gebhart/patrepeval huggingface dataset:
The nucleotide sequences recognized by endonucleases AvaI and AvaII from Anabaena variabilis (1980)

Determination of the 5'-terminal sequences flanking all the individual cleavage sites for endonuclease AvaI in bacteriophage-lambda DNA has shown that this enzyme recognizes the hexanucleotide sequences: (Formula: see text), This sequence is cut as shown by the arrows to give single-stranded 5'-tetranucleotide protrusions (cohesive ends). Endonucleases SmaI, XhoI and XmaI recognize different symmetrical subsets of this sequence and provide independent evidence for the occurrence of these subsets at particular endonuclease-AvaI cleavage sites in the bacteriophage-lambda genome. Further evidence for this structure came from the demonstration that DNA fragments generated by endonuclease AvaI can be ligated to form a discrete set of larger molecules and from nearest-neighbor analysis which showed that cytosine residues occurred at the 3'-side of cleavage points. The observation that endonuclease AvaII recognized a subset of the sites recognized by AsuI [Hughes, Bruce & Murray (1979) Biochem. J. 185, 59-63[ led to the deduction that AvaII recognize the pentanucleotide sequence: (Formula: see text), and breaks internucleotide bonds at the positions indicated by the arrows.
Systems biology of the 2-cell mouse embryo (2004)

The transcriptome of the 2-cell mouse embryo was analyzed to provide insight into the molecular networks at play during nuclear reprogramming and embryonic genome activation. Analysis of ESTs from a 2-cell cDNA library identified nearly 4,000 genes, over half of which have not been previously studied. Transcripts of mobile elements, especially those of LTR retrotransposons, are abundantly represented in 2-cell embryos, suggesting their possible role in introducing genomic variation, and epigenetic restructuring of the embryonic genome. Analysis of Gene Ontology of the 2-cell-stage expressed genes outlines the major biological processes that guide the oocyte-to-embryo transition. These results provide a foundation for understanding molecular control at the onset of mammalian development.
PAPR reduction using integer structures in OFDM systems (2005)

The problem of reducing the peak-to-average power ratio (PAPR) in an orthogonal frequency division multiplexing (OFDM) system is considered. We design a cubic constellation, called the Hadamard constellation, whose boundary is along the bases defined by the Hadamard matrix in the transform domain. Then, we further reduce the PAPR by applying a selective mapping (SLM) technique. The encoding method, following the method introduced by H.K. Kwok (see "Shape Up: Peak-Power Reduction via Constellation Shaping", PhD Dissertation, University of Illinois, 2001), is derived from a decomposition, known as the Smith normal form (SNF), and has a minimal complexity. This new technique offers a PAPR that is significantly lower than that of the best known techniques without any loss in terms of energy and/or spectral efficiency and without any side information being transmitted. Moreover, it has a low computational complexity.
Microscale to manufacturing scale‐up of cell‐free cytokine production—a new approach for shortening protein production development timelines (2011)

Engineering robust protein production and purification of correctly folded biotherapeutic proteins in cell-based systems is often challenging due to the requirements for maintaining complex cellular networks for cell viability and the need to develop associated downstream processes that reproducibly yield biopharmaceutical products with high product quality. Here, we present an alternative Escherichia coli-based open cell-free synthesis (OCFS) system that is optimized for predictable high-yield protein synthesis and folding at any scale with straightforward downstream purification processes. We describe how the linear scalability of OCFS allows rapid process optimization of parameters affecting extract activation, gene sequence optimization, and redox folding conditions for disulfide bond formation at microliter scales. Efficient and predictable high-level protein production can then be achieved using batch processes in standard bioreactors. We show how a fully bioactive protein produced by OCFS from optimized frozen extract can be purified directly using a streamlined purification process that yields a biologically active cytokine, human granulocyte-macrophage colony-stimulating factor, produced at titers of 700 mg/L in 10 h. These results represent a milestone for in vitro protein synthesis, with potential for the cGMP production of disulfide-bonded biotherapeutic proteins.
Ng-CAM, A Neuron-Glia and Neuron-Neuron Cell Adhesion Molecule. (1992)

ニューロン-グリア細胞接着分子 (Ng-CAM) は、ニューロン-リア間及びニューロン-ニューロン聞の接着に関与する。Ng-CAMは、ニューロンにおいて6kbの大きさのmRNAから、先ず約200kDaの大きさの蛋白質として合成され、切断されて135kDa及び80kDaのふたつの構成蛋白質となる。そのアミノ酸配列から、6個のイムノグロブリン・ドメイン、5個のフィブロネクチンIII型繰り返し構造、膜貫通ドメイン、そして細胞内ドメインから構成されていることがわかった。Ng-CAMによる接着は、ニユーロンーニューロン間の接着については同種分子間機構によって、またニューロン・アストロサイト間の接着については異種分子間機構によって行われている。Ng-CAMは、ニューロンやシュワン細胞には発現されているが、アストロサイトではその発現は認められない。発生時に伸長しているニューロン細胞体や、神経形成時の神経細胞軸索にもっとも多く認められる。また、神経系が傷害を被った後にもNg-CAMの発現は増加する。抗Ng-CAM抗体によって、小脳組織培養系での Bergmann グリア細胞に沿った顆粒細胞の移動や、後根神経節組織培養系での神経細胞軸索の束形成が阻害される。ニューロンのNg-CAMは、隣接するニューロンに存在するNg-CAM分子と、またアストロサイトに存在する未だ同定されていないリガンド分子と結合することによって細胞接着に関与する分子である。
Is targeting of CD47-SIRPα enough for treating hematopoietic malignancy? (2012)

To the editor:

With interest we have read the report by Chao et al,[1][1] which is the most recent of a pioneering and impressive series of publications by the same group of researchers over the past 2 years,[2][2][⇓][3][⇓][4][⇓][5]–[6][6] in which the interaction between the broadly
Joint Estimation of Effective Brain Wave Activation Modes Using EEG/MEG Sensor Arrays and Multimodal MRI Volumes (2018)

In this letter, we present a new method for integration of sensor-based multifrequency bands of electroencephalography and magnetoencephalography data sets into a voxel-based structural-temporal magnetic resonance imaging analysis by utilizing the general joint estimation using entropy regularization (JESTER) framework. This allows enhancement of the spatial-temporal localization of brain function and the ability to relate it to morphological features and structural connectivity. This method has broad implications for both basic neuroscience research and clinical neuroscience focused on identifying disease-relevant biomarkers by enhancing the spatial-temporal resolution of the estimates derived from current neuroimaging modalities, thereby providing a better picture of the normal human brain in basic neuroimaging experiments and variations associated with disease states.
DeviceEditor visual biological CAD canvas (2012)

Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.
A master-slave system to acquire biometric imagery of humans at distance (2003)

The Distant Human Identification (DHID) system is a master-slave, real-time surveillance system designed to acquire biometric imagery of humans at distance. A stationary wide field of view master camera is used to monitor an environment at distance. When the master camera detects a moving person, a narrow field of view slave camera is commanded to turn to that direction, acquire the target human, and track them while recording zoomed-in images. These zoomed-in views provide meaningful biometric imagery of the distant humans, who are not recognizable in the master view. Based on the lenses we currently use, the system can detect and track moving people at distances up to 50 meters, within a 60° field of regard.
Serum hepcidin: reference ranges and biochemical correlates in the general population (2011)

To date, concentrations of the promising biomarker hepcidin have only been assessed in serum of relatively small series of healthy volunteers and patients. We assessed age- and sex-stratified reference ranges of serum hepcidin concentration in a selected reference set and performed regression analyses to study associations between hepcidin and (biochemical) variables in a large, well-phenotyped sample of the general population (n = 2998). All participants filled out a questionnaire on lifestyle, health status, and medical history. Serum measurements of iron parameters, liver enzyme alanine aminotransferase, creatinine and C-reactive protein were available. Serum hepcidin concentrations were lower for premenopausal than for postmenopausal women (median, 4.1 nM vs 8.5 nM, respectively). Hepcidin concentrations in men were constant over age (median, 7.8 nM). Serum hepcidin was strongly associated with serum ferritin in men and women: β-coefficient of log-transformed variables (95% confidence interval): 0.78 (0.74-0.82) and 0.83 (0.78-0.88), respectively. Additional significant, though less strong, associations were observed for C-reactive protein and total iron binding capacity in men and for total iron binding capacity, alanine aminotransferase, and glomerular filtration rate in women. Our study provides age- and sex-specific reference ranges of serum hepcidin concentration and indicates ferritin as the primary correlate of serum hepcidin concentration.
Effect of Cold Shock on Lipid A Biosynthesis inEscherichia coli (1999)

Palmitoleate is not present in lipid A isolated from Escherichia coli grown at 30 degrees C or higher, but it comprises approximately 11% of the fatty acyl chains of lipid A in cells grown at 12 degrees C. The appearance of palmitoleate at 12 degrees C is accompanied by a decline in laurate from approximately 18% to approximately 5.5%. We now report that wild-type E. coli shifted from 30 degrees C to 12 degrees C acquire a novel palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase that acts on the key lipid A precursor Kdo2-lipid IVA. The palmitoleoyl transferase is induced more than 30-fold upon cold shock, as judged by assaying extracts of cells shifted to 12 degrees C. The induced activity is maximal after 2 h of cold shock, and then gradually declines but does not disappear. Strains harboring an insertion mutation in the lpxL(htrB) gene, which encodes the enzyme that normally transfers laurate from lauroyl-ACP to Kdo2-lipid IVA (Clementz, T., Bednarski, J. J., and Raetz, C. R. H. (1996) J. Biol. Chem. 271, 12095-12102) are not defective in the cold-induced palmitoleoyl transferase. Recently, a gene displaying 54% identity and 73% similarity at the protein level to lpxL was found in the genome of E. coli. This lpxL homologue, designated lpxP, encodes the cold shock-induced palmitoleoyl transferase. Extracts of cells containing lpxP on the multicopy plasmid pSK57 exhibit a 10-fold increase in the specific activity of the cold-induced palmitoleoyl transferase compared with cells lacking the plasmid. The elevated specific activity of the palmitoleoyl transferase under conditions of cold shock is attributed to greatly increased levels of lpxP mRNA. The replacement of laurate with palmitoleate in lipid A may reflect the desirability of maintaining the optimal outer membrane fluidity at 12 degrees C.
Loop distribution using coherent detection (fiber optic networks) (1988)

A novel architecture is described for point-to-multipoint distribution using coherent detection and a totally passive fiber bus. Coherent technology is used initially to provide transmission at rates of a few hundred Mb/s without the need for a local oscillator at each station. It is expected that this architecture can then be expanded via WDM (wavelength-division multiplexing) to transport multiple wavelengths as coherent technology matures. The performance of the proposed topology is analyzed and compared to that of previous bus structures using variable and fixed taps with direct-detection receivers. This performance analysis consists essentially of a loss budget calculation intended to determine the relative numbers of stations which each of the architectures could support. Because the rates and loop lengths are modest and the spectral width of the sources associated with coherent communication are very small, dispersion (or rise-time budgeting) is not expected to present any real limitation for the systems considered here. A performance analysis and comparison of three tree structures is presented. Engineering issues and open questions are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Demonstration of phase correlation in multiwavelength mode-locked semiconductor diode lasers (1999)

Wideband spectral phase correlation is demonstrated from a multiwavelength mode-locked semiconductor laser. By use of frequency-resolved optical gating techniques, significant phase correlation was observed between multiple intracavity oscillating wavelengths, with wavelength separations of ~1 nm . The resultant temporal characteristics show a substantial modulation owing to the spectral coupling induced by intracavity-generated four-wave mixing. This result may lead to novel methods for directly generating ultrafast subpicosecond optical pulse sequences with spectrally tailored amplitude and phase characteristics from actively mode-locked semiconductor lasers.
A Collaborative Filtering Approach to Real-Time Hand Pose Estimation (2015)

Collaborative filtering aims to predict unknown user ratings in a recommender system by collectively assessing known user preferences. In this paper, we first draw analogies between collaborative filtering and the pose estimation problem. Specifically, we recast the hand pose estimation problem as the cold-start problem for a new user with unknown item ratings in a recommender system. Inspired by fast and accurate matrix factorization techniques for collaborative filtering, we develop a real-time algorithm for estimating the hand pose from RGB-D data of a commercial depth camera. First, we efficiently identify nearest neighbors using local shape descriptors in the RGB-D domain from a library of hand poses with known pose parameter values. We then use this information to evaluate the unknown pose parameters using a joint matrix factorization and completion (JMFC) approach. Our quantitative and qualitative results suggest that our approach is robust to variation in hand configurations while achieving real time performance (≈ 29 FPS) on a standard computer.
Oral administration of cholera toxin B subunit conjugated to myelin basic protein protects against experimental autoimmune encephalomyelitis by inducing transforming growth factor-β-secreting cells and suppressing chemokine expression (2000)

The efficacy and mechanism of immunosuppression against experimental autoimmune encephalomyelitis (EAE) by oral low-dose administration of myelin basic protein (MBP) conjugated to cholera toxin B subunit (CTB) were investigated in Lewis rats immunized with MBP together with complete Freund's adjuvant 4 days before the start of treatment. Oral treatment with CTB-MBP conjugate gave almost complete protection against disease, an effect that was totally abrogated by including a low dose of cholera holotoxin (CT). The protection by CTB-MBP was associated with a dramatic reduction in the number of leukocytes staining for CD4, CD8, IL-2R or MHC class II in the spinal cord as examined by immunohistochemistry. The mRNA expressions of T(h)1 cytokines IFN-gamma, IL-12 and tumor necrosis factor-alpha, as well as of chemokines monocyte chemotactic protein (MCP)-1 and RANTES in the spinal cord were also reduced by 76-94%, as assessed by in situ hybridization. In contrast, transforming growth factor (TGF)-beta mRNA-expressing cells were strongly increased in the spinal cord from animals treated orally with the CTB-MBP conjugate. In the draining peripheral lymph nodes, the number of MBP-specific TGF-beta mRNA-expressing cells was also increased, whereas there was a decrease in cells expressing T(h)1 or T(h)2 cytokine mRNA. Protection against EAE could be transferred by injection of cells from the mesenteric lymph nodes of animals fed with CTB-MBP into naive animals exposed to encephalitogenic T cells. The results indicate that the protective anti-inflammatory effect by oral treatment with CTB-MBP conjugate is, to a large extent, due to the induction of TGF-beta-secreting suppressive-regulatory T cells and to local down-regulation of MCP-1 and RANTES in the spinal cord.
Survivin-Driven and Fiber-Modified Oncolytic Adenovirus Exhibits Potent Antitumor Activity in Established Intracranial Glioma (2007)

The poor prognosis of patients with malignant gliomas necessitates the development of novel therapies. Virotherapy, using genetically engineered adenovectors that selectively replicate in and kill neoplastic cells, represents one such strategy. In this study, we examined several oncolytic vectors with modified transcriptional and transductional control of viral replication. First, we incorporated the survivin promoter (S) to drive E1A gene expression. We then modified the adenovirus serotype 5 (Ad5) fiber protein via genetic knob switching or incorporation of peptide ligands to target the following glioma-associated receptors: the Ad3 attachment protein, or CD46, alpha(v) beta(3)/alpha(v)beta(5) integrins, or heparan sulfate proteoglycans. The three conditionally replicative adenoviruses, CRAd-S-5/3, CRAd-S-RGD, and CRAd-S-pk7, were then examined in vitro with respect to transduction efficiency and tissue specificity. The most promising virus was then tested in vivo for evidence of tumor growth inhibition. CRAd-S-pk7 provided the highest level of viral replication and tumor oncolysis in glioma cell lines. At the same time, we observed minimal viral replication and toxicity in normal human brain. Injection of CRAd-S-pk7 inhibited xenograft tumor growth by more than 300% (p < 0.001). Sixty-seven percent of treated mice with intracranial tumors were long-term survivors (>110 days; p < 0.005). Analysis of tumor tissue indicated increased adenoviral infectivity, decreased mitotic activity, and enhanced tumor apoptosis. These findings demonstrate the effectiveness of CRAd-S-pk7 and provide the rationale for further development of this novel oncolytic virus for glioma gene therapy.
Summarizing the predictive power of a generalized linear model (2000)

This paper studies summary measures of the predictive power of a generalized linear model, paying special attention to a generalization of the multiple correlation coefficient from ordinary linear regression. The population value is the correlation between the response and its conditional expectation given the predictors, and the sample value is the correlation between the observed response and the model predicted value. We compare four estimators of the measure in terms of bias, mean squared error and behaviour in the presence of overparameterization. The sample estimator and a jack-knife estimator usually behave adequately, but a cross-validation estimator has a large negative bias with large mean squared error. One can use bootstrap methods to construct confidence intervals for the population value of the correlation measure and to estimate the degree to which a model selection procedure may provide an overly optimistic measure of the actual predictive power.
Direct Link Between mhc Polymorphism, T Cell Avidity, and Diversity in Immune Defense (2002)

Major histocompatibility complex (mhc)-encoded molecules govern immune responses by presenting antigenic peptides to T cells. The extensive polymorphism of genes encoding these molecules is believed to enhance immune defense by broadening the array of antigenic peptides available for T cell recognition, but direct evidence supporting the importance of this mechanism in combating pathogens is limited. Here we link mhc polymorphism-driven diversification of the cytotoxic T lymphocyte (CTL) repertoire to the generation of high-avidity, protective antiviral T cells and to superior antiviral defense. Thus, much of the beneficial effect of the mhc polymorphism in immune defense may be due to its critical influence on the properties of the selected CTL repertoire.
Framework for practical hexagonal-image processing (2002)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Role of genetic factors in human sexual behavior based on studies of tourette syndrome and ADHD probands and their relatives (1994)

Most significant variations in the expression of human sexuality are considered to be the result of learned behavior or psychological problems. Tourette syndrome (TS) is a common, hereditary tic and disinhibition disorder sometimes associated with compulsive use of obscene words (coprolalia) and previously reported to be occasionally associated with exhibitionism. To further explore the relationship between the Gts genes and sexual behavior, questions concerning a wide range of such behaviors were administered to 1,040 subjects, 14 years of age or older, consisting of 358 TS probands, 101 non-proband relatives with TS, 359 non-TS first degree relatives, 79 attention deficit hyperactivity disorder (ADHD) probands, 70 unaffected relatives of the ADHD probands, and 73 controls. The behaviors included magnitude of sex drive, sex orientation, exhibitionism, transvestitism, transsexualism, sadism, masochism, pedophilia, fetishism, aversion to being touched, and aversion to sex. While most of these behaviors occurred in a distinct minority of TS subjects, there was a significant positive correlation between each behavior examined and the degree of genetic loading for the Gts gene(s). The nature of these behaviors and their association with TS suggests many are variants of obsessive-compulsive disorder. Studies in animals indicate that changes in serotonin and dopamine play a significant role in the sexual behavior and many lines of evidence are consistent with the hypothesis that TS is due to genetic changes in serotonin and dopamine metabolism. These studies suggest that genetic factors play a much greater role in a wide range of forms of sexual expression than previously thought.