gebhart/patrepeval huggingface dataset:
Advanced instantaneous shifted‐excitation Raman difference spectroscopy (iSERDS) using a laser pointer (2015)

Shifted‐excitation Raman difference spectroscopy (SERDS) is an established experimental method for obtaining Raman spectra from fluorescing samples. However, great care must be taken when the experiment is carried out. Some experimental parameters such as the intensity and the wavelength shift are very sensitive, and small inaccuracies in the settings can result in significant artifacts in the reconstructed Raman spectrum. Instantaneous shifted‐excitation Raman difference spectroscopy (iSERDS) using a broadband light source provides a certain flexibility regarding the parameter settings because there are multiple pairs of shifted wavelength spectra recorded simultaneously. The present work demonstrates the first experimental implementation of iSERDS using a commercial laser pointer as a moderately broadband excitation source. Employing a transmission grating for spatially dispersing the laser radiation in the measurement volume simplifies the experiment significantly compared with the previous iSERDS method that employs two reflection gratings for this purpose. Moreover, an evaluation strategy is developed based on a systematic investigation of the influence the main experimental parameters (i.e. the wavelength shift, the intensity, and noise) have on the SERDS spectrum and on the derived Raman spectrum. Recommendations on the optimal choice of settings in iSERDS and conventional SERDS experiments are made. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Engineering the haemogenic niche mitigates endogenous inhibitory signals and controls pluripotent stem cell-derived blood emergence (2017)

Efforts to recapitulate haematopoiesis, a process guided by spatial and temporal inductive signals, to generate haematopoietic progenitors from human pluripotent stem cells (hPSCs) have focused primarily on exogenous signalling pathway activation or inhibition. Here we show haemogenic niches can be engineered using microfabrication strategies by micropatterning hPSC-derived haemogenic endothelial (HE) cells into spatially-organized, size-controlled colonies. CD34+VECAD+ HE cells were generated with multi-lineage potential in serum-free conditions and cultured as size-specific haemogenic niches that displayed enhanced blood cell induction over non-micropatterned cultures. Intra-colony analysis revealed radial organization of CD34 and VECAD expression levels, with CD45+ blood cells emerging primarily from the colony centroid area. We identify the induced interferon gamma protein (IP-10)/p-38 MAPK signalling pathway as the mechanism for haematopoietic inhibition in our culture system. Our results highlight the role of spatial organization in hPSC-derived blood generation, and provide a quantitative platform for interrogating molecular pathways that regulate human haematopoiesis.
An Intronic Silencer of the Mouse Perforin Gene (2002)

We have previously shown that the perforin gene locus is comprised of eight DNase I hypersensitive sites (DHS). Seven (DHS I-DHS VII) of them were CTL-specific whereas one (DHS VIII) in the second intron was expressed in a wide range of cell types. DHS VIII was highly AT-rich (75%) and was comprised of multiple sets of high mobility group (HMG)-I/Y binding site, two potential Special AT-rich Binding protein (SATB-1)-binding sites, and a long stretch of CTAT repeats, indicating that DHS VIII may relate to nuclear matrix-associated region (MAR). When DHS VIII was inserted into the perforin promoter-driven luciferase gene, it silenced the reporter gene transcription in CTLL-R8 cells in an orientation- and distance-independent manner. Moreover, this silencing effect was also observed in other promoters in a variety of non-CTL cell lines, suggesting that DHS VIII exerted a global silencing effect. Deletion analysis and gel-shift assays indicated that the silencing effect was mediated by the CTAT repeats and its binding protein called CTAT repeats-binding protein (CRBP).
Gene delivery through cell culture substrate adsorbed DNA complexes (2005)

Efficient gene delivery is a fundamental goal of biotechnology and has numerous applications in both basic and applied science. Substrate-mediated delivery and reverse transfection enhance gene transfer by increasing the concentration of DNA in the cellular microenvironment through immobilizing a plasmid to a cell culture substrate prior to cell seeding. In this report, we examine gene delivery of plasmids that were complexed with cationic polymers (polyplexes) or lipids (lipoplexes) and subsequently immobilized to cell culture or biomaterial substrates by adsorption. Polyplexes and lipoplexes were adsorbed to either tissue culture polystyrene or serum-adsorbed tissue culture polystyrene. The quantity of DNA immobilized increased with time of exposure, and the deposition rate and final amount deposited depended upon the properties of the substrate and complex. For polyplexes, serum modification enhanced reporter gene expression up to 1500-fold relative to unmodified substrates and yielded equivalent or greater expression compared to bolus delivery. For lipoplexes, serum modification significantly increased the number of transfected cells relative to unmodified substrates yet provided similar levels of expression. Immobilized complexes transfect primary cells with improved cellular viability relative to bolus delivery. Finally, this substrate-mediated delivery approach was extended to a widely used biomaterial, poly(lactide-co-glycolide). Immobilization of DNA complexes to tissue culture polystyrene substrates can be a useful tool for enhancing gene delivery for in vitro studies. Additionally, adapting this system to biomaterials may facilitate application to fields such as tissue engineering.
Gene Expression in Blood Changes Rapidly in Neutrophils and Monocytes after Ischemic Stroke in Humans: A Microarray Study (2006)

Ischemic brain and peripheral white blood cells release cytokines, chemokines and other molecules that activate the peripheral white blood cells after stroke. To assess gene expression in these peripheral white blood cells, whole blood was examined using oligonucleotide microarrays in 15 patients at 2.4+/-0.5, 5 and 24 h after onset of ischemic stroke and compared with control blood samples. The 2.4-h blood samples were drawn before patients were treated either with tissue-type plasminogen activator (tPA) alone or with tPA plus Eptifibatide (the Combination approach to Lysis utilizing Eptifibatide And Recombinant tPA trial). Most genes induced in whole blood at 2 to 3 h were also induced at 5 and 24 h. Separate studies showed that the genes induced at 2 to 24 h after stroke were expressed mainly by polymorphonuclear leukocytes and to a lesser degree by monocytes. These genes included: matrix metalloproteinase 9; S100 calcium-binding proteins P, A12 and A9; coagulation factor V; arginase I; carbonic anhydrase IV; lymphocyte antigen 96 (cluster of differentiation (CD)96); monocarboxylic acid transporter (6); ets-2 (erythroblastosis virus E26 oncogene homolog 2); homeobox gene Hox 1.11; cytoskeleton-associated protein 4; N-formylpeptide receptor; ribonuclease-2; N-acetylneuraminate pyruvate lyase; BCL6; glycogen phosphorylase. The fold change of these genes varied from 1.6 to 6.8 and these 18 genes correctly classified 10/15 patients at 2.4 h, 13/15 patients at 5 h and 15/15 patients at 24 h after stroke. These data provide insights into the inflammatory responses after stroke in humans, and should be helpful in diagnosis, understanding etiology and pathogenesis, and guiding acute treatment and development of new treatments for stroke.
Simulation of Torso Posture and Motion in Seating (1998)

&lt;div class="htmlview paragraph"&gt;Since the 1960's, automotive seats have been designed and evaluated with tools and procedures described in the SAE Recommended Practice J826. The SAE J826 design template and testing manikin each have a torso with a flat lower back shape and with a single joint at the H-point.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The JOHN models provide a more anatomically detailed representation of human shape and movement. The articulations of the JOHN torso (pelvic, lumbar, and thoracic) segments are coupled so that their relative positions are determined by a single parameter related to spinal curvature. This paper describes the development and use of the JOHN biomechanical models for seating design.&lt;/div&gt;
ChemInform Abstract: Substituted 1‐Alkoxy‐2‐methyl‐2H‐isoindoles. Part 1. Reactive o‐Quinonoid Hetarenes with Unsymmetrical Molecular Structure. (1989)

Abstract Starting with the substituted phthalic acid anhydrides (I), the 2‐methylisoindolin‐1‐ones (IV) are prepared by chemoselective reduction of the intermediate phthalic acid amides (III).
High-Performance Plastic Transistors Fabricated by Printing Techniques (1997)

A printed field-effect transistor (FET) is reported, in which all the essential components are screen-printed for the first time. This transistor has a polyimide dielectric layer, a regioregular poly(3-alkythiophene) semiconducting layer, and two silver electrodes, all of which are printed on an ITO-coated plastic substrate.
A 100-kbps power-line modem for household applications (2003)

Communication using power line as a medium provides a convenient and inexpensive way for data transmission and control signaling in households. In this paper we introduce a power-line channel model as well as architecture of a spread-spectrum baseband transceiver IC for a powerline modem. The modulation and spreading scheme used in the proposed transceiver is MBOK. This transceiver runs at the carrier frequency of 256 kHz and provides 100 kbps data rate. Simulation results verify the effectiveness of the proposed architecture in household data communication.
A new case of dihydropyrimidine dehydrogenase deficiency (1989)

We present the clinical and biochemical features of a boy with dihydropyrimidine dehydrogenase deficiency, which seem to underline a disease entity of developmental retardation, epilepsy and muscular hypertonia.
Phosphorylation of human replication protein A by the DNA-dependent protein kinase is involved in the modulation of DNA replication (1996)

The single-stranded DNA-binding protein, Replication Protein A (RPA), is a heterotrimeric complex with subunits of 70, 32 and 14 kDa involved in DNA metabolism. RPA may be a target for cellular regulation; the 32 kDa subunit (RPA32) is phosphorylated by several cellular kinases including the DNA-dependent protein kinase (DNA-PK). We have purified a mutant hRPA complex lacking amino acids 1-33 of RPA32 (rhRPA x 32delta1-33). This mutant bound ssDNA and supported DNA replication; however, rhRPA x 32delta1-33 was not phosphorylated under replication conditions or directly by DNA-PK. Proteolytic mapping revealed that all the sites phosphorylated by DNA-PK are contained on residues 1-33 of RPA32. When wild-type RPA was treated with DNA-PK and the mixture added to SV40 replication assays, DNA replication was supported. In contrast, when rhRPA x 32delta1-33 was treated with DNA-PK, DNA replication was strongly inhibited. Because untreated rhRPA x 32delta1-33 is fully functional, this suggests that the N-terminus of RPA is needed to overcome inhibitory effects of DNA-PK on other components of the DNA replication system. Thus, phosphorylation of RPA may modulate DNA replication indirectly, through interactions with other proteins whose activity is modulated by phosphorylation.
Role of target antigen in bispecific-antibody-mediated killing of human glioblastoma cells: A pre-clinical study (1999)

Bispecific antibodies (bsAbs) directed to tumor-associated antigens and to receptors mediating T-cell activation, such as the TCR/CD3 complex and the co-stimulatory CD28 molecule, are capable of activating T cells at the surface of tumor cells, resulting in tumor-cell killing. Here we report the pre-clinical characterization of bispecific-antibody fragments (bsFab2) directed to 2 different glioblastoma-associated antigens: the EGF receptor (EGFR) and a chondroitin-sulfate proteoglycan (CSPG). Using cultured glioblastoma cells expressing both target antigens, we found that the ability of anti-tumor × anti-CD28 bsFab2 to mediate “targeted T-cell co-stimulation” is superior for constructs targeting the CSPG molecule, correlating with an approximately 6-fold higher expression level of this antigen on the cell surface. In contrast, bsFab2 triggering CD3 are more effective if they contain EGFR-target specificity. This indicates that the activity of anti-tumor × anti-CD3 constructs critically depends on properties of the antigen other than its expression level on the cell surface, e.g., its mobility in the membrane. These findings prompted us to use EGFR-targeting bsFab2 in an ongoing clinical trial with glioma patients. Int. J. Cancer 80:612–616, 1999. © 1999 Wiley-Liss, Inc.
Detection and Quantification of Biologically Active Botulinum Neurotoxin Serotypes A and B Using a Förster Resonance Energy Transfer-Based Quantum Dot Nanobiosensor (2017)

Botulinum neurotoxin (BoNT) is the most potent toxin known. The ingestion of food contaminated with biologically active BoNT causes foodborne botulism, which can lead to respiratory paralysis, coma, and death after ingestion of as little as 70 μg for a 70 kg human. Because of its lethality and challenges associated with current detection methods, there is an urgent need for highly sensitive rapid screening techniques capable of detecting biologically active BoNT. Here, we describe a Förster resonance energy transfer-based nanobiosensor that uses quantum dots (QDs) and two specific quencher-labeled peptide probes to detect and differentiate two biologically active forms of BoNT, serotypes A and B, which were responsible for 80% of human foodborne botulism cases in the U.S. from 2012 to 2015. Each peptide probe contains an enzymatic cleavage site specific to only one serotype. QDs were selected based on the spectral overlap with the quenchers. In the presence of the target BoNT serotype, the peptide probe is cleaved and the quenching of QD photoluminescence (PL) is reduced, giving a signal that is easily detected by a PL spectrophotometer. This sensor performance was evaluated with light chains of BoNT/A and BoNT/B (LcA and LcB), catalytic domains of the respective serotypes. LcA and LcB were detected in 3 h with limits of detection of 0.2 and 2 ng/mL, respectively. The specificity of the sensor was evaluated, and no cross-reactivity from nontarget serotypes was observed with 2 h of incubation. Because each serotype-specific peptide is conjugated to a QD with a unique emission wavelength, multiple biologically active BoNT serotypes could be detected in one PL spectrum. The sensor was also shown to be responsive to BoNT/A and BoNT/B holotoxins. Good performance of this sensor implies its potential application as a rapid screening method for biologically active BoNT/A and BoNT/B in the laboratory and in the field.
Geoaccurate three-dimensional reconstruction via image-based geometry (2013)

Recent technological advances in computing capabilities and persistent surveillance systems have led to increased focus on new methods of exploiting geospatial data, bridging traditional photogrammetric techniques and state-of-the-art multiple view geometry methodology. The structure from motion (SfM) problem in Computer Vision addresses scene reconstruction from uncalibrated cameras, and several methods exist to remove the inherent projective ambiguity. However, the reconstruction remains in an arbitrary world coordinate frame without knowledge of its relationship to a xed earth-based coordinate system. This work presents a novel approach for obtaining geoaccurate image-based 3-dimensional reconstructions in the absence of ground control points by using a SfM framework and the full physical sensor model of the collection system. Absolute position and orientation information provided by the imaging platform can be used to reconstruct the scene in a xed world coordinate system. Rather than triangulating pixels from multiple image-to-ground functions, each with its own random error, the relative reconstruction is computed via image-based geometry, i.e., geometry derived from image feature correspondences. In other words, the geolocation accuracy is improved using the relative distances provided by the SfM reconstruction. Results from the Exelis Wide-Area Motion Imagery (WAMI) system are provided to discuss conclusions and areas for future work.
Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions. (1983)

A 1.6-kilobase-pair DNA fragment derived from the Escherichia coli chromosome was analyzed by Tn3 transposon insertion and deletion mapping to locate a mutator gene, dnaQ (mutD), and the rnh gene that codes for RNase H. When a strong promoter, PL of lambda phage, was placed at the right- and left-side of the cloned DNA fragment, the dnaQ protein and RNase H, respectively were overproduced. These results suggested that the two genes are transcribed in opposite directions and that their promoters are located in a narrow region between the genes. Nucleotide sequence analysis confirmed this and further revealed that transcriptional and translational initiation signals for the two genes overlap. From the sequence data it was deduced that the dnaQ protein and RNase H consist of 243 and 155 triplets and have molecular weights of 27,500 and 17,500, respectively. dnaQ81 amber mutant showed two codon alterations, CAG(glutamine-195) leads to TAG(amber) and ACA(threonine-193) leads to ATA(isoleucine). The dnaQ-lacZ and the rnh-lacZ fused genes were constructed and hybrid proteins with beta-galactosidase activity were produced. From beta-galactosidase levels it was estimated that the promoter for dnaQ is 5 times more active than that for rnh.
Glioblastoma: A Method for Predicting Response to Antiangiogenic Chemotherapy by Using MR Perfusion Imaging—Pilot Study (2010)

This pilot study derived an imaging metric (HPV) that reflects local perfusion changes in GBMs. This metric was found to show a significantly improved correlation to TTP as compared with more commonly used metrics.
SDSPM-based user interest prediction in collaborative graphics design systems under ubiquitous environment (2009)

Rapid advances in the enabling technologies for mobile and ubiquitous computing help portable devices to join collaborative graphics design conveniently. The limitation of display size and computational power of these embedded devices makes it hard for mobile users to browse large pattern that renewed in real time efficiently. We present a novel user interest region prediction algorithm and related system that use state duration based segmental probability model (SDSPM) to forecast user's intention in the near future. Related experiment was carried out to test the effectiveness of the algorithm. Based on the prediction, only sub-patterns that might be interested to user are issued to the embedded sites. The proposed user interest prediction system is effective and the feasibility of the collaborative graphics design system in ubiquitous environment is enhanced.
A maximum entropy approach to species distribution modeling (2004)

We study the problem of modeling species geographic distributions, a critical problem in conservation biology. We propose the use of maximum-entropy techniques for this problem, specifically, sequential-update algorithms that can handle a very large number of features. We describe experiments comparing maxent with a standard distribution-modeling tool, called GARP, on a dataset containing observation data for North American breeding birds. We also study how well maxent performs as a function of the number of training examples and training time, analyze the use of regularization to avoid overfitting when the number of examples is small, and explore the interpretability of models constructed using maxent.
Separate effects of caffeine and dbcAMP on macaque sperm motility and interaction with the zona pellucida (1994)

Capacitation of macaque sperm with caffeine and dbcAMP is required for fertilization in vitro. This study determined the separate effects of caffeine and dbcAMP on sperm-zona pellucida binding and the acrosome reaction of zona bound sperm. Semen from 6 cynomolgus macaques was washed through 60% Percoll, resuspended, and washed with BWW media and incubated for 2.5 hr. Caffeine, dbcAMP (2 mM each), or both (1 mM each) were added to aliquots of the sperm suspensions. Immature macaque oocytes were placed into drops of sperm suspensions, coincubated with sperm for 30 sec, and either fixed immediately or removed to sperm-free media and incubated 1 hr before fixation. There were no significant differences between groups in the percentage of live, acrosome-reacted sperm in suspension. Treatment with caffeine and dbcAMP or with caffeine alone, significantly increased the number of sperm bound to each zona pellucida (96 +/- 16 and 81 +/- 17, respectively) compared to control and dbcAMP treatment (15 +/- 4 and 28 +/- 13). However, treatment with dbcAMP, alone and with caffeine, resulted in a higher percentage of acrosome-reacted sperm on the zona (15.2 +/- 2.1 and 9.0 +/- 0.6) than control or caffeine treatment (3.0 +/- 1.4 and 2.4 +/- 0.5). Effects on sperm motility consistent with hyperactivation were detected only when both caffeine and dbcAMP were present. Although both caffeine and dbcAMP are presumed to increase or to produce the same effect as increased intracellular cAMP levels, these compounds have different effects on the ability of sperm to bind to the zona and to undergo the acrosome reaction.
Introduction to the cellular and molecular biology of cancer (1986)

L M Franks: What is cancer? I R Hart: The spread of tumours Melvyn F Greaves: Biology of human leukaemia M C Pike: Epidemiology of cancer W F Bodmer: Inherited susceptibility to cancer Beverley E Griffin: Structure of DNA and its relationship to carcinogenesis Caroline Wigley: Chemical carcinogenesis and precancer G E Adams: Radiation carcinogenesis J A Wyke: Viruses and cancer Natalie M Teich: Oncogenes and cancer D Sheer: Chromosomes and cancer M D Waterfield: The role of growth factors in cancer W I P Mainwaring: Hormones and cancer J M Polak & S R Bloom: The neuroendocrine system and its tumours Peter Beverley: Immunology of cancer I S Fentiman: The local treatment of cancer J S Malpas: Chemotherapy Edward J Wawrzynczak & Philip F Thorpe: Monoclonal antibodies and therapy Robin A Weiss: Some conclusions and prospects.
Selective Cleavage of AAVS1 Substrates by the Adeno-Associated Virus Type 2 Rep68 Protein Is Dependent on Topological and Sequence Constraints (2000)

The adeno-associated virus type 2 (AAV-2) Rep78 and Rep68 proteins are required for replication of the virus as well as its site-specific integration into a unique site, called AAVS1, of human chromosome 19. Rep78 and Rep68 initiate replication by binding to a Rep binding site (RBS) contained in the AAV-2 inverted terminal repeats (ITRs) and then specifically nicking at a nearby site called the terminal resolution site (trs). Similarly, Rep78 and Rep68 are postulated to trigger the integration process by binding and nicking RBS and trs homologues present in AAVS1. However, Rep78 and Rep68 cleave in vitro AAVS1 duplex-linear substrates much less efficiently than hairpinned ITRs. In this study, we show that the AAV-2 Rep68 endonuclease activity is affected by the topology of the substrates in that it efficiently cleaves in vitro in a site- and strand-specific manner the AAVS1 trs only if this sequence is in a supercoiled (SC) conformation. DNA sequence mutagenesis in the context of SC templates allowed us to elucidate for the first time the AAVS1 trs sequence and position requirements for Rep68-mediated cleavage. Interestingly, Rep68 did not cleave SC templates containing RBS from other sites of the human genome. These findings have intriguing implications for AAV-2 site-specific integration in vivo.