gebhart/patrepeval huggingface dataset:
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes (2001)

To investigate the occurrence of glycosylphosphatidylinositol (GPI) lipid anchor modification in various taxonomic ranges, potential substrate proteins have been searched for in completely sequenced genomes. We applied the big-pi predictor for the recognition of propeptide cleavage and anchor attachment sites with a new, generalized analytical form of the extreme-value distribution for evaluating false-positive prediction rates. (i) We find that GPI modification is present among lower and higher Eukaryota (approximately 0.5% of all proteins) but it seems absent in all eubacterial and three archaeobacterial species studied. Four other archaean genomes appear to encode such a fraction of substrate proteins (in the range of eukaryots) that they cannot be explained as false-positive predictions. This result supports the possible existence of GPI anchor modification in an archaean subgroup. (ii) The frequency of GPI-modified proteins on various chromosomes of a given eukaryotic species is different. (iii) Lists of potentially GPI-modified proteins in complete genomes with their predicted cleavage sites are available at http://mendel.imp.univie.ac.at/gpi/gpi_genomes.html. (iv) Orthologues of known transamidase subunits have been found only for EUKARYA: Inconsistencies in domain structure among homologues some of which may indicate sequencing errors are described. We present a refined model of the transamidase complex.
[Target groups for influenza vaccination]. (2007)

The ACIP has gradually expanded the target populations for routine influenza vaccination. The most notable change during past 10 years seems to be the recommendation for inclusion of all children aged 6-59 months and people in close contact with babies for active vaccination.
Specific inhibition of insulin receptor dephosphorylation by a synthetic dodecapeptide containing sulfotyrosyl residues as phosphotyrosyl mimetic. (1997)

We have synthesized a tris-sulfotyrosyl dodecapeptide (3S-peptide-I) that corresponds to the major autophosphorylation domain within the insulin receptor beta-subunit and showed that it potently inhibited insulin receptor dephosphorylation by protein tyrosine phosphatases (PTPases) in vitro. 3S-peptide-I also inhibited tyrosine dephosphorylation of a synthetic peptide by the recombinant PTPase PTP-1B, indicating that 3S-peptide-I interacts directly with PTPase, causing its inactivation. The peptide had no effect on the activity of serine/threonine phosphatases, PP-1 and PP-2A, or alkaline phosphatase. Furthermore, we found that the introduction of a N-stearyl derivative of 3S-peptide-I in CHO/HIRc cells caused a significant increase in insulin-stimulated phosphorylation of the insulin receptor. In contrast, ligand-stimulated phosphorylation of epidermal growth factor (EGF) receptor in CHO cells overexpressing EGF receptors was not affected by the presence of N-stearyl-3S-peptide-I. These data suggest that by inhibiting dephosphorylation of the insulin receptor in intact cells, 3S-peptide-I may specifically enhance insulin signalling.
Structure-Activity Relationships of KATP Channel Openers (2006)

Given their many physiological functions, K(ATP) channels represent promising drug targets. Sulfonylureas like glibenclamide block K(ATP) channels; they are used in the therapy of type 2 diabetes. Openers of K(ATP) channels (KCOs) e.g. relax smooth muscle and induce hypotension. KCOs are chemically heterogeneous and include as different classes as the benzopyrans, cyanoguanidines, thioformamides, thiadiazines and pyridyl nitrates. Examples for new chemical entities more recently developed as KCOs include cyclobutenediones, dihydropyridine related structures, and tertiary carbinols. Structure-activity relationships of the main chemical classes of KCOs are discussed.
On Genetically Determined Human Serum Cholinesterases (1976)

The existence of genetically determined human serum cholinesterase variants (actlcholine acyl-hydrolase; EC 3.1.1.8) has been recognized by the use of a short acting muscle relaxant, suxamethonium. This polymorphism is now explained by at least four alleles belonging to an autosomal locus Ch1 or E1 depending on the nomenclature. These are: the usual gene, the dibucaine-resistant gene, the fluoride-resistant gene and the silent gene. At present, the modes of transmission for the silent genes is confusing and lack proper understanding. Another variant, not an allele of the first group, is recognized by gel electrophoresis, belong to a second locus Ch2 or E2. Evidence has been presented that many more rare serum cholinesterase variants may exist. Besides these genetic variants, normal serum cholinesterase is known to exist in multiple molecular forms. The present article attempts to discuss the polymorphism of human cholinesterase in relation to their chemical and genetic characteristics and their possible function.
Deep gray matter structures in HIV infection: a proton MR spectroscopic study. (1996)

The findings suggest no NAA differences between groups, consistent with negligible neuron loss in the region of the brain that carries the heaviest HIV load. The trends toward increased Cho/Cr are consistent with histopathologic findings of infiltration of subcortical gray matter structures with foamy macrophages, microglia, and lymphocytes, or possibly with gliosis.
Three Conserved Transcriptional Repressor Domains Are a Defining Feature of the TIEG Subfamily of Sp1-like Zinc Finger Proteins (1999)

Sp1-like transcription factors are characterized by three highly homologous C-terminal zinc finger motifs that bind GC-rich sequences. These proteins behave as either activators or repressors and have begun to be classified into different subfamilies based upon the presence of conserved motifs outside the zinc finger domain. This classification predicts that different Sp1-like subfamilies share certain functional properties. TIEG1 and TIEG2 constitute a new subfamily of transforming growth factor-beta-inducible Sp1-like proteins whose zinc finger motifs also bind GC-rich sequences. However, regions outside of the DNA-binding domain that differ in structure from other Sp1-like family members remain poorly characterized. Here, we have used extensive mutagenesis and GAL4-based transcriptional assays to identify three repression domains within TIEG1 and TIEG2 that we call R1, R2, and R3. R1 is 10 amino acids, R2 is 12 amino acids, and R3 is approximately 80 amino acids long. None of these domains share homology with previously described transcriptional regulatory motifs, but they share strong sequence homology and are functionally conserved between TIEG1 and TIEG2. Together, these data demonstrate that TIEG proteins are capable of repressing transcription, define domains critical for this function, and further support the idea that different subfamilies of Sp1-like proteins have evolved to mediate distinct transcriptional functions.
An even wiring approach to the ball grid array package routing (2003)

An even-wiring router for the BGA package is presented to interconnect each I/O pad of a chip to a corresponding ball distributed on the substrate area. The major phases for the router consist of layer assignment, topological routing, and physical routing. Using this router, we can generate an even distribution of planar and any-angle wires to improve manufacturing yield. We have also conducted various testing examples to verify the efficiency of this router. Experiments show that the router produces very good results, far better than the manual design, thus it can be practically applied to VLSI packaging.
Smartkom: multimodal communication with a life- like character (2001)

SmartKom is a multimodal dialog system that combines speech, gesture, and mimics input and output.Spontaneous speech understanding is combined with the video-based recognition of natural gestures.One of the major scientific goals of SmartKom is to design new computational methods for the seamless integration and mutual disambiguation of multimodal input and output on a semantic and pragmatic level.SmartKom is based on the situated delegation-oriented dialog paradigm, in which the user delegates a task to a virtual communication assistant, visualized as a life-like character on a graphical display.We describe the SmartKom architecture, the use of an XML-based mark-up language for multimodal content, and some of the distinguishing features of the first fully operational SmartKom demonstrator.
Antibacterial Activity of Some Garcinia Benzophenone Derivatives against Methicillin-Resistant Staphylococcus aureus. (1996)

Benzophenone derivatives, garcinol (1) and isogarcinol (2) isolated from the pericarps of Garcinia purpurea (Guttiferae), and xanthochymol (3) and a mixture of isoxanthochymol (4) cycloxanthochymol (5) from the pericarps of G. subelliptica were evaluated for their antibacterial activity against methicillin-resistant Staphylococcus aureus. Among them, 3 showed the lowest minimum inhibitory concentration at 3.1-12.5 micrograms/ml. This concentration is nearly equal to that of the antibiotic, vancomycin.
Sampling of the Group Membership in RTP (2000)

In large multicast groups, the size of the group membership table maintained by RTP (Real Time Transport Protocol) participants may become unwieldy, particularly for embedded devices with limited memory and processing power. This document discusses mechanisms for sampling of this group membership table in order to reduce the memory requirements. Several mechanisms are proposed, and the performance of each is considered.
Speaker Diarization: A Review of Recent Research (2012)

Speaker diarization is the task of determining “who spoke when?” in an audio or video recording that contains an unknown amount of speech and also an unknown number of speakers. Initially, it was proposed as a research topic related to automatic speech recognition, where speaker diarization serves as an upstream processing step. Over recent years, however, speaker diarization has become an important key technology for many tasks, such as navigation, retrieval, or higher level inference on audio data. Accordingly, many important improvements in accuracy and robustness have been reported in journals and conferences in the area. The application domains, from broadcast news, to lectures and meetings, vary greatly and pose different problems, such as having access to multiple microphones and multimodal information or overlapping speech. The most recent review of existing technology dates back to 2006 and focuses on the broadcast news domain. In this paper, we review the current state-of-the-art, focusing on research developed since 2006 that relates predominantly to speaker diarization for conference meetings. Finally, we present an analysis of speaker diarization performance as reported through the NIST Rich Transcription evaluations on meeting data and identify important areas for future research.
Safety assessment of near infrared light emitting diodes for diffuse optical measurements (2004)

In this study, we demonstrate that the major risk source of the LED in direct contact with skin is the conducted heat of the LED semiconductor junction, which may cause serious skin burns. Adjusting operational parameters by amplitude modulating or time multiplexing the LED can keep the LED within safe temperature ranges.
Efficacy and Safety of Lisdexamfetamine for Treatment of Adults With Moderate to Severe Binge-Eating Disorder (2015)

clinicaltrials.gov Identifier: NCT01291173.
Adenovirus encoding vascular endothelial growth factor–D induces tissue-specific vascular patterns in vivo (2002)

The capacity of an adenovirus encoding the mature form of vascular endothelial growth factor (VEGF)-D, VEGF-D Delta N Delta C, to induce angiogenesis, lymphangiogenesis, or both was analyzed in 2 distinct in vivo models. We first demonstrated in vitro that VEGF-D Delta N Delta C encoded by the adenovirus (Ad-VEGF-D Delta N Delta C) is capable of inducing endothelial cell proliferation and migration and that the latter response is primarily mediated by VEGF receptor-2 (VEGFR-2). Second, we characterized a new in vivo model for assessing experimental angiogenesis, the rat cremaster muscle, which permits live videomicroscopy and quantitation of functional blood vessels. In this model, a proangiogenic effect of Ad-VEGF-D Delta N Delta C was evident as early as 5 days after injection. Immunohistochemical analysis of the cremaster muscle demonstrated that neovascularization induced by Ad-VEGF-D Delta N Delta C and by Ad-VEGF-A(165) (an adenovirus encoding the 165 isoform of VEGF-A) was composed primarily of laminin and VEGFR-2-positive vessels containing red blood cells, thus indicating a predominantly angiogenic response. In a skin model, Ad-VEGF-D Delta N Delta C induced angiogenesis and lymphangiogenesis, as indicated by staining with laminin, VEGFR-2, and VEGFR-3, whereas Ad-VEGF-A(165) stimulated the selective growth of blood vessels. These data suggest that the biologic effects of VEGF-D are tissue-specific and dependent on the abundance of blood vessels and lymphatics expressing the receptors for VEGF-D in a given tissue. The capacity of Ad-VEGF-D Delta N Delta C to induce endothelial cell proliferation, angiogenesis, and lymphangiogenesis demonstrates that its potential usefulness for the treatment of coronary artery disease, cerebral ischemia, peripheral vascular disease, restenosis, and tissue edema should be tested in preclinical models.
A mobile networking system based on Internet protocol (1994)

Users of portable computers would like to carry their laptops with them whenever they move from one place to another and yet maintain transparent network access through the wireless link. The existing set of network protocols do not meet this requirement since they were designed under the assumption of a stationary network topology in which hosts do not change their location over time. The authors' approach, which is based on the use of a natural model and an existing IP option, does not introduce any new protocol and achieves optimal routing. The solution is transparent to transport and higher layers, and does not require any changes to stationary hosts and routers. The model is natural, because the authors coordinate a collection of mobile hosts (MHs) as a new IP network. They route packets to the MHs by using a router. The router is special because once it receives a packet, it does special things to ensure its safe delivery to its destination (the MH). This special operation is invisible to existing hosts and routers, so all the routing difference due to movement of the hosts can be hidden and effected by mechanisms under the control of the special entities. The other part of the model, which is a very natural part of a physical wireless data communications system, is the transceiver (access point), which collects wireless packets from a MH for delivery to existing hosts along existing wired networks. This transceiver provides the reference point by which the location of the MH is known.
Alginate synthesis in Pseudomonas aeruginosa: environmental regulation of the algC promoter (1992)

The exopolysaccharide alginate is a major virulence factor of Pseudomonas aeruginosa strains that infect the lungs of cystic fibrosis patients. The synthesis of alginate is almost uniquely associated with the pathogenicity of P. aeruginosa within the environment of the cystic fibrosis lung. The gene algC is one of the essential alginate biosynthetic genes and codes for the enzyme phosphomannomutase. In this report, we present data on the transcriptional regulation of algC expression. The activity of the algC promoter is modulated by the response regulator, AlgR1, a member of the two-component signal transduction protein family, which also regulates other alginate-specific promoters. In both mucoid (alginate-positive) and nonmucoid (alginate-negative) P. aeruginosa strains, transcriptional activation of algC increased with the osmolarity of the culture medium. This osmolarity-induced activation was found to be dependent on AlgR1. AlgR1 was found to interact directly with the algC promoter. Deletion mapping, in conjunction with mobility shift assays, showed that AlgR1 specifically bound with two regions of algC upstream DNA. A fragment spanning nucleotide positions -378 to -73 showed strong specific binding, while a fragment located between positions -73 and +187 interacted relatively weakly with AlgR1. Phosphorylation of the AlgR1 protein resulted in the stimulation of its in vitro ability to bind to the algC promoter region (a fragment spanning nucleotides -378 to -73). Transcription from the algC promoter, which has significant homology with the RNA polymerase sigma-54 (RpoN) recognition sequence, decreased in an rpoN mutant of P. aeruginosa.
Targeting RET Receptor Tyrosine Kinase Activation in Cancer (2010)

After ligand binding induces dimerization, the RET receptor tyrosine kinase activates multiple signal transduction pathways. Constitutively activating mutations and chromosomal rearrangements are the primary oncogenic event in a significant number of medullary thyroid cancers (MTC) and papillary thyroid cancers (PTC), respectively. When specific germline mutations in RET are identified early, prophylactic thyroidectomy can be timed to remove at-risk tissue in patients with multiple endocrine neoplasia 2 (MEN2) syndromes who would otherwise develop MTC. Conventional therapy for progressive metastatic MTC is limited. Small-molecule tyrosine kinase inhibitors can target multiple kinases at nanomolar concentrations, including RET, and have shown efficacy against a variety of malignancies. Initial clinical evidence suggests that several of these inhibitors, including sorafenib, vandetanib, motesanib, sunitinib, and XL-184, may have some benefit in treating progressive MTC. Although initial success seen in these trials seems to be modest, it represents a major breakthrough in the treatment of patients with widespread metastatic MTC.
Design of CPU Cache Memories (1987)

We present an overview of the current issues in the design of CPU cache memories. Our stress is on those issues of greatest concern to cache designers and builders, including line size, associativity, real vs. virtual addressing, main memory update algorithm, split (data/instructions) cache vs. unified cache, cache consistency mechanisms, cache size and number of cache levels. Brief mention is made of other aspects of cache and S-unit design. The Fairchild CLIPPER(tm) is used as an example of modern cache memory design
Bioactivity and chemical characterisation of Lophostemon suaveolens – an endemic Australian Aboriginal traditional medicinal plant (2015)

Lophostemon suaveolens is a relatively unexplored endemic medicinal plant of Australia. Extracts of fresh leaves of L. suaveolens obtained from sequential extraction with n-hexane and dichloromethane exhibited antibacterial activity in the disc diffusion and MTT microdilution assays against Streptococcus pyogenes and methicillin sensitive and resistant strains of Staphylococcus aureus (minimum bactericidal concentration < 63 μg/mL). The dichloromethane extract and chromatographic fractions therein inhibited nitric oxide in RAW264.7 murine macrophages (IC50 3.7-11.6 μg/mL) and also PGE2 in 3T3 murine fibroblasts (IC50 2.8-19.7 μg/mL). The crude n-hexane, dichloromethane and water extracts of the leaves and chromatographic fractions from the dichloromethane extract also showed modest antioxidant activity in the ORAC assay. GC-MS analysis of the n-hexane fraction showed the presence of the antibacterial compounds aromadendrene, spathulenol, β-caryophyllene, α-humulene and α-pinene and the anti-inflammatory compounds β-caryophyllene and spathulenol. Fractionation of the dichloromethane extract led to the isolation of eucalyptin and the known anti-inflammatory compound betulinic acid.
α-Synuclein Aggregates Interfere with Parkin Solubility and Distribution (2008)

Parkinson disease (PD) belongs to a heterogeneous group of neurodegenerative disorders with movement alterations, cognitive impairment, and alpha-synuclein accumulation in cortical and subcortical regions. Jointly, these disorders are denominated Lewy body disease. Mutations in the parkin gene are the most common cause of familial parkinsonism, and a growing number of studies have shown that stress factors associated with sporadic PD promote parkin accumulation in the insoluble fraction. alpha-Synuclein and parkin accumulation and mutations in these genes have been associated with familial PD. To investigate whether alpha-synuclein accumulation might be involved in the pathogenesis of these disorders by interfering with parkin solubility, synuclein-transfected neuronal cells were transduced with lentiviral vectors expressing parkin. Challenging neurons with proteasome inhibitors or amyloid-beta resulted in accumulation of insoluble parkin and, to a lesser extent, alpha-tubulin. Similarly to neurons in the brains of patients with Lewy body disease, in co-transduced cells alpha-synuclein and parkin colocalized and co-immunoprecipitated. These effects resulted in decreased parkin and alpha-tubulin ubiquitination, accumulation of insoluble parkin, and cytoskeletal alterations with reduced neurite outgrowth. Taken together, accumulation of alpha-synuclein might contribute to the pathogenesis of PD and other Lewy body diseases by promoting alterations in parkin and tubulin solubility, which in turn might compromise neural function by damaging the neuronal cytoskeleton. These studies provide a new perspective on the potential nature of pathogenic alpha-synuclein and parkin interactions in Parkinson disease.
Travis Peak Core Permeability and Porosity Relationships at Reservoir Stress (1991)

Summary Relationships of permeability to porosity are shown from analyses of more than 2, 100 core plugs from nine wells in the Travis Peak, a low-permeability, tight-gas sandstone formation in northeast Texas. Effects of reservoir vs. ambient stress are shown for permeability, porosity, and the Klinkenberg factor. The relationship of brine permeability to gas permeability is also shown.
An immunoglobulin E‐reactive chimeric human immunoglobulin G1 anti‐idiotype inhibits basophil degranulation through cross‐linking of FcɛRI with FcγRIIb (2007)

The inhibition of basophil degranulation by the human IgG1 anti-idiotype 2G10 highlights the therapeutic potential of IgE-reactive IgG antibodies in restoring basophil integrity through recruitment of the inhibitory receptor FcgammaRIIb.
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes (2009)

Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several copy number variations (CNVs) that are associated with an increased risk of ASDs. Here we present the results from a whole-genome CNV study on a cohort of 859 ASD cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to comprehensively identify CNVs conferring susceptibility to ASDs. Positive findings were evaluated in an independent cohort of 1,336 ASD cases and 1,110 controls of European ancestry. Besides previously reported ASD candidate genes, such as NRXN1 (ref. 10) and CNTN4 (refs 11, 12), several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls (P = 9.5 x 10(-3)). Furthermore, CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls (P = 3.3 x 10(-3)). We also identified duplications 55 kilobases upstream of complementary DNA AK123120 (P = 3.6 x 10(-6)). Although these variants may be individually rare, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, indicating that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.