gebhart/patrepeval huggingface dataset:
Expression of mucin genes and carbohydrate epitopes in 19 human colon carcinoma cell lines. (1998)

The levels of mRNA corresponding to the MUC1, MUC2, MUC5AC, MUC5B, and MUC6 genes were determined in 19 human colon adenocarcinoma cell lines by the reverse transcriptase-polymerase chain reaction method using specific primers in an attempt to correlate to the levels of cell surface carbohydrate epitopes. All 19 cell lines expressed MUC1 and MUC5B mRNA, whereas MUC2, MUC5AC, or MUC6 mRNA were only detected in 8, 3, or 2 of 19 cell lines, respectively. Sialyl Lewis a carbohydrates, identified by the monoclonal antibody (mAb) CA19-9, and sialyl Lewis X carbohydrates. identified by mAb KM93, were observed, with most of the cell lines expressing multiple mucin core polypeptide genes but with few cell lines expressing only MUC1 and MUC5B. Sialyl Tn epitopes identified by mAb B195.3R11 and by mAb TKH-2 were strongly expressed on both of two MUC6-positive cells, whereas only a small portion of MUC6-negative cells expressed these epitopes. Strict correlation between mucin gene expression and any carbohydrate epitopes examined was not observed.
Correction of Location and Orientation Errors in Electromagnetic Motion Tracking (2007)

We describe a method for calibrating an electromagnetic motion tracking device. Algorithms for correcting both location and orientation data are presented. In particular, we use a method for interpolating rotation corrections that has not previously been used in this context. This method, unlike previous methods, is rooted in the geometry of the space of rotations. This interpolation method is used in conjunction with Delaunay tetrahedralization to enable correction based on scattered data samples. We present measurements that support the assumption that neither location nor orientation errors are dependent on sensor orientation. We give results showing large improvements in both location and orientation errors. The methods are shown to impose a minimal computational burden.
Three-dimensional reciprocal space mapping of diffuse scattering for the study of stacking faults in semipolar (\bf 11{\overline 2}2) GaN layers grown from the sidewall of anr-patterned sapphire substrate (2013)

Three-dimensional reciprocal space mapping of semipolar (11{\overline 2}2) GaN grown on stripe-patterned r -plane (1{\overline 1}02) sapphire substrates is found to be a powerful and crucial method for the analysis of diffuse scattering originating from stacking faults that are diffracting in a noncoplanar geometry. Additionally, by measuring three-dimensional reciprocal space maps (3D-RSMs) of several reflections, the transmission electron microscopy visibility criteria could be confirmed. Furthermore, similar to cathodoluminescence, the 3D-RSM method could be used in future as a reliable tool to distinguish clearly between the diffuse scattering signals coming from prismatic and from basal plane stacking faults and from partial dislocations in semipolar (11{\overline 2}2) GaN. The fitting of the diffuse scattering intensity profile along the stacking fault streaks with a simulation based on the Monte Carlo approach has delivered an accurate determination of the basal plane stacking fault density. A reduction of the stacking fault density due to the intercalation of an SiN interlayer in the GaN layer deposited on the sidewall of the pre-patterned sapphire substrate has led to an improvement of the optoelectronic properties, influenced by the crystal quality, as has been demonstrated by a locally resolved cathodoluminescence investigation.
Reflectance spectroscopy of organic compounds: 1. Alkanes (2009)

Reflectance spectra of the organic compounds comprising the alkane series are presented from the ultraviolet to midinfrared, 0.35 to 15.5 μ m. Alkanes are hydrocarbon molecules containing only single carbon‐carbon bonds, and are found naturally on the Earth and in the atmospheres of the giant planets and Saturn's moon, Titan. This paper presents the spectral properties of the alkanes as the first in a series of papers to build a spectral database of organic compounds for use in remote sensing studies. Applications range from mapping the environment on the Earth, to the search for organic molecules and life in the solar system and throughout the universe. We show that the spectral reflectance properties of organic compounds are rich, with major diagnostic spectral features throughout the spectral range studied. Little to no spectral change was observed as a function of temperature and only small shifts and changes in the width of absorption bands were observed between liquids and solids, making remote detection of spectral properties throughout the solar system simpler. Some high molecular weight organic compounds contain single‐bonded carbon chains and have spectra similar to alkanes even when they fall into other families. Small spectral differences are often present allowing discrimination among some compounds, further illustrating the need to catalog spectral properties for accurate remote sensing identification with spectroscopy.
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine (2012)

Beneficial microbes and probiotics show promise for the treatment of pediatric gastrointestinal diseases. However, basic mechanisms of probiosis are not well understood, and most investigations have been performed in germ-free or microbiome-depleted animals. We sought to functionally characterize probiotic-host interactions in the context of normal early development. Outbred CD1 neonatal mice were orally gavaged with one of two strains of human-derived Lactobacillus reuteri or an equal volume of vehicle. Transcriptome analysis was performed on enterocyte RNA isolated by laser-capture microdissection. Enterocyte migration and proliferation were assessed by labeling cells with 5-bromo-2'-deoxyuridine, and fecal microbial community composition was determined by 16S metagenomic sequencing. Probiotic ingestion altered gene expression in multiple canonical pathways involving cell motility. L. reuteri strain DSM 17938 dramatically increased enterocyte migration (3-fold), proliferation (34%), and crypt height (29%) compared to vehicle-treated mice, whereas strain ATCC PTA 6475 increased cell migration (2-fold) without affecting crypt proliferative activity. In addition, both probiotic strains increased the phylogenetic diversity and evenness between taxa of the fecal microbiome 24 h after a single probiotic gavage. These experiments identify two targets of probiosis in early development, the intestinal epithelium and the gut microbiome, and suggest novel mechanisms for probiotic strain-specific effects.
Numerical Methods for Inferring Evolutionary Trees (1982)

Despite a century of evolutionary theory, only in the last few decades have clearly defined procedures for inferring phylogenies been stated. For discrete characters whose ancestral states are known, the prescriptions of Henning are well defined, but they are applicable only when there is no incompatibility between different characters. This limitation has led to the elaboration of a number of methods for dealing with such incompatibilities. One category consists of the parsimony methods, which choose that phylogeny on which the fewest changes of character state need be assumed. Another category consists of the compatibility methods, which choose that phylogeny which is perfectly compatible with the largest number of characters, irrespective of how many changes need be assumed in other characters. Other approaches include the use of phenetic clustering algorithms and methods fitting trees to similarity or distance matrices. Each method has a different set of implicit assumptions concerning the biology of the characters and the information available from the data. If the methods are considered in a statistical framework as different estimators of an unknow quantity (the phylogeny), these asseumptions are more clearly seen. Standard statistical approaches, such as maximum likelihood, can be used to obtain methods whose properties are known and for which one can determine the amount of uncertainty in the resulting estimates of the phylogeny. Although existing statistical models are highly oversimplified and do not reflect the complexity of evolutionary processes, it is by viewing the problem as a statistical one that we can place all these methods in common fremework, within which their behavior and assumptions can be compared. It is essential that we not adopt a single methods as a universal panacea, but that an attempt be made to understand the biological assumptions and statistical behavior of each method.
Detecting and reading text in natural scenes (2004)

This paper gives an algorithm for detecting and reading text in natural images. The algorithm is intended for use by blind and visually impaired subjects walking through city scenes. We first obtain a dataset of city images taken by blind and normally sighted subjects. From this dataset, we manually label and extract the text regions. Next we perform statistical analysis of the text regions to determine which image features are reliable indicators of text and have low entropy (i.e. feature response is similar for all text images). We obtain weak classifiers by using joint probabilities for feature responses on and off text. These weak classifiers are used as input to an AdaBoost machine learning algorithm to train a strong classifier. In practice, we trained a cascade with 4 strong classifiers containing 79 features. An adaptive binarization and extension algorithm is applied to those regions selected by the cascade classifier. Commercial OCR software is used to read the text or reject it as a non-text region. The overall algorithm has a success rate of over 90% (evaluated by complete detection and reading of the text) on the test set and the unread text is typically small and distant from the viewer.
[Non-specific immunosuppression and multiple sclerosis]. (1998)

Several series of arguments favor at least partial efficacy of immunosuppression in multiple sclerosis. Immunosuppression can often treat experimental autoimmune encephalitis, and imperfect model of multiple sclerosis. Certain agents have been shown to affect the pathophysiological processes seen indirectly on magnetic resonance imaging (mitoxantrone and Campath, for example). Therapeutic trials have their methodological weaknesses but do allow certain conclusions. The progressive forms of multiple sclerosis are the most widely studied. Massive but short-term immunosuppression does not appear to affect the course of progression but prolonged immunosuppression would appear to slow down the process, at least in responders. The effect on disease progression is modest and preference should go to well-tolerated treatments. Immunosuppression appears to effectively decrease the number of acute episodes and reduce the number of new lesions detectable by magnetic resonance imaging. The effect of immunosuppression is limited however by the fact that the clinical course of progressive forms depends less on the development of new lesions than on an aggravation of the demyelinization process and possible axon loss within constituted lesions. This is a further argument favoring early immunosuppressive treatment at a stage when it can be most effective.
The Carboxy-Terminal Domain Is Essential for Stability and Not for Virion Incorporation of HIV-1 Vpr into Virus Particles (1995)

Vpr is one of the auxiliary gene products encoded by HIV-1 genome. Vpr is a 14-kDa protein and exhibits several interesting characteristics including incorporation into virus particles, oligomerization, localization in the nucleus, and positive regulation of virus replication in primary cells. In an effort to define the structure-function relationship of Vpr, the role of the C-terminus of Vpr was investigated. Site-specific mutagenesis involving deletion, insertion, and substitution of residues at the C-terminus was utilized to generate variants of Vpr. Mutations introduced at the C-terminus affected properties of Vpr in different ways: (i) Vpr containing amino acids 1-72 showed the virion incorporation phenotype, indicating that the C-terminus is not essential for this function, (ii) the C-terminus contributes to the stability of Vpr, and (iii) substitution mutagenesis involving the basic residues showed stability similar to that of wild type, indicating the lack of involvement of these residues in this biochemical property of Vpr. The data generated in this study and our early mutagenic analyses on Vpr suggest that domains noncontiguous in primary sequence contribute to the stability of Vpr through overall conformation of the protein.
Comparison of ethylene glycol, 1,2-propanediol and glycerol for cryopreservation of slow-cooled mouse zygotes, 4-cell embryos and blastocysts (2000)

The aim of the study was to analyse the toxicity, the osmolar and cryoprotective activity of ethylene glycol (ETG) in terms of survival rate (SR), cleavage rate (CR) and expanded blastocysts percentage (EBP) of mouse embryos. Early mouse embryos and blastocysts were slowly cooled with ETG, 1,2-propanediol (PROH) or glycerol, and thawed. The Van t'Hoff curve for 1.5 mol/l ETG showed recovery of initial volume within 4 min. No differences were observed in CR and EBP of ETG-exposed compared with non-exposed mouse zygotes. The SR of zygotes frozen with PROH was significantly better than with ETG (92% and 60% respectively; P < 0.01), and a significantly better EBP was achieved for blastocysts frozen with glycerol compared with ETG (75% and 50% respectively; P < 0.05). For 4-cell stage embryos, no differences were observed in SR and EBP between ETG and PROH. Higher EBP was observed for 4-cell stage embryos (53%) frozen with ETG compared with pronucleate stage (19%) and blastocysts (48%). Low toxicity, good SR and EBP were observed for mouse embryos frozen with ETG, the best results being obtained at the 4-cell stage. At other embryonic stages, PROH and glycerol respectively seemed to provide better results.
Exposure of the Dorsal Root Ganglion in Rats to Pulsed Radiofrequency Currents Activates Dorsal Horn Lamina I and II Neurons (2002)

Exposure of the dorsal ganglion to pulsed RF currents activates pain-processing neurons in the dorsal horn. This effect is not mediated by tissue heating.
Neighborhood denoising for learning high-dimensional grasping manifolds (2008)

Human control of high degree-of-freedom robotic systems, e.g. anthropomorphic robot hands, is often difficult due to the overwhelming number of variables that need to be specified. Previous work has addressed this sparse control problem by learning a high-dimensional manifold of robot poses to provide low-dimensional control subspaces. Such subspaces allow cursor control, or eventually decoding of neural activity, to drive a robotic hand. Considering previously identified problems related to noise in manifold learning, we introduce a method for denoising neighborhood graphs in order to embed hand motion into 2D spaces. We present results demonstrating our approach in the case of a synthetic swissroll as well as in the embeddings for interactive sparse control for several grasping tasks.
Metamodeling techniques for evolutionary optimization of computationally expensive problems: promises and limitations (1999)

It is often the case in many problems in science and engineering that the analysis codes used are computationally very expensive. This can pose a serious impediment to the successful application of evolutionary optimization techniques. Metamodeling techniques present an enabling methodology for reducing the computational cost of such optimization problems. We present here a general framework for coupling metamodeling techniques with evolutionary algorithms to reduce the computational burden of solving this class of optimization problems. This framework aims to balance the concerns of optimization with that of design of experiments. Experiments on test problems and a practical engineering design problem serve to illustrate our arguments. The practical limitations of this approach are also outlined. 1
Long-term expansion of human functional epidermal precursor cells: promotion of extensive amplification by low TGF-β1 concentrations (2003)

We have previously introduced the concept of high proliferative potential-quiescent (HPP-Q) cells to refer to primitive human hematopoietic progenitors, on which transforming growth factor-beta1 (TGF-beta1) exerts a pleiotropic effect. TGF-beta1 confers to these slow-dividing cells a mitogenic receptor(low) phenotype and maintains immature properties by preventing differentiation and apoptosis. However, the effect of TGF-beta1 on long-term expansion has not yet been clearly demonstrated. Here, we describe the characterization of a human skin keratinocyte subpopulation, highly enriched for primitive epidermal precursors, on the basis of high adhesion capacity (Adh+++) and low expression of the epidermal growth factor receptor (Adh+++EGF-Rlow). In our standard culture condition without feeder cells, the mean estimated output for cells from an unfractionated population of primary foreskin keratinocytes was 10(7)-10(8), increasing to 10(12)-10(13) in cultures initiated with selected Adh+++EGF-Rlow precursors. Characterization of these cells revealed a hitherto unknown property of TGF-beta1: its addition at a very low concentration (10 pg/ml) in long-term cultures induces a very significant additional increase of expansion. In this optimized system, outputs obtained in cultures initiated with Adh+++EGF-Rlow cells repeatedly reached 10(16)-10(17) ( approximately 60 population doublings, approximately 4 x 10(18) keratinocytes produced per clonogenic cell present in the initial population). At the molecular level, this effect is associated with an increase in Smad1, Smad2 and Smad3 phosphorylation and an increase in alpha6 and beta1 integrin expression. No such effect could be observed on mature keratinocytes with low adhesion capacity (Adh-/+). We finally demonstrated that the progeny of Adh+++EGF-Rlow precursors after long-term expansion is still capable of generating a pluristratified epidermis in a model for skin reconstruction. In conclusion, after further characterizing the phenotype of primitive epidermal precursors, we demonstrated a new function of TGF-beta1, which is to promote undifferentiated keratinocyte amplification.
A manifold lifting algorithm for multi-view compressive imaging (2009)

We consider a multi-view imaging scenario where a number of cameras observe overlapping, translated subimages of a larger scene. To simplify the acquisition and encoding of these images, we propose a non-collaborative compressive sensing protocol at each camera. We discuss a prototype algorithm for joint reconstruction of the images from the ensemble of random measurements, based on the geometric manifold structure that arises from the varying camera positions. Even when the camera positions are unknown, we demonstrate that it is possible to simultaneously resolve the images and register their positions using only the random measurements.
Cellular prion protein controls stem cell-like properties of human glioblastoma tumor-initiating cells (2016)

Prion protein (PrPC) is a cell surface glycoprotein whose misfolding is responsible for prion diseases. Although its physiological role is not completely defined, several lines of evidence propose that PrPC is involved in self-renewal, pluripotency gene expression, proliferation and differentiation of neural stem cells. Moreover, PrPC regulates different biological functions in human tumors, including glioblastoma (GBM). We analyzed the role of PrPC in GBM cell pathogenicity focusing on tumor-initiating cells (TICs, or cancer stem cells, CSCs), the subpopulation responsible for development, progression and recurrence of most malignancies. Analyzing four GBM CSC-enriched cultures, we show that PrPC expression is directly correlated with the proliferation rate of the cells. To better define its role in CSC biology, we knocked-down PrPC expression in two of these GBM-derived CSC cultures by specific lentiviral-delivered shRNAs. We provide evidence that CSC proliferation rate, spherogenesis and in vivo tumorigenicity are significantly inhibited in PrPC down-regulated cells. Moreover, PrPC down-regulation caused loss of expression of the stemness and self-renewal markers (NANOG, Sox2) and the activation of differentiation pathways (i.e. increased GFAP expression). Our results suggest that PrPC controls the stemness properties of human GBM CSCs and that its down-regulation induces the acquisition of a more differentiated and less oncogenic phenotype.
Learning to Generate Chairs with Generative Adversarial Nets (2018)

Generative adversarial networks (GANs) has gained tremendous popularity lately due to an ability to reinforce quality of its predictive model with generated objects and the quality of the generative model with and supervised feedback. GANs allow to synthesize images with a high degree of realism. However, the learning process of such models is a very complicated optimization problem and certain limitation for such models were found. It affects the choice of certain layers and nonlinearities when designing architectures. In particular, it does not allow to train convolutional GAN models with fully-connected hidden layers. In our work, we propose a modification of the previously described set of rules, as well as new approaches to designing architectures that will allow us to train more powerful GAN models. We show the effectiveness of our methods on the problem of synthesizing projections of 3D objects with the possibility of interpolation by class and view point.
Appearance of atypical 3α,6β,7β,12α-tetrahydroxy-5β-cholan-24-oic acid in spgp knockout mice (2003)

Bile formation and its canalicular secretion are essential functions of the mammalian liver. The sister-of-p-glycoprotein (spgp) gene was shown to encode the canalicular bile salt export protein, and mutations in spgp gene were identified as the cause of progressive familial intrahepatic cholestasis type 2. However, target inactivation of spgp gene in mice results in nonprogressive but persistent cholestasis and causes the secretion of unexpectedly large amounts of unknown tetrahydroxylated bile acid in the bile. The present study confirms the identity of this tetrahydroxylated bile acid as 3 alpha,6 beta,7 beta,12 alpha-tetrahydroxy-5 beta-cholan-24-oic acid. The data further show that in serum, liver, and urine of the spgp knockout mice, there is a significant increase in the concentration of total bile salts containing a large amount of tetrahydroxy-5 beta-cholan-24-oic acid. The increase in total bile acids was associated with up-regulation of the mRNA of cholesterol 7 alpha-hydroxylase in male mice only. It is suggested that the lower severity of the cholestasis in the spgp knockout mice may be due to the synthesis of 3 alpha,6 beta,7 beta,12 alpha-tetrahydroxy-5 beta-cholan-24-oic acid, which neutralizes in part the toxic effect of bile acids accumulated in the liver.