gebhart/patrepeval huggingface dataset:
Decision Analysis with SUPERTREE (1987)

Transcription activator-like effector nuclease (TALEN)-mediated genome editing is a powerful technique for analyzing gene functions in various cells and organisms. At target loci, TALENs can not only introduce short insertions and deletions, but also yield large deletions through the use of two TALEN pairs. Here, we report easy and efficient methods for enrichment of cells with TALEN-induced mutations and large deletions. First, we established the fluorescence-activated sorting of TALEN-induced deletions (FAST-id) system that enabled fluorescence-activated cell sorting-mediated enrichment of cells with TALEN-induced mutations. In the FAST-id system, either EGFP or mCherry and TALENs were co-expressed. Using dual fluorescence selection, both left and right TALEN-expressing cells were easily concentrated, resulting in enrichment of TALEN-mediated mutated cells. Next, to apply the FAST-id system to enrichment of cells with large deletions, we developed the fast unification of separate endonucleases (FUSE) method for assembly of two TALENs into a single expression vector. Using the FUSE method, we easily obtained a TALEN pair-expressing plasmid driven by a single promoter. By combining the FAST-id system and FUSE method, cells with large deletions were efficiently enriched. To the best of our knowledge, this is the first report of enrichment of cells with TALEN-induced large deletions.
The web in marketing : information cue usage in two commercial domains (2008)

\n\t\t\t\t\tThe study reported in this paper involves a comparison of Resnik &amp;amp; Stern&amp;rsquo;s (e.g., 1977) information cue usage in websites registered in two commercial domains of the World Wide Web (Web)&amp;mdash;.com (global domain managed by VeriSign) and .com.au (a country domain, auDomain, managed by the Australian Domain Name Administrator&amp;mdash;AUDA). The hypothesised higher use of information cues by digital marketers with .com registered domain names relative to .com.au registered domain names is not supported. Examination of the audited websites in the two-domain comparison confirms that the Web provides a richer marketing communication medium than other media analysed in a meta-analysis of 117 datasets by Abernethy &amp;amp; Franke (1996). The study is important given the acknowledged influence of advertising information on consumer responses to ads and the brands they relate, to both in traditional and new media (Aaker &amp;amp; Stayman, 1990; Brown &amp;amp; Stayman, 1992; Bruner &amp;amp; Kumar, 2000).&lt;br /&gt;\n\t\t\t\t
A novel method for the preparation of highly tritiated methyl iodide, and its use for the syntheses of methyl‐3H‐labelled diazepam and the methiodides of (+)‐ and (−)‐bicuculline (1978)

Abstract The syntheses of methyl‐ 3 H‐labelled diazepam (4) and the methiodides of (+)‐ and (−)‐bicuculline (5) labelled with tritium in their methyl groups are described. Also reported here is a novel method for the preparation of triti‐ated methyl iodide (3) serving as the radioactive precursor for the substances mentioned above.
Triplet Repeat Expansion Mutations: The Example of Fragile X Syndrome (1995)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
A learning architecture for control based on back-propagation neural networks (1988)

A neural-network-based control architecture has been developed which can autonomously learn to perform kinematic control of an unknown system and/or adapt to a system which changes over time. It can control continuous-valued system variables to arbitrary accuracy using a small number of neurons. It learns to control the system more accurately than an analytically calculated controller. It is fault-tolerant in the presence of a large number (e.g., 30%) of component failures. The architecture has been used to learn to control a simulated robot arm of initially unknown characteristics. The simulations run in near real time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Salivary proteomic and genomic biomarkers for primary Sjögren's syndrome (2007)

Our preliminary study has indicated that WS from patients with primary SS contains molecular signatures that reflect damaged glandular cells and an activated immune response in this autoimmune disease. These candidate proteomic and genomic biomarkers may improve the clinical detection of primary SS once they have been further validated. We also found that WS contains more informative proteins, peptides, and mRNA, as compared with gland-specific saliva, that can be used in generating candidate biomarkers for the detection of primary SS.
A complex of glycoproteins is associated with VpreB/lambda 5 surrogate light chain on the surface of mu heavy chain-negative early precursor B cell lines. (1993)

Monoclonal antibodies (mAbs) have been made specific for the pre-B cell-specific proteins VpreB and lambda 5 which together form the surrogate light (L) chain. mAbs specific for VpreB protein identified the 16-kD molecule associated on precursor B cell lines with lambda 5 protein as the product of the VpreB gene. Surrogate L chain was detectable even in the absence of mu heavy (H) chain on the surface of early precursor cell lines such as pro-B cell lines where all immunoglobulin (Ig) loci are in the germline configuration, as well as early pre-B cell lines where Ig H chain loci are DHJH rearranged in reading frame I or III, which does not allow the expression of a DHJHC mu protein. A complex of glycoproteins (200, 130, 105, and 65-35 kD) was identified as coprecipitated with the Vpreb/lamba 5 surrogate L chain in mu H chain-negative precursor B cell lines. The 130-kD protein was most strongly labeled with iodine and most consistently detected in noncovalent association with surrogate L chain. This protein turned out to be a N-linked glycoprotein with a 100-kD protein core and isoelectric point 5.8, indicating that it is distinct from CD43 and the BP-1/6C3 antigen. The surface deposition of the surrogate L chain in association with the newly identified glycoproteins suggests that the surrogate L chain may function as a receptor even before the association with mu H chain in early precursor B cells.
Chitin metabolism in insects: structure, function and regulation of chitin synthases and chitinases (2003)

Chitin is one of the most important biopolymers in nature. It is mainly produced by fungi, arthropods and nematodes. In insects, it functions as scaffold material, supporting the cuticles of the epidermis and trachea as well as the peritrophic matrices lining the gut epithelium. Insect growth and morphogenesis are strictly dependent on the capability to remodel chitin-containing structures. For this purpose, insects repeatedly produce chitin synthases and chitinolytic enzymes in different tissues. Coordination of chitin synthesis and its degradation requires strict control of the participating enzymes during development. In this review, we will summarize recent advances in understanding chitin synthesis and its degradation in insects.
Abcb11 Deficiency Induces Cholestasis Coupled to Impaired β-Fatty Acid Oxidation in Mice (2012)

Background: Defective ABCB11 causes severe progressive cholestatic liver disease from early infancy.
Extracellular Vesicles Isolated from the Brains of rTg4510 Mice Seed Tau Protein Aggregation in a Threshold-dependent Manner (2016)

The microtubule-associated protein tau has a critical role in Alzheimer disease and related tauopathies. There is accumulating evidence that tau aggregates spread and replicate in a prion-like manner, with the uptake of pathological tau seeds causing misfolding and aggregation of monomeric tau in recipient cells. Here we focused on small extracellular vesicles enriched for exosomes that were isolated from the brains of tau transgenic rTg4510 and control mice. We found that these extracellular vesicles contained tau, although the levels were significantly higher in transgenic mice that have a pronounced tau pathology. Tau in the vesicles was differentially phosphorylated, although to a lower degree than in the brain cells from which they were derived. Several phospho-epitopes (AT8, AT100, and AT180) thought to be critical for tau pathology were undetected in extracellular vesicles. Despite this, when assayed with FRET tau biosensor cells, extracellular vesicles derived from transgenic mice were capable of seeding tau aggregation in a threshold-dependent manner. We also observed that the dye used to label extracellular vesicle membranes was still present during nucleation and formation of tau inclusions, suggesting either a role for membranes in the seeding or in the process of degradation. Together, we clearly demonstrate that extracellular vesicles can transmit tau pathology. This indicates a role for extracellular vesicles in the transmission and spreading of tau pathology. The characteristics of tau in extracellular vesicles and the seeding threshold we identified may explain why tau pathology develops very slowly in neurodegenerative diseases such as Alzheimer disease.
Prospective evaluation of dexmedetomidine for noninvasive procedural sedation in children* (2005)

Dexmedetomidine provided effective sedation in children undergoing noninvasive procedures and represents an alternative sedative choice for this population.
Efficient Analysis, Design and Decoding of Low-Density Parity-Check Codes (2004)

This dissertation presents new methods for the analysis, design and decoding of low-density parity-check (LDPC) codes. We start by studying the simplest class of decoders: the binary message-passing (BMP) decoders. We show that the optimum BMP decoder must satisfy certain symmetry and isotropy conditions, and prove that Gallager’s Algorithm B is the optimum BMP algorithm. We use a generalization of extrinsic information transfer (EXIT) charts to formulate a linear program that leads to the design of highly efficient irreg-ular LDPC codes for the BMP decoder. We extend this approach to the design of irregular LDPC codes for the additive white Gaussian noise channel. We introduce a “semi-Gaussian” approximation that very accurately predicts the behaviour of the decoder and permits code design over a wider range of rates and code parameters than in previous approaches. We then study the EXIT chart properties of the highest rate LDPC code which guarantees a certain convergence behaviour. We also introduce and analyze gear-shift decoding in which the decoder is permitted to select the decoding rule from among a predefined set. We show that this flexibility can give rise to significant reductions in decoding complexity. Finally, we
Immunological relatedness of high mobility group chromosomal proteins from calf thymus. (1978)

The non-histone proteins HMG-1, HMG-2, HMG-3, HMB-8, HMG-14, and HMG-17 (Goodwin, G. H., SANDERS, C., and Johns, E. W. (1973) Eur. J. Biochem. 38, 14) were purified from calf thymus. The apparent molecular weights on polyacrylamide gels run in the presence of sodium dodecyl sulfate of the high mobility group (HMB) proteins were determined. Those for HBG-1 and HMG-2 agreed with the molecular weights determined by sedimentation; that for HMG-17 was anomalously high. Antibodies against HMG-1 were elicited in rabbits. The interaction between HMG-1 and anti-HBG-1 was measured by quantitative precipitation and by the microcomplement fixation technique. Quantitative microcomplement fixation assays revealed that the indices of dissimilarity between HMG-1 and HMG-2, HMG-3, HMG-8, HMG-14, and HMG-17 were 2.0, 1.0, 3.8, 10.0, and 6.1, respectively. These correspond to 6%, 0%, 12%, 20%, and 16% sequence difference between HMG-1 and the other five HMG proteins, although the immunological distance between HMG-1 and HMG-14 may be too large to allow a good correlation between the sequence and the immunological reaction. Antibodies to HMB-1 bind to chromatin purified from calf thymus. Therefore, we suggest that the in situ organization of HMG proteins in chromatin and chromosomes may be studied by serological techniques.
Serum Anti-carbonic Anhydrase Antibodies and Oxidant–Antioxidant Balance in Patients with Acute Anterior Uveitis (2013)

These results suggest that autoimmune responses against CA I and CA II and an altered serum oxidant-antioxidant balance may be involved in the pathogenesis of AAU.
SPECIAL FEATURE : TUTORIAL Mass Spectrometry and the Age of the Proteome (1998)

Mass spectrometry has become an important technique to correlate proteins to their genes. This has been achieved, in part, by improvements in ionization and mass analysis techniques concurrently with large-scale DNA sequencing of whole genomes. Genome sequence information has provided a convenient and powerful resource for protein identi‐cation using data produced by matrix-assisted laser desorption/ionization time-of-Night (MALDI/TOF) and tandem mass spectrometers. Both of these approaches have been applied to the identi‐cation of electrophoretically separated protein mixtures. New methods for the direct identi‐cation of proteins in mixtures using a combination of enzymatic proteolysis, liquid chromatographic separation, tandem mass spectrometry and computer algorithms which match peptide tandem mass spectra to sequences in the database are also emerging. This tutorial review describes the principles of ionization and mass analysis for peptide and protein analysis and then focuses on current methods employing MALDI and electrospray ionization for protein identi‐cation and sequencing. Database searching approaches to identify proteins using data produced by MALDI/TOF and tandem mass spectrometry are also discussed. 1998 John Wiley & Sons, Ltd. ( J. Mass Spectrom. Vol. 33 ,1 E19 (1998)
Mortality in Elderly Patients with Acute Renal Failure (1996)

In a retrospective study, we identified 55 elderly patients with acute renal failure (ARF) admitted to our hospital during an 8-year period from 1985 to 1993. Information about the etiology, complications, laboratory data, and treatment course were obtained from the clinical history. Of the 200 patients with ARF admitted to the hospital during this period, 28% were patients more than 60 years old (41 male and 14 female) with an average age of 68.5 +/- 7 years. The main causes of ARF were sepsis, volume depletion, low cardiac output, arterial hypotension, nephrotoxicity by antibiotics, and obstructive uropathy. The global mortality of elderly patients with ARF was 53%. The mortality rate of the different types of the ARF were: prerenal 35%, intrinsic 64% (oliguric 76%, nonoliguric 50%), and postrenal 40%. Mortality as a result of sepsis occurred in 18 patients (62%), by cardiovascular disease in 4 patients (13%), by acute respiratory failure in 2 patients (7%), and by other causes in 5 patients (18%). In the cases of sepsis, Pseudomonas was detected in 7 cases (39%), Escherichia coli in 2 cases (11%), Gram-negative nonspecific in 3 cases (17%), Klebsiella in 1 case (5%), and in 5 cases (16%), the hemoculture was negative. The patient survival rate was 47% (26 of 55 patients). Of these patients, 19 recovered their normal renal function (73%), but 7 patients remained with renal failure (27%). In conclusion, the global mortality in the elderly patients without considering the types of ARF was 53%. The oliguric form had the highest mortality rate with 76%. The main causes for mortality were sepsis with 62%, cardiovascular disease with 13%, and other causes 18%.
Treatment of Condyloma Acuminata by Autogenous Vaccine (1970)

The authors successfully have used an autogenous vaccine in two dozen treatment-resistant cases of this disease. Though such treatment had been described some decades ago, it had fallen into disuse.
9 ps Gate Delay Josephson OR Gate with Modified Variable Threshold Logic (1985)

A Josephson logic OR gate suitable for high speed logic circuits is proposed and tested. This gate has a structure modified from Variable Threshold Logic (VTL) to obtain large operating margin and small occupation area. The operating margin is calculated as ±19% for fan-out of 2, even with the critical current variation of ±20%. The circuit area is 40×60 µm 2 . A chain of 5-stage OR gates was fabricated. The gates had Josephson junctions of 4 µm and 7 µm diameter made with Pb-alloy technology. The minimum gate delay of 9 ps was measured using a Josephson sampler.
Microwave-assisted organic synthesis: one hundred reaction procedures (2006)

1. Preface 2. Interaction of microwaves with different materials 3. Microwave effect vs. thermal effect 3.1. Thermal activation during microwave irradiation 3.2. Non-thermal activation during microwave irradiation 4. Microwave equipment 4.1. Microwave generators 4.2. Transmission lines (waveguides) 4.3. Microwave applicators (cavities) 4.4. Microwave reactors 4.5. Temperature monitoring 4.6. Reaction vessels and glassware 5. Techniques for conducting chemical reactions under microwave irradiation 6. Safety precautions on the application of microwaves in laboratory 7. Reactions under microwave conditions 7.1. Reactions in homogenous media 7.2. Reactions of reagents supported on mineral supports 7.3. Solid-liquid solvent-free phase transfer catalysis (PTC) reactions 7.4. Reactions of neat reagents 7.5. Polymerization reactions 8. Concluding remarks
Molecular Targeting of Lymphatics for Therapy (2004)

The dysfunction or proliferation of lymphatic vessels (lymphangiogenesis) is linked to a number of pathological conditions including lymphedema and cancer. The recent discovery and characterisation of the lymphangiogenic growth factors vascular endothelial growth factor-C (VEGF-C) and VEGF-D and of their receptor on lymphatic endothelial cells, VEGFR-3, has provided an understanding of the molecular mechanisms controlling the growth of lymphatic vessels. In addition, other genes and protein markers have been identified with specificity for lymphatic endothelium that have enhanced the characterization and isolation of lymphatic endothelial cells. Our growing understanding of the molecules that control lymphangiogenesis allows us to design more specific drugs with which to manipulate the relevant signalling pathways. Modulating these pathways and other molecules with specificity to the lymphatic system could offer alternative treatments for a number of important clinical conditions.
Spatial management of data. (1977)

Thesis. 1977. M.S.--Massachusetts Institute of Technology. Dept. of Architecture.
ProteinN-Glycosylation along the Secretory Pathway:  Relationship to Organelle Topography and Function, Protein Quality Control, and Cell Interactions (2002)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProtein N-Glycosylation along the Secretory Pathway: Relationship to Organelle Topography and Function, Protein Quality Control, and Cell InteractionsJürgen RothView Author Information Division of Cell and Molecular Pathology, Department of Pathology, University of Zurich, CH-8091 Zurich, Switzerland Cite this: Chem. Rev. 2002, 102, 2, 285–304Publication Date (Web):January 22, 2002Publication History Received16 July 2001Published online22 January 2002Published inissue 1 February 2002https://pubs.acs.org/doi/10.1021/cr000423jhttps://doi.org/10.1021/cr000423jresearch-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views3741Altmetric-Citations328LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cancer,Cells,Oligosaccharides,Peptides and proteins,Quality control Get e-Alerts
The role of oxidative stress and NF‐κB activation in late diabetic complications (1999)

A common endpoint of hyperglycemia dependent cellular changes is the generation of reactive oxygen intermediates (ROIs) and the presence of elevated oxidative stress. Therefore, oxidative stress is supposed to play an important role in the development of late diabetic complications. Formation of advanced glycation end products (AGE's) due to elevated nonenzymatic glycation of proteins, lipids and nucleic acids is accompanied by oxidative, radical-generating reactions and thus represents a major source for oxygen free radicals under hyperglycemic conditions. Once formed, AGE's can influence cellular function by binding to several binding sites including the receptor for AGE's, RAGE. Binding of AGE's (and other ligands) to RAGE results in generation of intracellular oxidative stress and subsequent activation of the redox-sensitive transcription factor NF-kappaB in vitro and in vivo. Consistently, activation of NF-kappaB in diabetic patients correlates with the quality of glycemic control and can be reduced by treatment with the antioxidant alpha-lipoic acid. The development of techniques allowing for a tissue culture independent measurement of NF-kappaB activation in patients with diabetes mellitus gives insights into the molecular mechanisms linking diabetes mellitus and hyperglycemia with formation of advanced glycated endproducts and generation of oxidative stress finally resulting in oxidative stress mediated cellular activation.
Extracellular Renal Guanosine Cyclic 3′5′-Monophosphate Modulates Nitric Oxide– and Pressure-Induced Natriuresis (2007)

This study addresses the hypothesis that NO- and pressure-induced natriuresis are inhibited when guanosine cyclic 3',5'-monophosphate (cGMP) is prevented from being transported outside its renal synthesizing cells in vivo. Rats received a renal interstitial (RI) infusion of NO donor S-nitroso-N-acetylpenicillamine (SNAP) or SNAP+organic anion transporter inhibitor probenecid (PB) or SNAP+PB+cGMP. SNAP alone increased U(Na)V (P<0.05 at 1 hour and P<0.005 at 2 hours). In contrast, SNAP failed to increase U(Na)V when coinfused with PB, but cGMP coinfused with SNAP+probenecid restored the natriuretic response. SNAP alone increased RI cGMP (P<0.05) during the second experimental period. PB abolished the increase in RI cGMP in response to SNAP (P<0.01), but cGMP levels were restored by coinfusion with cGMP. PB also abolished SNAP-induced increases in fractional excretion of Na(+) (FE(Na)) and lithium (FE(Li)) (both P<0.01). PB also abolished the rise in RI cGMP and natriuresis induced by raising renal perfusion pressure (RPP) from 100 to 160 mm Hg in rats subjected to a standard pressure-natriuresis protocol and the natriuretic response was rescued by coinfusion with cGMP. RI administration of phosphodiesterase type V (PDE V) reduced both RIcGMP and U(Na)V in parallel (both P<0.01) without altering RIcAMP. The data demonstrate that export of cGMP from its renal synthesizing cells into the extracellular RI compartment is critical for the natriuretic action of NO donor SNAP or increased RPP and that RI cGMP controls basal Na(+) excretion. Extracellular cGMP modulates NO- and pressure-induced natriuresis.