gebhart/patrepeval huggingface dataset:
Selection of antibodies for intracellular function using a two-hybridin vivosystem (1999)

Expression of antibodies inside cells has been used successfully to ablate protein function. This finding suggests that the technology should have an impact on disease treatment and in functional genomics where proteins of unknown function are predicted from genomic sequences. A major hindrance is the paucity of antibodies that function in eukaryotic cells, presumably because the antibodies fold incorrectly in the cytoplasm. To overcome this problem, we have developed an in vivo assay for functional intracellular antibodies using a two-hybrid approach. In this assay, antibody, as single-chain Fv (scFv) linked to a transcriptional transactivation domain, can interact with a target antigen, linked to a LexA-DNA binding domain, and thereby activate a reporter gene. We find that several characterized antibodies can bind their target antigen in eukaryotic cells in this two-hybrid format, and we have been able to isolate intracellular binders from among sets of scFv that can bind antigen in vitro. Furthermore, we show a model selection in which a single scFv was isolated from a mixture of half a million clones, indicating that this is a robust procedure that should facilitate capture of antibody specificities from complex mixtures. The approach can provide the basis for de novo selection of intracellular scFv from libraries, such as those made from spleen RNA after immunization with antigen, for intracellular analysis of protein function based only on genomic or cDNA sequences.
Photoaffinity Labeling of Sialidase with a Biotin-Conjugated Phenylaminodiazirine Derivative of 2,3-Didehydro-2-deoxy-N-acetylneuraminic Acid (2008)

A biotin-conjugated photoactivatable phenylaminodiazirine derivative of 2,3-didehydro-2-deoxy-N-acetylneuraminic acid (DANA) was synthesized to identify sialidase. The free carboxylic group and N-acetyl substituent of sialic acid, which are important for recognition and enzymatic activity of sialidase, were conserved by the photolabeling compound as confirmed using analytical methods. The synthesized compound and DANA competitively inhibited starfish sialidase with a Ki value of 7.6 microM and 4.6 microM, respectively. Photo incorporation of the labeling compound to sialidase increased with irradiation time; 90% photo incorporation was achieved with more than 10-min irradiation, and labeling was completely inhibited by the addition of a competitive inhibitor. Starfish sialidase purified using high-performance gel filtration chromatography was subjected to photoaffinity labeling. A 50-kDa band was revealed to contain the sialidase active site by the photolabeling compound, and labeling was completely hindered in presence of the competitive inhibitor. Labeling specificity was ensured by the addition of the heat-deactivated standard protein chymotrypsinogen A to the reaction mixture.
A hybrid approach to nanoelectronics (2005)

The definition of features on the nanometre length scale (NLS) is impossible via conventional lithography, but can be done using extreme ultraviolet, synchrotron-radiation, or electron beam lithography. However, since these techniques are very expensive and still in their infancy, their exploitation in integrated circuit (IC) processing is still highly putative. Geometries on the NLS can however be produced with relative ease using the spacer patterning technique, i.e. transforming vertical features (like film thickness) in the vicinity of a step of a sacrificial layer into horizontal features. The ultimate length that can be produced in this way is controlled by the steepness of the step defining the sacrificial layer, the uniformity of the deposited or grown films, and the anisotropy of its etching. While useful for the preparation of a few devices with special needs, the above trick does not allow by itself the development of a nanotechnology where each layer useful for defining the circuit should be on the NLS and aligned on the underlying geometries with tolerances on the NLS. Setting up such a nanotechnology is a major problem which will involve the IC industry in the post-Roadmap era. Irrespective of the detailed structure of the basic constituents (molecules, supramolecular structures, clusters, etc), ICs with nanoscopic active elements can hardly be prepared without the ability to produce arrays of conductive strips with pitch on the NLS. This work is devoted to describing a scheme (essentially based on the existing microelectronic technology) for their production without the use of advanced lithography and how it can be arranged to host molecular devices.
Substrate Specificity of NovM:  Implications for Novobiocin Biosynthesis and Glycorandomization (2003)

[reaction: see text] In an effort to expand the scope of natural product in vitro glycorandomization (IVG), the substrate specificity of NovM was investigated. A test of four aglycon analogues and over 40 nucleotide sugars revealed NovM has a surprisingly stringent substrate specificity and provided only three new "unnatural" natural products. On the basis of the determined substrate specificity, an alternative to the sugar nucleotide biosynthetic dogma and a cautionary note for the general applicability of IVG are introduced.
Effects of Cilastatin on the Pharmacokinetics of a New Carbapenem, DA-1131, in Rats, Rabbits, and Dogs (1999)

DA-1131, a new carbapenem antibiotic, undergoes renal metabolism by renal dehydropeptidase I (DHP-I), located on the brush border of the proximal tubular cell. Species differences with regard to the effects of cilastatin, a renal DHP-I inhibitor, were investigated after a 1-min intravenous infusion of DA-1131, with or without cilastatin, to rats, rabbits, and dogs. After intravenous infusion, the nonrenal clearance (CL(NR)) of DA-1131 was significantly slower in rats (3.00 versus 8.01 ml/min/kg) and rabbits (2.41 versus 6.77 ml/min/kg) when the drug was coadministered with cilastatin; this could be due to the slower metabolism of DA-1131 by rat and rabbit kidney DHP-I. This indicated that renal metabolism of DA-1131 by renal DHP-I was inhibited by cilastatin. However, coadministration with cilastatin to dogs did not affect the CL(NR) of DA-1131.
Lactate Racemization as a Rescue Pathway for Supplying d -Lactate to the Cell Wall Biosynthesis Machinery in Lactobacillus plantarum (2005)

Lactobacillus plantarum is a lactic acid bacterium that produces d- and l-lactate using stereospecific NAD-dependent lactate dehydrogenases (LdhD and LdhL, respectively). However, reduction of glycolytic pyruvate by LdhD is not the only pathway for d-lactate production since a mutant defective in this activity still produces both lactate isomers (T. Ferain, J. N. Hobbs, Jr., J. Richardson, N. Bernard, D. Garmyn, P. Hols, N. E. Allen, and J. Delcour, J. Bacteriol. 178:5431-5437, 1996). Production of d-lactate in this species has been shown to be connected to cell wall biosynthesis through its incorporation as the last residue of the muramoyl-pentadepsipeptide peptidoglycan precursor. This particular feature leads to natural resistance to high concentrations of vancomycin. In the present study, we show that L. plantarum possesses two pathways for d-lactate production: the LdhD enzyme and a lactate racemase, whose expression requires l-lactate. We report the cloning of a six-gene operon, which is involved in lactate racemization activity and is positively regulated by l-lactate. Deletion of this operon in an L. plantarum strain that is devoid of LdhD activity leads to the exclusive production of l-lactate. As a consequence, peptidoglycan biosynthesis is affected, and growth of this mutant is d-lactate dependent. We also show that the growth defect can be partially restored by expression of the d-alanyl-d-alanine-forming Ddl ligase from Lactococcus lactis, or by supplementation with various d-2-hydroxy acids but not d-2-amino acids, leading to variable vancomycin resistance levels. This suggests that L. plantarum is unable to efficiently synthesize peptidoglycan precursors ending in d-alanine and that the cell wall biosynthesis machinery in this species is specifically dedicated to the production of peptidoglycan precursors ending in d-lactate. In this context, the lactate racemase could thus provide the bacterium with a rescue pathway for d-lactate production upon inactivation or inhibition of the LdhD enzyme.
Raman amplifiers for telecommunications (2002)

Raman amplifiers are being deployed in almost every new long-haul and ultralong-haul fiber-optic transmission systems, making them one of the first widely commercialized nonlinear optical devices in telecommunications. This paper reviews some of the technical reasons behind the wide-spread acceptance of Raman technology. Distributed Raman amplifiers improve the noise figure and reduce the nonlinear penalty of fiber systems, allowing for longer amplifier spans, higher bit rates, closer channel spacing, and operation near the zero-dispersion wavelength. Lumped or discrete Raman amplifiers are primarily used to increase the capacity of fiber-optic networks, opening up new wavelength windows for wavelength-division multiplexing such as the 1300 nm, 1400 nm, or short-wavelength S-band. As an example, using a cascade of S-band lumped amplifiers, a 20-channel, OC-192 system is shown that propagates over 867 km of standard, single-mode fiber. Raman amplifiers provide a simple single platform for long-haul and ultralong-haul amplifier needs and, therefore, should see a wide range of deployment in the next few years.
Neurofilament protein in cerebrospinal fluid: a potential marker of activity in multiple sclerosis (1998)

The neurofilament protein is a major structural protein of neurons and a marker for axonal damage. The concentrations of the light subunit of the neurofilament triplet protein (NFL) in CSF were significantly increased in patients with relapsing-remitting multiple sclerosis compared with healthy controls (p<0.001). Seventy eight per cent of patients with multiple sclerosis showed increased NFL concentrations. Significant correlations between the NFL concentration in CSF and clinical indices were discerned for disability, exacerbation rate, and time from the start of the previous exacerbation to the time of the lumbar puncture. The results suggest that axonal damage occurs during relapsing-remitting multiple sclerosis and that the damage contributes to disability and the appearance of clinical exacerbations. The concentration of NFL in CSF is a potential marker of disease activity in multiple sclerosis and might be useful in future clinical trials of multiple sclerosis.
Toll-like receptors and NOD-like receptors in rheumatic diseases (2009)

The past 10 years have seen the description of families of receptors that drive proinflammatory cytokine production in infection and tissue injury. Two major classes have been examined in the context of inflammatory joint disease--the Toll-like receptors (TLRs) and NOD-like receptors (NLRs). TLRs such as TLR2 and TLR4 are being implicated in the pathology of rheumatoid arthritis, ankylosing spondylitis, lyme arthritis and osteoarthritis. Nalp3 has been identified as a key NLR for IL-1beta production and has been shown to have a particular role in gout. These findings present new therapeutic opportunities, possibly allowing for the replacement of biologics with small molecule inhibitors.
Glioma, glutamate (SLC7A11) and seizures—a commentary (2017)

Glioma, a common type of adult primary brain tumor and also the most dreaded, often presents to the clinic with seizures. These seizures are usually difficult to control with the standard anti-epileptics. Some of the patients presenting with medically refractory epilepsy due to a low grade glioma, achieve seizure control by surgical resection but some remain symptomatic despite surgery. Excitability in the human CNS is predominantly mediated by glutamate and recent compelling evidence points to the role of glutamate in excitotoxic damage resulting in seizures as well as maintenance and invasion of malignant glioma (1). Furthermore, recent studies have shown that excitotoxicity favours glioma preservation, progression and invasion in cases of malignant glioma (2-4). For instance, necrosis in glioblastoma was reported to result due to glutamate excitotoxicity through inhibition of system XC- (SXC), which normally exchanges intracellular glutamate with extracellular cystine, causing deficient intracellular cystine or through change in calcium homeostasis eventually leading to cell death resulting from reactive oxygen species damage (5). Thus, targeting excitotoxicity in glioma patients not only helps in symptomatic management of the seizures but may, possibly, play a role in altering the underlying tumor pathogenesis.
Sequence-specific DNA recognition by the thyroid transcription factor-1 homeodomain (1994)

The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivatives of TTF-1HD indicate a precise correspondence of some of its amino acid residues with specific bases in its binding site, allowing a crude orientation of the TTF-1HD within the protein-DNA complex. TTF-1HD shows an overall geometry of interaction with DNA similar to that previously observed for Antennapedia class HDs, even though the binding specificities of these two types of HDs are distinct. We demonstrate that the crucial difference between the binding sites of Antennapedia class and TTF-1 HDs is in the motifs 5'-TAAT-3', recognized by Antennapedia, and 5'-CAAG-3', preferentially bound by TTF-1. Furthermore, the binding of wild type and mutants TTF-1 HD to oligonucleotides containing either 5'-TAAT-3' or 5'-CAAG-3' indicate that only in the presence of the latter motif the Gln50 in TTF-1 HD is utilized for DNA recognition. Since the Gln at position 50 is an essential determinant for DNA binding specificity for several other HDs that bind to 5'-TAAT-3' containing sequences, we suggest that utilization by different HDs of key residues may depend on the sequence context and probably follows a precise hierarchy of contacts.
An IC Piezoresistive Pressure Sensor for Biomedical Instrumentation (1973)

A thin-diaphragm piezoresistive pressure sensor for biomedical instrumentation has been developed using monolithic integratedcircuit (IC) techniques. The piezoresistive effect has been chosen for this device because it provides an observable resistance change that is a linear function of pressure and is observable at low stress levels. A diaphragm is used as a stress magnifying device; its magnification is proportional to the square of the ratio of the diaphragm diameter to its thickness. The pressure-induced stresses in the diaphragm are sensed by properly oriented piezoresistors interconnected to form a bridge.
Intranasal Verapamil in Allergen‐Induced Rhinitis (1983)

Twenty-six pollen-allergic subjects participated in a double-blind, placebo-controlled trial of the protective effect of the calcium antagonist, verapamil, on allergen-provoked nasal symptoms. Intranasal verapamil, 1 mg. had a weak protective effect in that "tickling score" was 22% lower (P less than 0.01) and the number of sneezes 29% lower (nonsignificant) after verapamil as compared with placebo pretreatment. There were no differences with regard to nasal blockage or discharge. It is concluded that the verapamil spray used, cannot be recommended for clinical trials, but that further investigations of other formulations of calcium antagonist are justified in order to analyse the potential role of this type of drugs in the treatment of allergic rhinitis.
Evaluation of the Key Odorants of Foods by Dilution Experiments, Aroma Models and Omission (2001)

The state of the art in aroma analysis is reviewed with emphasis on aroma-recombination studies using synthetic blends of odorants (aroma models) which have been prepared on the basis of analytical data. The model that matches the original aroma is the starting material for omission experiments which are performed to establish the odorants that actually contribute to the aroma. These experiments are discussed in detail for the aromas of two wine varieties, three olive oils of different provenance, French fries, boiled beef and coffee. The results indicate that odorants with higher odour activity values (OAV, the ratio of the concentration to the odour threshold) are frequently essential for the aroma. However, there are exceptions where odorants with high OAVs are suppressed in the aroma and compounds with lower OAVs are important contributors. These findings are discussed in the light of model experiments which have been reported in the literature to obtain an insight into the perceptual interactions of odorants in mixtures.
Complexities of Prostate-Cancer Risk (2008)

As men age, prostate epithelial cells are subjected to substantial stresses, and these stresses can damage DNA, thereby causing cellular transformation. The aging prostate gland acquires numerous foci of cancer cells that arise from distinct clonal transformation events.1 That most of these foci never develop into clinically detectable cancer is consistent with the frequent finding of prostate cancer during autopsies of asymptomatic men in whom the condition was never diagnosed.2 Susceptibility to prostate cancer has a clear heritable component: men are at an increased risk for the disease if they have a first-degree relative with prostate cancer. The more relatives . . .
Production of hydrogen by autothermal reforming of biogas (2017)

In this paper the results of the operation of a pilot-plant with a hydrogen output of 50 Nm³/h are discussed. This plant shows the possibility of distributed production of hydrogen for the powertrains based on hydrogen. The focus of the investigations is the long-term behavior of the novel Nickel-based catalyst. This includes experimental studies of the impact of the start-up sequence on the reforming performance after the necessary activation of the catalyst. Additionally the prospective demand of hydrogen requires an analysis of the start-up time of the plant. The focus was a short start-up time without harming the catalyst.
Effects of egg storage time on spread of hatch, chick quality, and chick juvenile growth (2003)

A total of 1,800 incubating eggs produced by a commercial flock of Cobb broiler breeders was used to determine the effects of storage duration (3 or 18 d) on spread of hatch and chick quality. Chick relative growth (RG) at the end of 7 d of rearing was also determined as a measure of the chick performance. Chick quality was defined to encompass several qualitative characteristics and scored according to their importance. Eggs stored for 3 d hatched earlier than those stored for 18 d (P < 0.05). Hatching was normally distributed in both categories of eggs, and the spread of hatch was not affected by storage time (P = 0.69). Storage duration of 18 d reduced the percentage of day-old chick with high quality as well as average chick quality score (P < 0.05). RG varied with length of egg storage, quality of day-old chick, and the incubation duration (P < 0.05). Eighteen-day storage of eggs not only resulted in longer incubation duration and lower quality score but also depressed RG. Chick quality as defined in this study was correlated to RG and storage time. It was concluded that day-old chick quality may be a relatively good indicator of broiler performance. The results suggest however that in order to improve performance prediction power of chick quality, it would be better to define it as a combination of several qualitative aspects of the day-old chick and the juvenile growth to 7 d.
Complete amino acid sequence and predicted membrane topology of phenobarbital-induced cytochrome P-450 (isozyme 2) from rabbit liver microsomes. (1983)

The complete amino acid sequence of phenobarbital-induced isozyme 2 of rabbit liver microsomal cytochrome P-450 (P-450LM2) is presented. The polypeptide consists of 491 residues with a calculated Mr of 55,755. The rabbit isozyme is 77% identical to the corresponding rat cytochrome, P-450b, as deduced from cDNA, with 96% of the hydrophobic, 88% of the anionic, and 83% of the cationic positions conserved. The secondary structure of isozyme 2 was predicted and a model was developed for the membrane topology of this cytochrome. Of the two highly conserved cysteinyl peptides in P-450LM2, P-450b, and bacterial P-450cam, we favor, on the basis of our model, the one nearer the NH2 terminus (Cys-152 in P-450LM2) as the source of the thiolate ligand to the heme iron atom. The recently reported sequence of the apparently identical protein [Heinemann, F. S. & Ozols, J. (1983) J. Biol. Chem. 258, 4195-4201] has two fewer residues and differs in 14 other amino acid assignments.
Regulation of CD40 function by its isoforms generated through alternative splicing (2001)

CD40 is a member of the tumor necrosis factor receptor superfamily. The interaction between CD40 and CD40 ligand (CD154) activates NF-kappa B, Jun N-terminal kinase, and Janus kinase/signal transducers and activators of transcription pathways and promotes B cell growth, differentiation, and survival as well as IL-12 production in macrophages and dendritic cells. We demonstrate here the existence of multiple isoforms of CD40 mRNA generated by alternative splicing and show that their expression is regulated differentially in activated macrophages and dendritic cells. Pre-CD40 RNA is spliced preferentially out to signal-transducible CD40 mRNA in the early stage of activation; half of the CD40 mRNA is replaced by the signal-nontransducible CD40 mRNAs in the later stages (24 h). Using IL-12 p40 gene expression as a reporter for CD40 signaling, we show that three of the alternative isoforms can disable signaling through CD40. The major alternative isoform lacks the membrane-associated endodomain and seems to reduce the amount of the signal-transducible form available on the cell surface. It would seem, therefore, that CD40 expression is controlled by posttranscriptional and posttranslational regulation through alternative splicing. Modulation of isoform expression may provide a mechanism by which cells regulate their susceptibility to CD40L signaling.
Erythromycin contracts rabbit colon myocytes via occupation of motilin receptors (1992)

Erythromycin stimulates gastroduodenal motility via action on motilin receptors. We evaluated erythromycin as a colonic muscle motilin agonist using in vitro rabbit colon studies. Isolated myocytes contracted to erythromycin with a half-maximal effective concentration of 2 pM and peak shortening of 22.4 +/- 2.5% at 1 nM, which was superimposable with the response to motilin. 125I-labeled motilin binding to colon muscle homogenates was saturable and specific with a dissociation constant (Kd) of 0.39 nM and maximal binding (Bmax) of 41 +/- 3 fmol/mg protein. Motilin displaced specifically bound 125I-motilin, with a Kd of 0.31 nM. Erythromycin displaced 125I-motilin but was less potent, with an inhibitory constant of 84.0 nM. Bmax values from displacement studies were similar to the Scatchard data. Motilin receptor protection from alkylation by N-ethylmaleimide preserved contraction to motilin and erythromycin but not acetylcholine or cholecystokinin, whereas protection with erythromycin preserved contraction to motilin but not other agonists. In conclusion, erythromycin binds to colon muscle motilin receptors present in densities similar to reported values for the upper gut. Furthermore, erythromycin contracts colonic myocytes via specific action on motilin receptors. Thus erythromycin may have colonic motor-stimulating properties by action on motilin receptors.