gebhart/patrepeval huggingface dataset:
Absolute position measurement using pseudo-random binary encoding (1998)

This paper will present a non-traditional encoding method which represents a more efficient alternative to absolute position measurement applications. The new method is based on the properties of pseudo-random binary sequences and has the notable advantage of requiring only one bit of code per quantization interval. This advantage makes absolute position measurement more accessible for very high resolution applications.
A Chip-Based Biosensor for the Functional Analysis of Single Ion Channels (2000)

Stabile elektrische Abdichtungen („Giga-seals“) wurden zwischen mikrostrukturierten Silicium-Chips (1) und elektrophoretisch positionierten Riesenvesikeln (2) erhalten. Das geringe Hintergrundrauschen (im Mittel <80 fA) der resultierenden planaren Lipiddoppelschicht (3) ermöglicht die Aufzeichnung einzelner Ionenkanalereignisse.
Does oxidative damage to DNA increase with age? (2001)

The levels of 8-oxo-2-deoxyguanosine (oxo8dG) in DNA isolated from tissues of rodents (male F344 rats, male B6D2F1 mice, male C57BL/6 mice, and female C57BL/6 mice) of various ages were measured using sodium iodide to prevent oxidative damage to DNA during DNA isolation. Oxo8dG was measured in nuclear DNA (nDNA) isolated from liver, heart, brain, kidney, skeletal muscle, and spleen and in mitochondrial DNA (mtDNA) isolated from liver. We observed a significant increase in oxo8dG levels in nDNA with age in all tissues and strains of rodents studied. The age-related increase in oxo8dG in nDNA from old mice was shown not to the result of the tissue's reduced ability to remove the oxo8dG lesion. Rather, the increase in oxo8dG levels appears to arise from an age-related increase in the sensitivity of these tissues to oxidative stress. We also observed an age-related increase in oxo8dG in mtDNA isolated from the livers of the rats and mice. Dietary restriction, which is known to retard aging and increase the lifespan of rodents, was shown to significantly reduce the age-related accumulation of oxo8dG levels in nDNA in all tissues of male B6D23F1 mice and in most tissues of male F344 rats. Our study also showed that dietary restriction prevented the age-related increase in oxo8dG levels in mtDNA isolated from the livers of both rats and mice.
Catalytic hydroboration by an imido-hydrido complex of Mo(iv) (2011)

The imido-hydrido complex (ArN)Mo(H)(Cl)(PMe(3))(3) catalyses a variety of hydroboration reactions, including the first example of catalytic addition of HBCat to nitriles to form the bis(borylated) amines RCH(2)N(BCat)(2). The latter species easily undergoes chemoselective coupling with aldehydes R'C(O)H to yield imines RCH(2)N=C(H)R'.
Sequential Element Design With Built-In Soft Error Resilience (2006)

This paper presents a built-in soft error resilience (BISER) technique for correcting radiation-induced soft errors in latches and flip-flops. The presented error-correcting latch and flip-flop designs are power efficient, introduce minimal speed penalty, and employ reuse of on-chip scan design-for-testability and design-for-debug resources to minimize area overheads. Circuit simulations using a sub-90-nm technology show that the presented designs achieve more than a 20-fold reduction in cell-level soft error rate (SER). Fault injection experiments conducted on a microprocessor model further demonstrate that chip-level SER improvement is tunable by selective placement of the presented error-correcting designs. When coupled with error correction code to protect in-pipeline memories, the BISER flip-flop design improves chip-level SER by 10 times over an unprotected pipeline with the flip-flops contributing an extra 7-10.5% in power. When only soft errors in flips-flops are considered, the BISER technique improves chip-level SER by 10 times with an increased power of 10.3%. The error correction mechanism is configurable (i.e., can be turned on or off) which enables the use of the presented techniques for designs that can target multiple applications with a wide range of reliability requirements
Oncogenomic analysis of mycosis fungoides reveals major differences with Sézary syndrome (2008)

Mycosis fungoides (MF), the most common cutaneous T-cell lymphoma, is a malignancy of mature, skin-homing T cells. Sézary syndrome (Sz) is often considered to represent a leukemic phase of MF. In this study, the pattern of numerical chromosomal alterations in MF tumor samples was defined using array-based comparative genomic hybridization (CGH); simultaneously, gene expression was analyzed using microarrays. Highly recurrent chromosomal alterations in MF include gain of 7q36, 7q21-7q22 and loss of 5q13 and 9p21. The pattern characteristic of MF differs markedly from chromosomal alterations observed in Sz. Integration of data from array-based CGH and gene-expression analysis yielded several candidate genes with potential relevance in the pathogenesis of MF. We confirmed that the FASTK and SKAP1 genes, residing in loci with recurrent gain, demonstrated increased expression. The RB1 and DLEU1 tumor suppressor genes showed diminished expression associated with loss. In addition, it was found that the presence of chromosomal alterations on 9p21, 8q24, and 1q21-1q22 was associated with poor prognosis in patients with MF. This study provides novel insight into genetic alterations underlying MF. Furthermore, our analysis uncovered genomic differences between MF and Sz, which suggest that the molecular pathogenesis and therefore therapeutic requirements of these cutaneous T-cell lymphomas may be distinct.
Cortistatin A is a High‐Affinity Ligand of Protein Kinases ROCK, CDK8, and CDK11 (2009)

Antiproliferative alkaloid: Cortistatin A is a high-affinity ligand for a small set of protein kinases including Rho-associated, coiled-coil-containing protein kinase (ROCK), cyclin-dependent kinase 8 (CDK8), and cyclin-dependent kinase 11 (CDK11). Models of cortistatin A bound to a crystallographic structure of ROCK (see picture) and a homology model of CDK8 are presented. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Determination of adeno-associated virus Rep68 and Rep78 binding sites by random sequence oligonucleotide selection (1995)

To further define the canonical binding site for the P5-promoted Rep proteins of the adeno-associated virus, a modified random oligonucleotide selection procedure was performed, using purified recombinant Rep protein. These results may explain the effects of Rep on cellular gene expression.
Meal‐stimulated gastric acid secretion and integrated gastric acidity in gastro‐oesophageal reflux disease (2003)

As post-prandial gastric acidity is increased in subjects with gastro-oesophageal reflux disease, it seems likely that increased gastric acidity is an important aetiological factor in this disease.
Stealth Polycyanoacrylate Nanoparticles as Tumor Necrosis Factor-.ALPHA. Carriers: Pharmacokinetics and Anti-tumor Effects. (2001)

The objective of this study was to investigate the pharmacokinetics and in vivo anti-tumor effect of recombinant human tumor necrosis factor-alpha (rHuTNF-alpha) encapsulated in poly(methoxypolyethyleneglycol cyanoacrylate-co-n-hexadecyl cyanoacrylate) (PEG-PHDCA) nanoparticles. Our experimental results showed that PEG-PHDCA nanoparticles could extend the half-life of rHuTNF-alpha to 7.42 h and obviously change the protein biodistribution in tissues, and in particular, increase accumulation of rHuTNF-alpha in tumor. Compared with PHDCA nanoparticles and free rHuTNF-alpha, PEG-PHDCA nanoparticles loaded with rHuTNF-alpha showed higher antitumor potency at the same dose, which might be related to its higher accumulation in tumor tissues and longer plasma circulation time. Therefore, PEG-PHDCA nanoparticles could be an effective carrier for rHuTNF-alpha.
Nucleotide sequence of constant and 3' untranslated regions of a kappa immunoglobulin light chain mRNA of a homozygous b4 rabbit. (1981)

A homozygous a2/a2 and b4/b4 rabbit has been hyperimmunized with Micrococcus lysodeikticus. Poly(A)-containing RNA has been isolated from the spleen and translated in vitro, and translation products have been analyzed by NaDodSO4/polyacrylamide gel electrophoresis. Double-stranded cDNA has been synthesized from poly(A)-containing RNA template and inserted in the Pst I endonuclease site of plasmid pBR322 by using the oligo(dC).oligo(dG) tailing procedure. Tetracycline-resistant ampicillin-sensitive clones containing cDNA complementary to a kappa light chain mRNA have been selected by differential screening and their ability to hybridize to a spleen mRNA having the same size as a mouse kappa light chain mRNA. Two clones, pRk-15 and pRk-32, have been selected to determine the nucleotide sequence of the constant and 3' untranslated regions of kappa light chain mRNA, by the Maxam and Gilbert partial degradation method. Comparison of homologous regions of mouse kappa chain mRNA and b4 rabbit kappa chain mRNA reveals 61% homology in the constant region and 59% homology in the 3' untranslated region.
Emerging Biomarkers of Acute Kidney Injury (2007)

As they represent tandem biomarkers, it is likely that the AKI panels will be useful for timing the initial insult and assessing the duration and severity of AKI. Based on the differential expression of the biomarkers, it is also likely that the AKI panels will distinguish between the various types and etiologies of AKI. It will be important in future studies to validate the sensitivity and specificity of these biomarker panels in clinical samples from large cohorts and from multiple clinical situations.
Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 Directly Regulates the Genes That Govern Programmed Cell Death and Secondary Wall Formation during Xylem Differentiation (2010)

Xylem consists of three types of cells: tracheary elements (TEs), parenchyma cells, and fiber cells. TE differentiation includes two essential processes, programmed cell death (PCD) and secondary cell wall formation. These two processes are tightly coupled. However, little is known about the molecular mechanisms underlying these processes. Here, we show that VASCULAR-RELATED NAC-DOMAIN6 (VND6), a master regulator of TEs, regulates some of the downstream genes involved in these processes in a coordinated manner. We first identified genes that are expressed downstream of VND6 but not downstream of SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1), a master regulator of xylem fiber cells, using transformed suspension culture cells in microarray experiments. We found that VND6 and SND1 governed distinct aspects of xylem formation, whereas they regulated a number of genes in common, specifically those related to secondary cell wall formation. Genes involved in TE-specific PCD were upregulated only by VND6. Moreover, we revealed that VND6 directly regulated genes that harbor a TE-specific cis-element, TERE, in their promoters. Thus, we found that VND6 is a direct regulator of genes related to PCD as well as to secondary wall formation.
Dipeptidyl-peptidase IV secreted by Aspergillus fumigatus, a fungus pathogenic to humans (1997)

A dipeptidyl-peptidase IV was purified from the culture medium of the human-pathogenic fungus Aspergillus fumigatus. The enzyme has an apparent molecular mass of 95 kDa and contained approximately 10 kDa of N-linked carbohydrate. This glycoprotein is antigenic and has all characteristics of the class IV dipeptidyl-peptidases: removal of Xaa-Pro and to a lesser extent Xaa-Ala dipeptides from the N termini of peptides, including bioactive peptides such as neuropeptide Y, [des-Arg1] bradykinin, and glucagon-like peptide 1, activity at neutral pH, and presence in the amino acid sequence of the Gly-X-Ser-X-Gly consensus motif of the serine-hydrolases and the putative catalytic triad (Ser613, Asp690, His725) of the dipeptidyl-peptidases. Moreover, the last 200 amino acids displayed 60 to 65% similarity with the other dipeptidyl-peptidases IV from rat, mouse, human, and yeast. However, unlike the other dipeptidyl-peptidases, the dipeptidyl-peptidase IV of A. fumigatus is a secreted enzyme with a cleavable signal peptide. Expression of a recombinant dipeptidyl-peptidase IV of A. fumigatus has been attained in the yeast Pichia pastoris.
Effect of microwave irradiation on antibody labeling efficiency when applied to ultrathin cryosections through fixed biological material (1998)

To study the effect of microwaves on immunolabeling, ultrathin cryosections or diluted antibodies were irradiated prior to antibody application, and gold labeling was quantified. In addition, affinity purified, polyclonal antibodies and protein A-gold were applied to ultrathin cryosections of aldehyde-fixed material in the presence and absence of microwaves. Amylase, a soluble protein secreted by pancreatic acinar cells, MHC class II, an integral membrane protein, and 3-(2,4-dinitroanilino)-3-amino-N-methyldipropylamine (DAMP), an exogenously added antigen, were localized with monospecific antibodies. Each was chosen for their contrasting subcellular characteristics. Results demonstrated that for some antigens, antibody labeling efficiency was quantitatively improved by microwave irradiation of sections prior to antibody application. Irradiation of diluted antibodies prior to their application also resulted in improved labeling. In contrast, the results obtained using rapid immunolabeling protocols in the presence of microwaves resulted in labeling levels similar to those obtained in the absence of microwaves. We conclude that microwave irradiation can improve the labeling efficiency of some antibodies. However, improvements in labeling density are dependent on the antigen under study and on variable irradiation times, unique to each antibody. This suggests that the routine use of microwaves to reduce incubation times may not be a viable alternative to bench protocols.
Transected dorsal column axons within the guinea pig spinal cord regenerate in the presence of an applied electric field (1986)

Using an implanted battery and electrodes, we have imposed a weak, steady electrical field across partially severed guinea pig spinal cords. We have analyzed regeneration of dorsal column axons in experimental animals and sham-treated controls at 50-60 days postinjury by anterograde filling of these axons with the intracellular marker horseradish peroxidase and by employing a marking device to identify precisely the original plane of transection (J. Comp. Neurol. 250: 157-167, '86). In response to electric field applications, axons grew into the glial scar, as far as the plane of transection in most experimental animals. In a few animals axons could be traced around the margins of the lesion (but never through it). Moreover, these fibers returned to their approximate positions within the rostral spinal cord before turning toward the brain. In sham-treated controls, ascending axons were found to terminate caudal to the glial scar, and rarely were any fibers found within the scar itself. Axons were never observed to cross into the rostral cord segment. These findings suggest that an imposed electrical field promotes growth of axons within the partially severed mammalian spinal cord, that a steady voltage gradient may be an environmental component necessary for axonal development and regeneration, and that some component(s) of the scar impede or deflect axonal growth and projection.
Prevention of arterial reocclusion after thrombolysis with recombinant lipoprotein-associated coagulation inhibitor. (1991)

Inhibition of the extrinsic pathway of coagulation with LACI prevents thrombotic arterial reocclusion after thrombolysis in vessels subjected to extensive vascular injury. Our results demonstrate that activation of the extrinsic pathway plays a critical role in thrombotic reocclusion and that LACI provides a highly targeted approach to facilitate sustained recanalization without directly inhibiting platelets.
A Novel Segmentation Algorithm for Volumetric Analysis of Macular Hole Boundaries Identified with Optical Coherence Tomography (2012)

The computerized segmentation algorithm enables rapid volumetric analysis of MH geometry and correlates with baseline and postoperative visual function. Further research is needed to better understand the algorithm's role in prognostication and clinical management.
Interconversion of two oxidized forms of taurine/α-ketoglutarate dioxygenase, a non-heme iron hydroxylase: Evidence for bicarbonate binding (2003)

Taurinealpha-ketoglutarate (alphaKG) dioxygenase, or TauD, is a mononuclear non-heme iron hydroxylase that couples the oxidative decarboxylation of alphaKG to the decomposition of taurine, forming sulfite and aminoacetaldehyde. Prior studies revealed that taurine-free TauD catalyzes an O(2)- and alphaKG-dependent self-hydroxylation reaction involving Tyr-73, yielding an Fe(III)-catecholate chromophore with a lambda(max) of 550 nm. Here, a chromophore (lambda(max) 720 nm) is described and shown to arise from O(2)-dependent self-hydroxylation of TauD in the absence of alphaKG, but requiring the product succinate. A similar chromophore rapidly develops with the alternative oxidant H(2)O(2). Resonance Raman spectra indicate that the approximately 700-nm chromophore also arises from an Fe(III)-catecholate species, and site-directed mutagenesis studies again demonstrate Tyr-73 involvement. The approximately 700-nm and 550-nm species are shown to interconvert by the addition or removal of bicarbonate, consistent with the alphaKG-derived CO(2) remaining tightly bound to the oxidized metal site as bicarbonate. The relevance of the metal-bound bicarbonate in TauD to reactions of other members of this enzyme family is discussed.
Cure of Burkitt's lymphoma in severe combined immunodeficiency mice by T cells, tetravalent CD3 x CD19 tandem diabody, and CD28 costimulation. (2000)

To increase the valency, stability, and therapeutic potential of bispecific antibodies, we have constructed a tetravalent tandem diabody (Tandab) that is specific to both human CD3 (T-cell antigen) and CD19 (B-cell marker; S. M. Kipriyanov et al., J. Mol. Biol., 293: 41-56, 1999). It was generated by the functional dimerization of a single chain molecule that contained four antibody variable domains (V(H) and V(L)) in an orientation that prevented intramolecular pairing. Compared with a previously constructed heterodimeric CD3 x CD19 diabody, the Tandab exhibited a higher apparent affinity to both CD3+ and CD19+ cells and longer blood retention when injected into mice. Biodistribution studies in mice bearing Burkitt's lymphoma xenografts demonstrated specific accumulation of the radioiodinated Tandab in a tumor site with tumor-to-blood ratios of 1.5, 8.1, and 13.3 at 3, 18, and 24 h, respectively. Treatment of severe combined immunodeficiency mice bearing established Burkitt's lymphoma (5 mm in diameter) with human peripheral blood lymphocytes, Tandab, and anti-CD28 MAbs resulted in the complete elimination of tumors in all of the animals within 10 days. In contrast, mice receiving human peripheral blood lymphocytes in combination with either the diabody alone or the diabody plus anti-CD28 MAbs showed only partial tumor regression. These data demonstrate that the CD3 x CD19 Tandab may be a promising tool for the immunotherapy of human B-cell leukemias and lymphomas.
A Small Molecule Microarray Platform To Select RNA Internal Loop−Ligand Interactions (2007)

Herein, we report the development of a microarray platform to select RNA motif-ligand interactions that allows simultaneous screening of both RNA and chemical space. We used this platform to identify the RNA internal loops that bind 6'- N-5-hexynoate kanamycin A ( 1). Selected internal loops that bind 1 were studied in detail and commonly display an adenine across from a cytosine independent of the size of the loop. Additional preferences are also observed. For 3 x 3 nucleotide loops, there is a preference for purines, and for 2 x 2 nucleotide loops there is a preference for pyrimidines neighbored by an adenine across from a cytosine. This technique has several advantageous features for selecting RNA motif-ligand interactions: (1) higher affinity RNA motif-ligand interactions are identified by harvesting bound RNAs from lower ligand loadings; (2) bound RNAs are harvested from the array via gel extraction, mitigating kinetic biases in selections; and (3) multiple selections are completed on a single array surface. To further demonstrate that multiple selections can be completed in parallel on the same array surface, we selected the RNA internal loops from a 4096-member RNA internal loop library that bound a four-member aminoglycoside library. These experiments probed 16,384 (4 aminoglycoside x 4096-member RNA library) interactions in a single experiment. These studies allow for parallel screening of both chemical and RNA space to improve our understanding of RNA-ligand interactions. This information may facilitate the rational and modular design of small molecules targeting RNA.
On the power of universal bases in sequencing by hybridization (1999)

Article Free Access Share on On the power of universal bases in sequencing by hybridization Authors: Franco P. Preparata Computer Science Department, Brown University, Box 1910, Providence, RI Computer Science Department, Brown University, Box 1910, Providence, RIView Profile , Alan M. Frieze Department of Mathematics, Carnegie-Mellon University, Pittsburgh PA Department of Mathematics, Carnegie-Mellon University, Pittsburgh PAView Profile , Eli Upfal Computer Science Department, Brown University, Box 1910, Providence, RI Computer Science Department, Brown University, Box 1910, Providence, RIView Profile Authors Info & Claims RECOMB '99: Proceedings of the third annual international conference on Computational molecular biologyApril 1999 Pages 295–301https://doi.org/10.1145/299432.299505Online:01 April 1999Publication History 12citation285DownloadsMetricsTotal Citations12Total Downloads285Last 12 Months1Last 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 SiteeReaderPDF
In vivo targeting of dendritic cells for activation of cellular immunity using vaccine carriers based on pH-responsive microparticles (2005)

Activating the immune system to trigger a specific response is a major challenge in vaccine development. In particular, activating sufficient cytotoxic T lymphocyte-mediated cellular immunity, which is crucial for the treatment of many diseases including cancer and AIDS, has proven to be especially challenging. In this study, antigens were encapsulated in acid-degradable polymeric particle carriers to cascade cytotoxic T lymphocyte activation. To target dendritic cells, the most potent antigen-presenting cells, the particle carriers, were further conjugated with monoclonal antibodies. A series of ex vivo and in vivo studies have shown increased receptor-mediated uptake of antibody-conjugated particles by dendritic cells as well as migration of particle-carrying dendritic cells to lymph nodes and stimulation of naïve T cells leading to enhanced cellular immune response as confirmed by specific cell lysis and IFN-gamma secretion.