavage, Yps1p-deficient strains were constructed and their antibody production was evaluated. As a result, the partial degradation of the antibody was suppressed in the O. minuta multiple-protease-deficient strains.
Stabbing and ray shooting in 3 dimensional space (1990)

In this paper we consider the following problems: given a set T of triangles in 3-space, with |T| = n,
Genetic control of responses to bacterial lipopolysaccharides in mice. II. A gene that influences a membrane component involved in the activation of bone marrow-derived lymphocytes by lipipolysaccharides. (1975)

C3H/HeJ mice contain a defect in a single autosomal locus which is not linked to the H-2 histocompatibility or the heavy chain allotype loci that restrict immune, mitogenic, and polyclonal responses to bacterial lipopolysaccharides (LPS). Adult thymectomized C3H/HeJ mice that have been irradiated and reconstituted with C3HeB/FeJ bone marrow cells respond well to LPS. Cell-mixing experiments using C3H/HEJ-C3HeB/FeJ spleen cultures show that the failure of C3H/HeJ spleen cells to support responses to LPS is not due to nonspecific or LPS-induced suppressive events, or the lack of accessory cell types. C3H/HeJ and C3HeB/FeJ spleen cells bind LPS and respond to other B cell mitogens equally well. We suggest that the B lymphocytes of C3H/HeJ mice have a defect in a membrane component that is activated via interaction with LPS, and initiates the intracellular events that lead to cell proliferation.
On the algorithmic implementation of multiclass kernel-based vector machines (2002)

In this paper we describe the algorithmic implementation of multiclass kernel-based vector machines. Our starting point is a generalized notion of the margin to multiclass problems. Using this notion we cast multiclass categorization problems as a constrained optimization problem with a quadratic objective function. Unlike most of previous approaches which typically decompose a multiclass problem into multiple independent binary classification tasks, our notion of margin yields a direct method for training multiclass predictors. By using the dual of the optimization problem we are able to incorporate kernels with a compact set of constraints and decompose the dual problem into multiple optimization problems of reduced size. We describe an efficient fixed-point algorithm for solving the reduced optimization problems and prove its convergence. We then discuss technical details that yield significant running time improvements for large datasets. Finally, we describe various experiments with our approach comparing it to previously studied kernel-based methods. Our experiments indicate that for multiclass problems we attain state-of-the-art accuracy.
Contextual advertising by combining relevance with click feedback (2008)

Contextual advertising supports much of the Web's ecosystem today. User experience and revenue (shared by the site publisher and the ad network) depend on the relevance of the displayed ads to the page content. As with other document retrieval systems, relevance is provided by scoring the match between individual ads (documents) and the content of the page where the ads are shown (query). In this paper we show how this match can be improved significantly by augmenting the ad-page scoring function with extra parameters from a logistic regression model on the words in the pages and ads. A key property of the proposed model is that it can be mapped to standard cosine similarity matching and is suitable for efficient and scalable implementation over inverted indexes. The model parameter values are learnt from logs containing ad impressions and clicks, with shrinkage estimators being used to combat sparsity. To scale our computations to train on an extremely large training corpus consisting of several gigabytes of data, we parallelize our fitting algorithm in a Hadoop framework [10]. Experimental evaluation is provided showing improved click prediction over a holdout set of impression and click events from a large scale real-world ad placement engine. Our best model achieves a 25% lift in precision relative to a traditional information retrieval model which is based on cosine similarity, for recalling 10% of the clicks in our test data.
Explaining nonlinear classification decisions with deep Taylor decomposition (2016)

Nonlinear methods such as Deep Neural Networks (DNNs) are the gold standard for various challenging machine learning problems, e.g., image classification, natural language processing or human action recognition. Although these methods perform impressively well, they have a significant disadvantage, the lack of transparency, limiting the interpretability of the solution and thus the scope of application in practice. Especially DNNs act as black boxes due to their multilayer nonlinear structure. In this paper we introduce a novel methodology for interpreting generic multilayer neural networks by decomposing the network classification decision into contributions of its input elements. Although our focus is on image classification, the method is applicable to a broad set of input data, learning tasks and network architectures. Our method is based on deep Taylor decomposition and efficiently utilizes the structure of the network by backpropagating the explanations from the output to the input layer. We evaluate the proposed method empirically on the MNIST and ILSVRC data sets.
Sensor Networks for Agent Based Distributed Energy Resources (2005)

We are developing agents for the control of distributed energy resources (DERS) in the electricity network. These resources consist of both generators and loads, physically located close to load centres. Although traditionally DERs have operated independently, we have been able to demonstrate an architecture whereby DERs collaborate to present an aggregated response. This aggregated response can be used to support the network at times of peak demand, increasing efficiency and robustness. In this paper, we focus on one such DER agent, which provides control of a commercial cool room. This agent utilizes a wireless sensor network to collect information on various products in the cool room, allowing the control system to respond based on aggregated conditions across the sensor network. Through development of new software and protocols, the sensor network is able to exist on the same control channel as traditional control hardware and provide extra reliability and fault tolerance.
Quantitative Microwave Imaging for Breast Cancer Detection Using a Planar 2.45 GHz System (2010)

Microwave imaging is recognized as a potential candidate for biomedical applications, such as breast tumor detection. In this context, the capability of a planar microwave camera to produce quantitative imaging of high-contrast inhomogeneous objects is investigated. The image reconstruction is achieved by means of an iterative Newton-Kantorovich algorithm. Promising numerical simulation results indicate that the planar geometry is suitable for quantitative imaging, as long as the signal-to-noise ratio is higher than 40 dB. Such a requirement is satisfied with the camera due to appropriate data averaging. Furthermore, different calibration techniques are discussed, aiming to reduce the model error, which results from the limitations of the numerical model involved in the reconstruction to accurately reproduce the experimental setup. The experimental work also includes the development of a phantom using a new fluid tissue equivalent mixture based on Triton X-100. As a final result, this paper shows the first reconstructed quantitative images of a high-contrast inhomogeneous 2-D object obtained by using experimental data from the camera.
Distinct, Cross-Reactive Epitope Specificities of CD8 T Cell Responses Are Induced by Natural Hepatitis B Surface Antigen Variants of Different Hepatitis B Virus Genotypes (2006)

We investigated the specific and cross-reactive CD8 T cell immunity to three natural variants (of different geno/serotype) of the small hepatitis B surface Ag (or S protein). The D(d)-binding variants of the S(201-209) epitope showed different immunogenicity. The loss of the consensus C-terminal (P9) anchor abrogated its immunogenicity. In contrast, a conservative (serine vs asparagine) exchange at P7 primed cross-reactive CD8 T cells that preferentially recognized the priming variant. Cross-reactive CD8 T cell responses to a variant could be primed in mice tolerant to an alternative variant of the D(d)-binding S(201-209) peptide. Loss of the C-terminal (P10) anchor in S(185-194) eliminated its immunogenicity in HLA-A*0201(A2)-transgenic mice but two conservative exchanges (leucine vs valine in P2, and leucine vs isoleucine in P6) in S(208-216) generated cross-reactive CD8 T cell responses with strong preference for the priming variant. Similar cross-reactive recognition of variant envelope epitopes were also found in S(208-216)-specific CD8 T cells from hepatitis B virus (HBV)-infected patients. Distinct CD8 T cell populations cross-reactive to natural variants of class I-restricted HBV epitopes can be primed by vaccination (of mice) or natural infection (of humans), and they may play a role in the "spontaneous remission" or the specific immunotherapy of chronic HBV infection.
Mechanical characterization of bulk Sylgard 184 for microfluidics and microengineering (2014)

Polydimethylsiloxane (PDMS) elastomers are extensively used for soft lithographic replication of microstructures in microfluidic and micro-engineering applications. Elastomeric microstructures are commonly required to fulfil an explicit mechanical role and accordingly their mechanical properties can critically affect device performance. The mechanical properties of elastomers are known to vary with both curing and operational temperatures. However, even for the elastomer most commonly employed in microfluidic applications, Sylgard 184, only a very limited range of data exists regarding the variation in mechanical properties of bulk PDMS with curing temperature. We report an investigation of the variation in the mechanical properties of bulk Sylgard 184 with curing temperature, over the range 25 C to 200 C. PDMS samples for tensile and compressive testing were fabricated according to ASTM standards. Data obtained indicates variation in mechanical properties due to curing temperature for Young's modulus of 1.32-2.97 MPa, ultimate tensile strength of 3.51-7.65 MPa, compressive modulus of 117.8-186.9 MPa and ultimate compressive strength of 28.4-51.7 GPa in a range up to 40% strain and hardness of 44-54 Sh A .
Expanding the Range of Substrate Acceptance of Enzymes: Combinatorial Active‐Site Saturation Test (2005)

CASTing for success: The traditional problem of expanding the range of substrate acceptance of enzymes can be solved by creating focused libraries of mutants resulting from randomization of pairs of properly chosen amino acids around the active site (see example with the lipase from Pseudomonas aeruginosa, amino acid pairs are shown in the same color). CAST=combinatorial active-site saturation test.
Part 2 Revised nomenclature for serum amyloid A(SAA) (1999)

(1999). Part 2 Revised nomenclature for serum amyloid A(SAA) Amyloid: Vol. 6, No. 1, pp. 67-70.