gebhart/patrepeval huggingface dataset:
DNA Interaction and Dual Topoisomerase I and II Inhibition Properties of the Anti-Tumor Drug Prodigiosin (2005)

Prodigiosin is a red pigment produced by Serratia marcescens with apoptotic activity. We examined the mechanism of action of this tripyrrole alkaloid, focusing on its interaction with DNA and its ability to inhibit both topoisomerase I and topoisomerase II. We also evaluated the DNA damage induced in cancer cell lines. Prodigiosin-DNA intercalation was analyzed using a competition dialysis assay with different DNA base sequences. Topoisomerase I and II inhibition was studied in vitro by a cleavage assay, and in cultured cells, by analysis of its ability to form covalent complexes. Furthermore, we analyzed DNA damage by pulse-field gel electrophoresis and by immunocytochemistry. Apoptosis inducing factor (AIF)/phospho-H2AX (p-H2AX) double labeling by confocal microscopy was performed to determine the possible implication of AIF in the prodigiosin-DNA damage. Finally, we studied the ability of this drug to induce copper-mediated DNA damage at different pH by a DNA cleavage assay. Our results demonstrate prodigiosin-DNA interaction in vitro and in cultured cells. It involves prodigiosin-DNA intercalation, with some preference for the alternating base pairs but with no discrimination between AT or CG sequences, dual abolition of topoisomerase I and II activity and, as consequence, DNA cleavage. Prodigiosin-DNA damage is independent of AIF. Furthermore, we found that copper-mediated cleavage activity is associated with pH (occurring at pH 6.8 rather than pH 7.4) and with the Cu(2+) ion concentration. These results indicate DNA a therapeutic target for prodigiosin and could explain the apoptosis mechanism of action induced by this antineoplastic drug.
Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients (2020)

SUMMARY The SARS-CoV-2 pandemic has unprecedented implications for public health, social life, and world economy. Since approved drugs and vaccines are not available, new options for COVID-19 treatment and prevention are highly demanded. To identify SARS-CoV-2 neutralizing antibodies, we analysed the antibody response of 12 COVID-19 patients from 8 to 69 days post diagnosis. By screening 4,313 SARS-CoV-2-reactive B cells, we isolated 255 antibodies from different time points as early as 8 days post diagnosis. Among these, 28 potently neutralized authentic SARS-CoV-2 (IC 100 as low as 0.04 μg/ml), showing a broad spectrum of V genes and low levels of somatic mutations. Interestingly, potential precursors were identified in naïve B cell repertoires from 48 healthy individuals that were sampled before the COVID-19 pandemic. Our results demonstrate that SARS-CoV-2 neutralizing antibodies are readily generated from a diverse pool of precursors, fostering the hope of rapid induction of a protective immune response upon vaccination.
Three-dimensional television system based on spatial imaging method using integral photography (2012)

A three-dimensional (3-D) television based on the spatial imaging method using integral photography (integral 3-D television) has three main advantages; displaying 3-D images without having to use special 3-D glasses, being viewable without restricting viewer posture, having a system applicable to live broadcasting service. I describe the principle of an integral 3-D television and introduce an experimental integral 3-D television with 33-mega-pixel imaging devices. In this experimental television, a lens array is configured of 400 lenses in the horizontal direction and 250 lenses in the vertical direction. The results from capture and display experiments confirm 3-D video reproduction that changes seamlessly with viewing position.
Metal‐Mediated Cross‐Linking in the Generation of a Marine‐Mussel Adhesive (2004)

In the Communication “Metal-Mediated Cross-Linking in the Generation of a Marine-Mussel Adhesive” by J. J. Wilker and co-workers (1), three relevant citations discussing atomic force microscopy (“Adhesion of Mytilus edulis Foot Protein 1 on Silica: Ionic Effects on Biofouling”, B. P. Frank, G. Belfort, Biotechnol. Prog. 2002, 18, 580–586), iron binding to the Mefp-1 protein (“Ferric Ion Complexes of a DOPA-Containing Adhesive Protein from Mytilus edulis”, S. W. Taylor, D. B. Chase, M. H. Emptage, M. J. Nelson, J. H. Waite, Inorg. Chem. 1996, 35, 7572–7577) and hydrolyzed peptides thereof (“Polarographic and Spectrophotometric Investigation of Iron(III) Complexation to 3,4-Dihydroxyphenylalanine-Containing Peptides and Proteins from Mytilus edulis”, S. W. Taylor, G. W. Luther III, J. H. Waite, Inorg. Chem. 1994, 33, 5819-5824) should have been included. The authors apologize for this oversight and point out that the novelty of their work lies in comparing spectroscopic data from live mussel glue to those of a protein-based adhesive film and peptide models of potential cross-links, thereby providing direct characterization of marine adhesive bonding.
Bone Marrow Stromal Cells and Their Use in Regenerating Bone (2003)

Tissue engineering approaches have recently been devised to repair large bone losses. Tissue engineering takes advantages of the combined use of cultured living cells and 3D scaffolds to deliver vital cells to the damaged site of the patient. Cultured bone marrow stromal cells (BMSCs) can be regarded as a mesenchymal progenitor/precursor cell population derived from adult stem cells. When implanted in immunodeficient mice, BMSCs combined with mineralized 3D scaffolds to form a primary bone tissue that is highly vascularized. We have used autologous BMSC/bioceramic composites to treat full-thickness gaps of tibial diaphysis in sheep. The healing process has been investigated. The sequence of events is as follows: (1) bone formation on the outer surface of the implant; (2) bone formation in the inner cylinder canal; (3) formation of fissures and cracks in the implant body; (4) bone formation in the bioceramic pores. Similar composites whose size and shape reflected each bone defect have been implanted at the lesion sites of three patients. External fixation was used. Patients have been followed for more than three years. The results obtained are very promising and we propose the use of culture-expanded osteoprogenitor cells in conjunction with hydroxyapatite bioceramics as a significant improvement in the repair of critical size long bone defects.
High dose eicosapentaenoic acid ethyl ester: effects on lipids and neutrophil leukotriene production in normal volunteers. (1990)

1. A 93% pure ethyl ester of eicosapentaenoic acid was investigated for tolerability and biochemical effects on neutrophil leukotriene synthesis and plasma lipoproteins when given in high dose. Six healthy volunteers received 6 g eicosapentaenoic acid ethyl ester daily for 6 weeks, followed by a 4 week wash-out and then 18 g daily for 6 weeks. 2. There was inhibition of neutrophil leukotriene B4 and 5-hydroxyeicosatetraenoic acid synthesis, with no significant differences between low and high dose. 3. There was a dose dependent increase in leukotriene B5 and 5-hydroxyeicosatetraenoic acid acid synthesis. 4. Plasma triglycerides were reduced maximally on 6 g daily, with no greater suppression at 18 g daily. 5. Plasma cholesterol was only suppressed significantly at 18 g daily. 6. The 6 g daily dose was well tolerated but the 18 g daily dose produced diarrhoea and steatorrhoea.
Multi-mode fibre correction for applications in optomechanics using a digital micromirror device (2014)

We discuss the development of a digital micromirror based adaptive optical system that corrects for the propagation of coherent light through multimode fibres with the aim to achieve optical trapping in vacuum.
PointRight (2002)

We describe the design of and experience with PointRight, a peer-to-peer pointer and keyboard redirection system that operates in multi-machine, multi-user environments. PointRight employs a geometric model for redirecting input across screens driven by multiple independent machines and operating systems. It was created for interactive workspaces that include large, shared displays and individual laptops, but is a general tool that supports many different configurations and modes of use. Although previous systems have provided for re-routing pointer and keyboard control, in this paper we present a more general and flexible system, along with an analysis of the types of re-binding that must be handled by any pointer redirection system This paper describes the system, the ways in which it has been used, and the lessons that have been learned from its use over the last two years.
Dysregulation of long non-coding RNA profiles in human colorectal cancer and its association with overall survival (2016)

Long non-coding RNAs (lncRNAs) emerged as key regulators of diverse roles during colorectal cancer (CRC) carcinogenesis, but their specific function still remains to be explored. The present study aimed to re-annotate the Affymetrix Human Exon 1.0 ST Array for defining differential lncRNAs in CRC. Their prognostic relevance was also developed for screening key regulators in CRC. The CRC datasets E-GEOD-31737, E-MATB-829, Affymetrix colon cancer dataset and E-GEOD-24550 were re-purposed for searching differential lncRNAs and exploring their association with overall survival (OS). The identified lncRNAs were validated in CRC tissues or cell lines. As a result, 462, 286 and 166 differential lncRNAs were identified, respectively, in three predictive datasets. Among them, 48 lncRNAs were commonly observed to exhibit differential expression in the three datasets. Notably, the overexpression of family with sequence similarity 83 member H (FAM83H)-antisense (AS) 1 (P=0.038) and VPS9 domain containing 1 (VPS9D1)-AS1 (P=0.020) indicated shorter OS time than lower expression. The overexpression of FAM83H-AS1 (P=0.033) and VPS9D1-AS1 (P=0.011) was validated in cancerous tissues. Thus, FAM83H-AS1 and VPS9D1-AS1 may potentially enhance carcinogenesis or may be developed as prognostic biomarkers for CRC. In conclusion, a total of 48 CRC-related lncRNAs were identified, the majority of which were confirmed to exhibit dysregulation. FAM83H-AS1 and VPS9D1-AS1 could have a potential use as prognostic biomarkers for CRC patients.
Flow Cytometry, Amped Up (2011)

The novel technique of mass cytometry opens a new chapter in single-cell biology.
Classification of PDZ domains (2001)

A diverse family of PDZ domains has been identified, but the rules that govern their ligand specificity are not clear. Here we propose a novel classification of PDZ domains based on the nature of amino acids in the two critical positions in the PDZ domain fold. Using these principles, we classified PDZ domains present in the SMART database. Using yeast two-hybrid, in vitro pull-down and plasmon surface resonance assays, we demonstrated that in agreement with their position in the proposed classification the Mint1-1, hINADL-5, and PAR6 PDZ domains display similar dual ligand specificity. The proposed classification helps to organize PDZ domain containing proteins.
Prion-Inducing Domain of Yeast Ure2p and Protease Resistance of Ure2p in Prion-Containing Cells (1995)

The genetic properties of the [URE3] non-Mendelian element of Saccharomyces cerevisiae suggest that it is a prion (infectious protein) form of Ure2p, a regulator of nitrogen catabolism. In extracts from [URE3] strains, Ure2p was partially resistant to proteinase K compared with Ure2p from wild-type extracts. Overexpression of Ure2p in wild-type strains induced a 20- to 200-fold increase in the frequency with which [URE3] arose. Overexpression of just the amino-terminal 65 residues of Ure2p increased the frequency of [URE3] induction 6000-fold. Without this "prion-inducing domain" the carboxyl-terminal domain performed the nitrogen regulation function of Ure2p, but could not be changed to the [URE3] prion state. Thus, this domain induced the prion state in trans, whereas in cis it conferred susceptibility of the adjoining nitrogen regulatory domain to prion infections.
The Fabrication and Bandgap Engineering of Photonic Multilayers (2001)

New opportunities for engineered photonic behaviorhave been found in the preparation of multilayer colloidal crystals (see Figure). Each layer of the crystal consists of a three-dimensionally ordered array of close-packed colloids. These multilayer samples are amenable to templating methods for tuning the dielectric contrast and mechanical properties of the material.
Vaccination with Dendritic Cells Pulsed with Peptides of Myelin Basic Protein Promotes Functional Recovery from Spinal Cord Injury (2003)

Injury-induced self-destructive processes cause significant functional loss after incomplete spinal cord injury (SCI). Cellular elements of both the innate (macrophage) and the adaptive (T-cell) immune response can, if properly activated and controlled, promote post-traumatic regrowth and protection after SCI. Dendritic cells (DCs) trigger activation of effector and regulatory T-cells, providing a link between the functions of the innate and the adaptive immune systems. They also initiate and control the body's response to pathogenic agents and regulate immune responses to both foreign and self-antigens. Here we show that post-injury injection of bone marrow-derived DCs pulsed with encephalitogenic or nonencephalitogenic peptides derived from myelin basic protein, when administered (either systemically or locally by injection into the lesion site) up to 12 d after the injury, led to significant and pronounced recovery from severe incomplete SCI. No significant protection was seen in DC recipients deprived of mature T-cells. Flow cytometry, RT-PCR, and proliferation assays indicated that the DCs prepared and used here were mature and immunogenic. Taken together, the results suggest that the DC-mediated neuroprotection was achieved via the induction of a systemic T-cell-dependent immune response. Better preservation of neural tissue and diminished formation of cysts and scar tissue accompanied the improved functional recovery in DC-treated rats. The use of antigen-specific DCs may represent an effective way to obtain, via transient induction of an autoimmune response, the maximal benefit of immune-mediated repair and maintenance as well as protection against self-destructive compounds.
Aminozuckersynthesen, XVI1). 2‐Amino‐2.6‐didesoxy‐D‐allose und 2‐Amino‐2.6‐didesoxy‐D‐gulose (1966)

Abstract Aus Benzyl‐ N ‐benzoyl‐3.4‐di‐ O ‐mesyl‐β‐D‐allosaminid bzw. aus Benzyl‐4‐ O ‐acetyl‐6‐ O ‐mesyl‐α‐D‐gulopyranosido[2.3 : 4′.5′]oxazolidon‐(2′) werden über die 6‐Jod‐Verbindungen 2‐Amino‐2.6‐didesoxy‐D‐allose und ‐D‐gulose synthetisiert. 6‐Jod‐benzyl‐glykoside werden selektiv zu 6‐Desoxy‐benzyl‐glykosiden reduziert, wobei O ‐Acetyl‐Gruppen erhalten bleiben.
Unbalanced alternative splicing and its significance in cancer (2006)

Alternative pre-mRNA splicing leads to distinct products of gene expression in development and disease. Antagonistic splice variants of genes involved in differentiation, apoptosis, invasion and metastasis often exist in a delicate equilibrium that is found to be perturbed in tumours. In several recent examples, splice variants that are overexpressed in cancer are expressed as hyper-oncogenic proteins, which often correlate with poor prognosis, thus suggesting improved diagnosis and follow up treatment. Global gene expression technologies are just beginning to decipher the interplay between alternatively spliced isoforms and protein-splicing factors that will lead to identification of the mutations in these trans-acting factors responsible for pathogenic alternative splicing in cancer.
Handbook of Non-Invasive Methods and the Skin (2006)

Firmly established as the leading international reference in this field, Non-Invasive Methods and the Skin broke new ground with its comprehensive coverage of methods used in both clinical and experimental dermatology. Completely revised and updated, containing more than twice as much information, the Second Edition continues the tradition. The aut
Candidate Biomarkers of Response to an Experimental Cancer Drug Identified through a Large-scale RNA Interference Genetic Screen (2009)

We propose that suppression of the activity of a RBX1 and DDB1-containing E3 ligase complex leads to the stabilization of certain proteins, the increased abundance of which is in turn responsible for resistance to R3200. Moreover, our data suggest that RBX1 and DDB1 could potentially be developed into biomarkers of resistance to acyl sulfonamide-based cancer drugs. This will require clinical validation in a series of patients treated with R3200.
Toward optimal feature selection (1996)

In this paper, we examine a method for feature subset selection based on Information Theory. Initially, a framework for defining the theoretically optimal, but computationally intractable, method for feature subset selection is presented. We show that our goal should be to eliminate a feature if it gives us little or no additional information beyond that subsumed by the remaining features. In particular, this will be the case for both irrelevant and redundant features. We then give an efficient algorithm for feature selection which computes an approximation to the optimal feature selection criterion. The conditions under which the approximate algorithm is successful are examined. Empirical results are given on a number of data sets, showing that the algorithm effectively handles datasets with large numbers of features. 1 Introduction In the classic supervised learning task, we are given a training set of labeled fixed-length feature vectors, or instances, from which to induce a classi...
Digital Predistortion for Envelope-Tracking Power Amplifiers Using Decomposed Piecewise Volterra Series (2008)

Due to dynamic changes of supply voltage, envelope-tracking (ET) power amplifiers (PAs) exhibit very distinct characteristics in different power regions. It is very difficult to compensate the distortion induced by these amplifiers by employing conventional digital predistortion techniques. In this paper, by introducing a new piecewise Volterra model based on a vector threshold decomposition technique, we first set several thresholds in the input power level according to the PA characteristics, and decompose the input complex envelope signal into several sub-signals by using these thresholds. We then process each sub-signal separately by employing the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dynamic</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deviation</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">reduction</i> -based Volterra series, and finally recombine them together to produce the predistorted output. Experimental results show that by using this new decomposed piecewise digital predistorter model, the distinct characteristics of the ET system at different signal power levels can be accurately modeled, and thus, the distortion, including both static nonlinearities and memory effects, caused by the amplifier nonlinear behavior can be effectively compensated.
Agreement Regarding Diagnosis of Transient Ischemic Attack Fairly Low Among Stroke-Trained Neurologists (2010)

TIA remains a highly subjective diagnosis, even among stroke subspecialists. The use of confirmatory testing beyond clinical judgment is needed to help solidify the diagnosis. Caution should be used when diagnosing an event as a possible TIA.
瓦尔德沃夫——一所培养动手能力、陶冶心灵的学校 (1995)

瓦尔德沃夫学校1919年由鲁道夫·斯特纳创始于德国,现在美国、荷兰、美国、瑞典等国家都有瓦尔德沃夫学校,并且每年都有新的学校出现。瓦尔德沃夫教育运动历经七十多个春秋,至今仍方兴未艾,这在教育史上是不多见的,也说明它是有生命力的。它的指导思想和教学方法对我们在教学中贯彻美育、充分发挥学生在学习中的主体作用、培养学生的创造能力,造就全面发展的人才等方面都有借鉴作用。在此译出,供广大教育工作者参考。初看起来,位于马萨诸塞州大巴灵顿的
Event-driven rules for sensing and responding to business situations (2007)

Event-based systems have been developed and used to implement networked and adaptive business environments based on loosely coupled systems in order to respond faster to critical business events. In this paper, we introduce a rule management system which is able to sense and evaluate events in order to respond to changes in a business environment or customer needs. It enables users to graphically compose comprehensive event-triggered rules, which can be used to control the processing of services. For the definition of a rule set, users can independently define event conditions, event patterns and correlation-related information which can be combined for modeling complex business situations. We have fully implemented the proposed system with a service-oriented approach and illustrate our approach with an order management business case.
Sugar and metabolic regulation of genes for sucrose metabolism: potential influence of maize sucrose synthase and soluble invertase responses on carbon partitioning and sugar sensing1 (1996)

Sugar responsiveness of genes for both paths of sucrose metabolism could provide a mechanism not only for transcriptional regulation of the first step in the use of imported carbon, but also for altering signals to the sugar-sensing system. This hypothesis was examined by comparison of (1) sugar regulation among maize genes for sucrose synthase and invertase, (2) their contrasting patterns of tissue expression, and (3) their influence on production of effectors for other sugar-responsive genes. Cloning and characterization of the Ivr1 and Ivr2 invertase genes of maize indicated that these genes belong to distinct subfamilies of the maize soluble invertase gene family. In addition, maize invertases can be grouped with the sucrose synthases (Sh1 and Sus1) on the basis of shared patterns of differential sugar-responsiveness and tissue-specific expression. Extension of this comparison to include genes for sucrose metabolism from other species revealed a more widespread association between starvation-tolerant expression and restricted patterns of tissue distribution. Consideration of current models for plant sugar-sensing systems and transport pathways suggested that the site and mechanism of sucrose cleavage in the cell could affect the magnitude and type of signal generated.
Visual masking and the design of magnetic resonance image acquisition (2002)

This paper presents novel data acquisition schemes for improving the quality of magnetic resonance images (MRI). These approaches determine the number of times that k-space (frequency domain) samples have to be acquired and averaged to form an MRI image, by taking into account the characteristics of the human visual system and the location in k-space of the data samples. They lead to dramatic reductions in imaging time (by a factor of 8 to 10) with no reduction in image quality. Alternatively, they produce higher quality imagery using the same amount of imaging time as conventional approaches.
Nitrogen regulation inCorynebacterium glutamicum: isolation of genes involved and biochemical characterization of corresponding proteins (1999)

The regulation of nitrogen assimilation was investigated in the Gram-positive actinomycete Corynebacterium glutamicum. Biochemical studies and site-directed mutagenesis revealed that glutamine synthetase activity is regulated via adenylylation in this organism. The genes encoding the central signal transduction protein PH (glnB) and the primary nitrogen sensor uridylyltransferase (glnD) were isolated and sequenced. Additionally, genes putatively involved in the degradation of ornithine (ocd) and sarcosine (soxA), ammonium uptake (amtP) and protein secretion (ftsY, srp) were identified in C. glutamicum. Based on these observations, the mechanism of N regulation in C. glutamicum is similar to that of the Gram-negative Escherichia coli. As deduced from data base searches, the described regulation may also hold true for the important pathogen Mycobacterium glutamicum.