gebhart/patrepeval huggingface dataset:
χ AND THE RecBC D ENZYME OF ESCHERICHIA COLI (1994)

The products of genes recB and recC are responsible for conjugal recombination and for the repair of chromosomal double chain breaks in Escherichia coli. The product of the recD gene, which combines with the RecB and RecC proteins to comprise the RecBCD enzyme, is not required for either recombination or repair. On the contrary, RecBCD enzyme is a potent exonuclease which inhibits recombination by destroying linear DNA. The RecD Ejection model supposes that RecBCD enzyme enters DNA at a double-chain end and travels destructively along the DNA until (typically) it encounters the recombination hotspot sequence chi. Chi then alters the RecBCD enzyme by weakening the affinity of the RecD subunit for the RecBC heterodimer. With the loss of the RecD subunit from the enzyme, the resulting protein, RecBC(D-), becomes deficient for exonuclease activity and proficient as a recombinagenic helicase. Thus, the RecD Ejection model proposes that chi participates in recombination by acting as a toggle to convert RecBCD (a powerful exonuclease) to RecBC(D-) (a recombinase). We review the properties of RecBCD and its cognate site chi, including recent results that support both the RecD Ejection model and the view that chi plays only an indirect role in recombination.
IL-7 surface-engineered lentiviral vectors promote survival and efficient gene transfer in resting primary T lymphocytes (2003)

Important gene therapy target cells such as resting human T cells are refractory to transduction with lentiviral vectors. Completion of reverse transcription, nuclear import, and subsequent integration of the lentiviral genome occur in these cells only if they have been activated. In T-cell-based gene therapy trials performed to date, cells have been activated via their cognate antigen receptor. To couple activation with gene transfer, we previously generated lentiviral vectors displaying an anti-CD3 scFv fragment that allowed up to 48% transduction of freshly isolated T cells. However, transduction of highly purified resting T cells with these anti-CD3-displaying lentiviral vectors was inefficient and shifted the T cells from the naive to the memory phenotype. Here, we describe interleukin-7 (IL-7)-displaying HIV-1-derived vectors. Like recombinant IL-7, these modified particles could promote the survival of primary T cells placed in culture without inducing a naive-to-memory phenotypic switch. Furthermore, a single exposure to the IL-7-displaying vectors resulted in efficient gene transfer in both resting memory adult T cells and naive cord blood T cells. With adult naive T cells, preactivation with recombinant IL-7 was necessary for efficient gene transfer. Altogether, these results suggest that IL-7-displaying vectors could constitute interesting tools for T-cell-targeted gene therapy.
ACM awards banquet 2000, vicariously (2000)

article ACM awards banquet 2000, vicariously Share on Author: Lynellen D. S. Perry View Profile Authors Info & Claims XRDS: Crossroads, The ACM Magazine for StudentsVolume 6Issue 5August 2000 - Late Summer Edition pp 9–eshttps://doi.org/10.1145/345107.345121Online:15 July 2000Publication History 0citation91DownloadsMetricsTotal Citations0Total Downloads91Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Lower bounds for orthogonal range searching: part II. The arithmetic model (1990)

Lower bounds on the complexity of orthogonal range searching in the static case are established. Specifically, we consider the following dominance search problem: Given a collection of n weighted points in d -space and a query point q , compute the cumulative weight of the points dominated (in all coordinates) by q . It is assumed that the weights are chosen in a commutative semigroup and that the query time measures only the number of arithmetic operations needed to compute the answer. It is proved that if m units of storage are available, then the query time is at least proportional to (log n /log(2 m / n )) d –*1 in both the worst and average cases. This lower bound is provably tight for m = Ω( n (log n ) d –1+ϵ) and any fixed ϵ &gt; 0. A lower bound of Ω( n /log log n ) d ) on the time required for executing n inserts and queries is also established. —Author's Abstract
Hydroxyanisole‐induced regression of the Harding‐Passey melanoma in mice (1977)

The drug p-hydroxyanisole (OHA) was found to inhibit the incorporation of 3H-thymidine in the Harding-Passey melanoma cells in culture. Because the cultured cells had lost some of their pigment-forming capacity, the enzyme tyrosinase was added to the culture. This greatly increased the sensitivity of the cells to OHA, strongly suggesting that cells producing the enzyme would be preferentially killed by the drug. An in-vivo study of the effect of OHA injected into tumour-bearing mice showed a beneficial effect, including increased survival time, reduction in tumour size and in many cases complete loss of tumour and no recurrence. An experiment with animals immunologically suppressed by radiation suggests that the effect is not an immunological one.
The Toxoplasma Micronemal Protein MIC4 Is an Adhesin Composed of Six Conserved Apple Domains (2001)

The initial stage of invasion by apicomplexan parasites involves the exocytosis of the micronemes-containing molecules that contribute to host cell attachment and penetration. MIC4 was previously described as a protein secreted by Toxoplasma gondii tachyzoites upon stimulation of micronemes exocytosis. We have microsequenced the mature protein, purified after discharge from micronemes and cloned the corresponding gene. The deduced amino acid sequence of MIC4 predicts a 61-kDa protein that contains 6 conserved apple domains. Apple domains are composed of six spacely conserved cysteine residues which form disulfide bridges and are also present in micronemal proteins from two closely related apicomplexan parasites, Sarcocystis muris and Eimeria species, and several mammalian serum proteins, including kallikrein. Here we show that MIC4 localizes in the micronemes of all the invasive forms of T. gondii, tachyzoites, bradyzoites, sporozoites, and merozoites. The protein is proteolytically processed both at the N and the C terminus only upon release from the organelle. MIC4 binds efficiently to host cells, and the adhesive motif maps in the most C-terminal apple domain.
The importance of being proline: the interaction of proline‐rich motifs in signaling proteins with their cognate domains (2000)

Acommon focus among molecular and cellular biologists is the identification of proteins that interact with each other. Yeast two-hybrid, cDNA expression library screening, and coimmunoprecipitation experiments are powerful methods for identifying novel proteins that bind to one's favorite protein for the purpose of learning more regarding its cellular function. These same techniques, coupled with truncation and mutagenesis experiments, have been used to define the region of interaction between pairs of proteins. One conclusion from this work is that many interactions occur over short regions, often less than 10 amino acids in length within one protein. For example, mapping studies and 3-dimensional analyses of antigen-antibody interactions have revealed that epitopes are typically 4-7 residues long (1). Other examples include protein-interaction modules, such as Src homology (SH) 2 and 3 domains, phosphotyrosine binding domains (PTB), postsynaptic density/disc-large/ZO1 (PDZ) domains, WW domains, Eps15 homology (EH) domains, and 14-3-3 proteins that typically recognize linear regions of 3-9 amino acids. Each of these domains has been the subject of recent reviews published elsewhere (2 3 4 5 6 7). Among the primary structures of many ligands for protein-protein interactions, the amino acid proline is critical. In particular, SH3, WW, and several new protein-interaction domains prefer ligand sequences that are proline-rich. In addition, even though ligands for EH domains and 14-3-3 domains are not proline-rich, they do include a single proline residue. This review highlights the analysis of those protein-protein interactions that involve proline residues, the biochemistry of proline, and current drug discovery efforts based on proline peptidomimetics.-Kay, B. K., Williamson, M. P., Sudol, M. The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains.
New Roles for Introns: Sites of Combinatorial Regulation of Ca2+- and Cyclic AMP-Dependent Gene Transcription (2001)

Because some proteins can facilitate cell division or the expression of many genes simultaneously, it comes as no surprise that the expression of very important gene products is a tightly controlled process. Although gene expression is often thought of in terms of complexes of transcription factors binding to promoter elements, some studies indicate that intronic DNA sequences may also regulate gene expression. Finkbeiner examines recent work by Schlegel and colleagues demonstrating that sequences within the first intron of the c-fos gene help to regulate Fos expression under different conditions.
Crystallization of Cyclic Polymers: Synthesis and Crystallization Behavior of High Molecular Weight Cyclic Poly(ε-caprolactone)s (2011)

High molecular weight poly(ε-caprolactone)s (PCL) were synthesized via zwitterionic polymerization of ε-caprolactone initiated with N-heterocyclic carbenes. Ring-opening polymerization of ε-caprolactone (1 M) with carbenes 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene (1) or 1,3,4,5-tetramethylimidazol-2-ylidene (3) affords cyclic PCL with molecular weights up to Mn = 114 000 g/mol. Crystallization of the cyclic PCL was investigated by synchrotron small-angle X-ray scattering experiments and differential scanning calorimetry. High molecular weight cyclic poly(ε-caprolactone) crystallizes with a similar lamellar thickness and long period spacing as linear poly(ε-caprolactone), but the crystallization of cyclic poly(ε-caprolactone) is faster than that of linear poly(ε-caprolactone) for molecular weights greater than 75 000 g/mol. These results imply that the polymer topology does not have a significant influence on the crystal structure or morphology but can have a significant influence on the rate of crystallization from the melt.
Immunochemical and biochemical evidence for distinct basement membrane heparan sulfate proteoglycans. (1993)

Two antigenically and structurally related heparan sulfate proteoglycans (HSPG), with masses of 200 and 350 kDa, have been isolated and characterized from bovine renal tubular basement membranes (BTBM) using DEAE-Sephacel, octyl-Sepharose CL-4B, and Propac PA-1 chromatography. Heparitinase treatment revealed core proteins of 145 and 125 kDa, with corresponding core proteins after trifluoromethanesulfonic acid treatment of 88 and 82 kDa, from the 200- and 350-kDa HSPGs, respectively. The separated HSPGs produced similar tryptic peptide maps, had similar amino acid compositions, and had similarly sized GAG chains. The 200-kDa HSPG had 2.1 mg of protein/mumol of hexuronic acid compared with 1.1 mg/mumol for the 350-kDa HSPG. Anti-BTBM HSPG monoclonal antibody (mAb A12) reacted with core proteins derived from the 200- and 350-kDa HSPGs, whereas anti-perlecan polyclonal and monoclonal antibodies did not bind to the BTBM HSPG core proteins described above but reacted with a 230-kDa core protein, which was nonreactive with mAb A12. Immunohistochemical studies of the kidney demonstrated differences in the distribution of BTBM HSPG and perlecan. Comparison of amino acid sequences from BTBM HSPG tryptic peptides with the sequence of perlecan revealed similarities but not extensive identity. Two tryptic peptides show homology to rat agrin, a basement membrane component of synaptic junctions. These data suggest that the two BTBM HSPGs are immunologically and structurally related and that differences in these molecules may arise from alternative splicing or posttranslational modifications. In addition, the two BTBM HSPGs are immunologically and structurally distinct from perlecan but may share homology with agrin.
Molecular Cloning and Characterization of the Mousetag7 Gene Encoding a Novel Cytokine (1998)

Cloning of the mouse tag7 gene encoding a novel cytokine is described. The Tag7 protein consists of 182 amino acids. Genomic organization of the tag7 gene and its promoter region remind those of the genes of the tumor necrosis factor locus, although the tag7 gene is not linked to this locus. The gene is located on chromosome 7 at the area that corresponds to band 7A3, which has genetic linkage with lupus-like disease in mouse models. tag7 transcription is essential for lymphoid organs. It is also detected in certain areas of lungs, brain, and intestine and in some tumors. Tag7 protein is detectable in both cell-associated and soluble forms. The soluble form of Tag7 triggers apoptosis in mouse L929 cells in vitro and does not involve NF-kappaB activation. The relationship between Tag7 and tumor necrosis factor family of ligands is discussed.
Amyloid P component is not present in the glomerular basement membrane in Alport-type hereditary nephritis. (1986)

Serum amyloid P component (SAP) is a normal plasma glycoprotein immunochemically indistinguishable from amyloid P, a glycoprotein found in all tissue amyloid deposits. SAP has also been shown to be a constituent of normal glomerular basement membrane (GBM). In this study the authors discovered a unique association between SAP and Goodpasture (GP) antigen. In those patients whose GBM lack GP antigen (those with Alport-type hereditary nephritis) SAP is also uniformly absent. Although the relationship between these two components is unknown, this association may provide clues to the abnormality of GBM in Alport-type hereditary nephritis.
<title>Tracking a head-mounted display in a room-sized environment with head-mounted cameras</title> (1990)

This paper presents our efforts to accurately track a Head-Mounted Display (HMD) in a large environment. We review our current benchtop prototype (introduced in {WCF9O]), then describe our plans for building the full-scale system. Both systems use an inside-oui optical tracking scheme, where lateraleffect photodiodes mounted on the user's helmet view flashing infrared beacons placed in the environment. Church's method uses the measured 2D image positions and the known 3D beacon locations to recover the 3D position and orientation of the helmet in real-time. We discuss the implementation and performance of the benchtop prototype. The full-scale system design includes ceiling panels that hold the infrared beacons and a new sensor arrangement of two photodiodes with holographic lenses. In the full-scale system, the user can walk almost anywhere under the grid of ceiling panels, making the working volume nearly as large as the room.
Design of a Quasi-Passive Parallel Leg Exoskeleton to Augment Load Carrying for Walking (2005)

Biomechanical experiments suggest that it may be possible to build a leg exoskeleton to reduce the metabolic cost of walking while carrying a load. A quasi-passive, leg exoskeleton is presented that is designed to assist the human in carrying a 75 lb. payload. The exoskeleton structure runs parallel to the legs, transferring payload forces to the ground. In an attempt to make the exoskeleton more efficient, passive hip and ankle springs are employed to store and release energy throughout the gait cycle. To reduce knee muscular effort, a variable damper is implemented at the knee to support body weight throughout early stance. In this thesis, the author hypothesizes that a quasi-passive leg exoskeleton of this design will improve metabolic walking economy for carrying a 75 lb. backpack compared with a leg exoskeleton without any elastic energy storage or variable-damping capability. He further anticipates that the quasi-passive leg exoskeleton will improve walking economy for carrying a 75 lb. backpack compared with unassisted loaded walking. To test these hypotheses, the rate of oxygen consumption is measured on one human test participant walking on a level surface at a self-selected speed. Pilot experimental data show that the quasi-passive exoskeleton increases the metabolic cost of carrying a 75 lb. backpack by 39% compared to carrying 75 lbs. without an exoskeleton. When the variable-damper knees are replaced by simple pin joints, the metabolic cost relative to unassisted load carrying decreases to 34%, suggesting that the dampening advantages of the damper knees did not compensate for their added mass. When the springs are removed from the aforementioned pin knee exoskeleton, the metabolic cost relative to unassisted load carrying increased to 83%. These results indicate that the implementation of springs is beneficial in exoskeleton design.
Nonenzymatic ligation of oligodeoxyribonucleotides on a duplex DNA template by triple-helix formation (1989)

We report that a double-stranded DNA template can direct the sequence-specific formation of a phosphodiester linkage between oligodeoxyribonucleotides in aqueous solution by juxtaposing the termini head-to-tail in a triple-helical complex (Figure 1). A triple-stranded complex can be formed when a pyrimidine oligodeoxynucleotide binds in the major groove of duplex DNA parallel to the purine Watson-Crick strand. In the complex, sequence specificity for the condensation of oligodeoxynucleotides is directed by Hoogsteen base pairing.
Real-Time Adaptive Image Compression (2017)

We present a machine learning-based approach to lossy image compression which outperforms all existing codecs, while running in real-time. Our algorithm typically produces files 2.5 times smaller than JPEG and JPEG 2000, 2 times smaller than WebP, and 1.7 times smaller than BPG on datasets of generic images across all quality levels. At the same time, our codec is designed to be lightweight and deployable: for example, it can encode or decode the Kodak dataset in around 10ms per image on GPU. Our architecture is an autoencoder featuring pyramidal analysis, an adaptive coding module, and regularization of the expected codelength. We also supplement our approach with adversarial training specialized towards use in a compression setting: this enables us to produce visually pleasing reconstructions for very low bitrates.
The clinical and pathological phenotype of C9ORF72 hexanucleotide repeat expansions (2012)

There is increasing evidence that frontotemporal dementia and amyotrophic lateral sclerosis are part of a disease continuum. Recently, a hexanucleotide repeat expansion in C9orf72 was identified as a major cause of both sporadic and familial frontotemporal dementia and amyotrophic lateral sclerosis. The aim of this study was to investigate clinical and neuropathological characteristics of hexanucleotide repeat expansions in C9orf72 in a large cohort of Dutch patients with frontotemporal dementia. Repeat expansions were successfully determined in a cohort of 353 patients with sporadic or familial frontotemporal dementia with or without amyotrophic lateral sclerosis, and 522 neurologically normal controls. Immunohistochemistry was performed in a series of 10 brains from patients carrying expanded repeats using a panel of antibodies. In addition, the presence of RNA containing GGGGCC repeats in paraffin-embedded sections of post-mortem brain tissue was investigated using fluorescence in situ hybridization with a locked nucleic acid probe targeting the GGGGCC repeat. Hexanucleotide repeat expansions in C9orf72 were found in 37 patients with familial (28.7%) and five with sporadic frontotemporal dementia (2.2%). The mean age at onset was 56.9 ± 8.3 years (range 39-76), and disease duration 7.6 ± 4.6 years (range 1-22). The clinical phenotype of these patients varied between the behavioural variant of frontotemporal dementia (n = 34) and primary progressive aphasia (n = 8), with concomitant amyotrophic lateral sclerosis in seven patients. Predominant temporal atrophy on neuroimaging was present in 13 of 32 patients. Pathological examination of the 10 brains from patients carrying expanded repeats revealed frontotemporal lobar degeneration with neuronal transactive response DNA binding protein-positive inclusions of variable type, size and morphology in all brains. Fluorescence in situ hybridization analysis of brain material from patients with the repeat expansion, a microtubule-associated protein tau or a progranulin mutation, and controls did not show RNA-positive inclusions specific for brains with the GGGGCC repeat expansion. The hexanucleotide repeat expansion in C9orf72 is an important cause of frontotemporal dementia with and without amyotrophic lateral sclerosis, and is sometimes associated with primary progressive aphasia. Neuropathological hallmarks include neuronal and glial inclusions, and dystrophic neurites containing transactive response DNA binding protein. Future studies are needed to explain the wide variation in clinical presentation.
Diagnosis influences response of cerebral near infrared spectroscopy to intracranial hypertension in children* (2009)

These data suggest that cerebral regional oxygen saturation is lower with intracranial hypertension. However, the relationship between cerebral regional oxygen saturation and intracranial pressure is strongly influenced by diagnosis.
Cyclodextrin chemistry. Selective modification of all primary hydroxyl groups of α‐ and β‐cyclodextrins (1978)

Abstract Two efficient methods are described for the selective modification of all six primary hydroxyl groups of α‐cyclodextrin (α‐CD, 1 1 ). One, using an indirect strategy, involves protection of all 18 hydroxyl functions as benzoate esters, followed by selective deprotection of the six primary alcohol groups. The other, using a direct strategy, involves selective activation of the primary hydroxyl groups via a bulky triphenylphosphonium salt, which is then substituted by azide anion as the reaction proceeds. A number of modified α‐cyclodextrin derivatives have been prepared and fully characterized, among which are: the useful intermediate α‐cyclodextrin‐dodeca (2, 3) benzoate ( 3 ); hexakis (6‐amino‐6‐deoxy)‐α‐cyclodextrin hexahydrochloride ( 7 ); hexakis (6‐amino‐6‐deoxy)‐dodeca (2, 3)‐ O ‐methyl‐α‐cyclodextrin hexahydrochloride ( 9 ), hexa (6)‐ O ‐methyl‐α‐cyclodextrin ( 13 ). The direct substitution is shown to be even more efficient for β‐cyclodextrin ( 16 ), giving the heptakis (6‐azido‐6‐deoxy)‐β‐CD‐tetradeca (2, 3)acetate ( 17 ), while the indirect strategy fails. The compounds are characterized by extensive use of 13 C‐ and 1 H‐NMR. spectroscopy. The steric and statistical problems of selective polysubstitution reactions for the cyclodextrins are discussed, and possible reasons for the observed differences in reactivity between α‐ and β‐cyclodextrins are examined. The dodecabenzoate 3 presents a very marked solvent effect on physical properties (IR. and NMR. spectra, optical rotation); the effects observed may be ascribed to an unusually strong intramolecular network of hydrogen bonds which severely distorts the α‐cyclodextrin ring and lowers the symmetry from six‐fold to three‐fold.