gebhart/patrepeval huggingface dataset:
Identification of cry1I- Type Genes from Bacillus thuringiensis Strains and Characterization of a Novel cry1I- Type Gene (2003)

A PCR-restriction fragment length polymorphism method for identification of cry1I-type genes from Bacillus thuringiensis was established by designing a pair of universal primers based on the conserved regions of the genes to amplify 1,548-bp cry1I-type gene fragments. Amplification products were digested with the Bsp119I and BanI enzymes, and four kinds of known cry1I-type genes were successfully identified. The results showed that cry1I-type genes appeared in 95 of 115 B. thuringiensis isolates and 7 of 13 standard strains. A novel cry1I-type gene was found in one standard strain and six isolates. The novel cry1I gene was cloned from B. thuringiensis isolate Btc007 and subcloned into vector pET-21b. Then it was overexpressed in Escherichia coli BL21(DE3). The expressed product was shown to be toxic to the diamondback moth (Plutella xylostella), Asian corn borer (Ostrinia furnacalis), and soybean pod borer (Leguminivora glycinivorella). However, it was not toxic to the cotton bollworm (Helicoverpa armigera), beet armyworm (Spodoptera exigua), or elm leaf beetle (Pyrrhalta aenescens) in bioassays. Subsequently, the Cry protein encoded by this novel cry gene was designated Cry1Ie1 by the B. thuringiensis delta-endotoxin nomenclature committee.
Digital PCR to Detect and Quantify Heteroresistance in Drug Resistant Mycobacterium tuberculosis (2013)

Drug resistance in Mycobacterium tuberculosis presents an enormous public health threat. It is typically defined as >1% of drug resistant colonies using the agar proportion method. Detecting small numbers of drug resistant Tb in a population, also known as heteroresistance, is challenging with current methodologies. Here we have utilized digital PCR to detect heteroresistance within M. tuberculosis populations with excellent accuracy versus the agar proportion method. We designed dual TaqMan-MGB probes to detect wild-type and mutant sequences of katG (315), rpoB (531), gyrA (94,95) and rrs (1401), genes that associate with resistance to isoniazid, rifampin, fluoroquinolone, and aminoglycoside respectively. We generated heteroresistant mixtures of susceptible and extensively drug resistant Tb, followed by DNA extraction and digital PCR. Digital PCR yielded a close approximation to agar proportion's percentages of resistant colonies, and yielded 100% concordance with agar proportion's susceptible/resistant results. Indeed, the digital PCR method was able to identify mutant sequence in mixtures containing as little as 1000∶1 susceptible:resistant Tb. By contrast, real-time PCR or PCR followed by Sanger sequencing were less sensitive and had little resolution to detect heteroresistance, requiring fully 1∶1 or 10∶1 susceptible:resistant ratios in order to detect resistance. Our assay can also work in sputum so long as sufficient quantities of Tb are present (>1000 cfu/ml). This work demonstrates the utility of digital PCR to detect and quantify heteroresistance in drug resistant Tb, which may be useful to inform treatment decisions faster than agar proportion.
Streptozotocin, an analog of N-acetylglucosamine, blocks the removal of O-GlcNAc from intracellular proteins. (1999)

Streptozotocin (STZ), an analog of N-acetylglucosamine (GlcNAc), is a specific toxin for the pancreatic beta cell. We found that treatment of rats with STZ results in an early beta-cell-specific increase in the level of intracellular protein modification by O-linked GlcNAc (O-GlcNAc). Using a model O-GlcNAc peptide based on the transcription factor Sp1, we show that treatment of cultured cells with STZ during peptide biosynthesis results in hyperglycosylation of the peptide as a result of the ability of STZ to specifically inhibit the activity of O-GlcNAc-selective N-acetyl-beta-D-glucosaminidase. Although this inhibitory activity of STZ probably can occur in all cells, we found, using in situ hybridization, that beta cells express very high levels of the mRNA encoding the enzyme responsible for cytoplasmic protein O-glycosylation, O-GlcNAc transferase (OGT). These findings suggest that the pancreatic beta cell is particularly sensitive to the toxicity of STZ because it expresses such high levels of OGT. When STZ blocks O-GlcNAc removal from intracellular proteins, the cell with the most rapid on-rate for O-GlcNAc, the beta cell, will experience the most rapid accumulation of this protein modification. Because we also show that the on-rate of O-GlcNAc is substrate driven in several cell types, we speculate that the beta cell, with its high level of OGT, may also respond to elevations of blood sugar with increased protein modification by O-GlcNAc. Thus, this proposed mechanism of STZ toxicity on the beta cell may result from an exaggeration of a heretofore unrecognized physiological response to glucose mediated through the high level of OGT in these cells.
Prediction of Postoperative Recurrence-Free Survival in Non–Small Cell Lung Cancer by Using an Internationally Validated Gene Expression Model (2011)

A 4-gene prognostic model incorporating the multivariate marker DBN1 exhibits potential clinical utility for risk stratification of stage I to III NSCLC patients.
Bacterial outer membranes as model systems (1987)

GENE AND GENE EXPRESSION: Transcriptional Control of Gene Expression: Osmoregulation of Porin Protein Synthesis Post-transcriptional Regulation of Gene Expression MEMBRANE PROTEINS: STRUCTURE AND FUNCTION: Export Localization of Escherichia Coli Envelope Proteins Three- Dimensional Structure of Membrane Proteins INTERACTION WITH OTHER SYSTEMS: Biosynthesis and Pharmacologic Properties of Escherichia Coli Lipid A The Structural Basis of Prokaryotic DNA Transfer Appendix Index.
[Activity and quality comparison of the engineered protein Staphylococcus aureus alpha-hemolysin purified with gel filtration chromatography and Ni-NTA]. (2009)

The alpha-hemolysin protein of Staphylococcus aureus, which was expressed in Escherichia coli BL21 (DE3) with recombinant pET32a(+)-alpha-HL plasmid, was purified with gel filtration chromatography (GFC) and Ni-NTA spin columns. The quality and biological characteristic were compared. First, the purified products were analyzed with SDS-PAGE, and the expected protein band was with a molecular mass of 53 kD. Second, protein concentration was determined by the method of Bradford, and the median hemolytic dose potency (HD50) was finally analyzed with rabbit erythrocyte. The protein purified with GFC was 0.337 mg/mL, its hemolysis activity was 1519 HU/mg, and hemolysin yield was 14.04%. Meanwhile, the protein purified with the Ni-NTA Spin Columns was 0.35 mg/mL, its hemolysis activity was 1463 HU/mg, and hemolysin yield was 17.5%, respectively. The results showed that there is no significant difference in the quality, hemolysis activity and yield of the recombinant proteins purified with Ni-NTA spin columns and GFC.
Adenoid cystic carcinoma: a third type of human salivary gland neoplasms characterized cytogenetically by reciprocal translocations. (1982)

Using G-banding technique, the chromosomes were studied in four consecutive preparations from cultured material from a human adenoid cystic carcinoma of the submandibular gland. The results indicated that the carcinoma had originated with a normal diploid stemline, and that reciprocal translocations played a predominant role in development of an abnormal stemline. The propensity of developing variant cells, as well as an abnormal stemline, characterized by various types of reciprocal translocations, was found to be a property shared by two other types of salivary gland neoplasms studied by banding techniques, namely the pleomorphic adenoma and the acinic cell tumour. The tissue of origin is suggested to be the crucial determinant responsible for this important cytogenetical similarity between different types of salivary gland tumours.
Perception-motivated high dynamic range video encoding (2004)

Due to rapid technological progress in high dynamic range (HDR) video capture and display, the efficient storage and transmission of such data is crucial for the completeness of any HDR imaging pipeline. We propose a new approach for inter-frame encoding of HDR video, which is embedded in the well-established MPEG-4 video compression standard. The key component of our technique is luminance quantization that is optimized for the contrast threshold perception in the human visual system. The quantization scheme requires only 10--11 bits to encode 12 orders of magnitude of visible luminance range and does not lead to perceivable contouring artifacts. Besides video encoding, the proposed quantization provides perceptually-optimized luminance sampling for fast implementation of any global tone mapping operator using a lookup table. To improve the quality of synthetic video sequences, we introduce a coding scheme for discrete cosine transform (DCT) blocks with high contrast. We demonstrate the capabilities of HDR video in a player, which enables decoding, tone mapping, and applying post-processing effects in real-time. The tone mapping algorithm as well as its parameters can be changed interactively while the video is playing. We can simulate post-processing effects such as glare, night vision, and motion blur, which appear very realistic due to the usage of HDR data.
NLRP4 Negatively Regulates Autophagic Processes through an Association with Beclin1 (2011)

Although more than 20 putative members have been assigned to the nucleotide-binding and oligomerization domain-like receptor (NLR) family, their physiological and biological roles, with the exception of the inflammasome, are not fully understood. In this article, we show that NLR members, such as NLRC4, NLRP3, NLRP4, and NLRP10 interact with Beclin1, an important regulator of autophagy, through their neuronal apoptosis inhibitory protein, MHC class II transcription activator, incompatibility locus protein from Podospora anserina, and telomerase-associated protein domain. Among such NLRs, NLRP4 had a strong affinity to the Beclin1 evolutionally conserved domain. Compromising NLRP4 via RNA interference resulted in upregulation of the autophagic process under physiological conditions and upon invasive bacterial infections, leading to enhancement of the autophagic bactericidal process of group A streptococcus. NLRP4 recruited to the subplasma membrane phagosomes containing group A streptococcus and transiently dissociated from Beclin1, suggesting that NLRP4 senses bacterial infection and permits the initiation of Beclin1-mediated autophagic responses. In addition to a role as a negative regulator of the autophagic process, NLRP4 physically associates with the class C vacuolar protein-sorting complex, thereby negatively regulating maturation of the autophagosome and endosome. Collectively, these results provide novel evidence that NLRP4, and possibly other members of the NLR family, plays a crucial role in biogenesis of the autophagosome and its maturation by the association with regulatory molecules, such as Beclin1 and the class C vacuolar protein-sorting complex.
Selection of Antisense Oligonucleotides on the Basis of Genomic Frequency of the Target Sequence (1994)

Antisense oligonucleotides (ASOs) are capable of blocking the expression of targeted genes and are potential antitumor and antiviral therapeutic agents. The specificity of ASO gene inhibition is compromised when homology to other sequences allows the selected ASO to bind to nontargeted mRNAs. To reduce this nonspecific activity, an ASO should target a sequence that is predicted to be unlikely to occur in other mRNAs. The probability of a sequence being unique can be predicted by determining the genomic frequency of short stretches of sequences contained within the target sequence. Two computer programs, OLIGOMER and HEXAGRAPH, were developed for this analysis. OLIGOMER was used to analyze the genomic frequencies of di-, tri-, and hexamers in more than 24 million nucleotides from 8 different genomes in GenBank. A mathematical model was developed that predicts the genomic frequency of longer oligomers on the basis of the observed frequencies of shorter oligomers. The second program, HEXAGRAPH, was used to graphically display the genomic frequency data of a selected target gene. The computational tools developed in this study may help to design more efficient ASOs by decreasing their nonspecific binding activity.
The Application of Stable Isotopes to Studies of Drug Bioavailability and Bioequivalence (1986)

The increased availability of chemical intermediates and automated instrumentation has resulted in expanded use of stable isotopes for bioavailability and bioequivalence studies in recent years. Initially, stable isotopes were confined to the labeling of mass internal standard compounds for gas chromatography/mass spectrometry. More recently, their in vivo use has expanded and proved to be a powerful pharmacologic tool. The lack of toxicity of stable isotopes, particularly deuterium and carbon-13, make them ideally suited for human studies. The primary advantage of the isotopic methods is that the drug can be administered concomitantly either by two routes (e.g., parenteral and oral) or in two formulations (e.g., solution and solid dosage). Thus, a single set of blood samples serves to describe the time course of the routes or formulations being compared. The concomitant administration reduces variability inherent in dual administration, the single assay for both forms further reduces variation, and the method minimizes both drug exposure and discomfort to the subject. In addition to single-dose administration, in which two routes or dosage forms are compared, the technique is well suited to "pulse" administration, wherein the kinetics of a single dose, during multiple or chronic dosing regimens, can be compared with single-dose kinetics.
Chondrogenic Differentiation of Bone Marrow-Derived Mesenchymal Stem Cells: Tips and Tricks (2011)

It is well known that adult cartilage lacks the ability to repair itself; this makes articular cartilage a very attractive target for tissue engineering. The majority of articular cartilage repair models attempt to deliver or recruit reparative cells to the site of injury. A number of efforts are directed to the characterization of progenitor cells and the understanding of the mechanisms involved in their chondrogenic differentiation. Our laboratory has focused on cartilage repair using mesenchymal stem cells and studied their differentiation into cartilage. Mesenchymal stem cells are attractive candidates for cartilage repair due to their osteogenic and chondrogenic potential, ease of harvest, and ease of expansion in culture. However, the need for chondrogenic differentiation is superposed on other technical issues associated with cartilage repair; this adds a level of complexity over using mature chondrocytes. This chapter will focus on the methods involved in the isolation and expansion of human mesenchymal stem cells, their differentiation along the chondrogenic lineage, and the qualitative and quantitative assessment of chondrogenic differentiation.
LIPID-TRANSFER PROTEINS IN PLANTS (1996)

Lipid-transfer proteins (LTP) are basic, 9-kDa proteins present in high amounts (as much as 4% of the total soluble proteinss) in higher plants. LTPs can enhance the in vitro transfer of phospholipids between membranes and can bind acyl chains. On the basis of these properties, LTPs were thought to participate in membrane biogenesis and regulation of the intracellular fatty acid pools. However, the isolation of several cDNAs and genes revealed the presence of a signal peptide indicating that LTPs could enter the secretory pathway. They were found to be secreted and located in the cell wall. Thus, novel roles were suggested for plant LTPs: participation in cutin formation, embryogenesis, defense reactions against phytopathogens, symbiosis, and the adaptation of plants to various environmental conditions. The validity of these suggestions needs to be determined, in the hope that they will elucidate the role of this puzzling family of plant proteins.
Outside-inside translocation of aminophospholipids in the human erythrocyte membrane is mediated by a specific enzyme (1986)

When human erythrocytes are incubated with spin-labeled analogues of sphingomyelin, phosphatidylcholine, phosphatidylserine, or phosphatidylethanolamine, with a short beta chain (C5) bearing a doxyl group at the fourth carbon position, the labeled lipids incorporate readily in the outer monolayer. The incorporation is followed in fresh erythrocytes by a selective inward diffusion of the amino derivatives. This observation led us to postulate the existence of a selective ATP-dependent system that would flip aminophospholipids from the outer to the inner monolayer [Seigneuret, M., & Devaux, P. F. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 3751-3755]. This study further examines the nature of this selective transport and demonstrates that it is mediated by a specific membrane protein. By measurement of the initial rate of transverse diffusion of spin-labeled lipids incorporated at various concentrations in the membrane outer leaflet of packed erythrocytes, apparent Km values were determined for the phosphatidylserine and phosphatidylethanolamine analogues. A ratio of approximately equal to 1/9.4 [corrected] was obtained (KmPS/KmPE). Using spin-labels bearing either a 14N or a 15N isotope, we have carried out competition experiments allowing us to measure simultaneously the transport of two different phospholipids. By this procedure, we show that phosphatidylserine and phosphatidylethanolamine compete for the same transport site but that phosphatidylserine has a higher affinity, in agreement with a lower apparent Km. On the other hand, the slow diffusion of the phosphatidylcholine or sphingomyelin analogues has no influence on the transport of phosphatidylserine or phosphatidylethanolamine. Experiments carried out in ghosts loaded with ATP enabled us to determine the activation energies for phosphatidylserine and phosphatidylcholine transverse diffusion.(ABSTRACT TRUNCATED AT 250 WORDS)
Measurement of carbon nanotube–polymer interfacial strength (2003)

The force required to separate a carbon nanotube from a solid polymer matrix has been measured by performing reproducible nanopullout experiments using atomic force microscopy. The separation stress is found to be remarkably high, indicating that carbon nanotubes are effective at reinforcing a polymer. These results imply that the polymer matrix in close vicinity of the carbon nanotube is able to withstand stresses that would otherwise cause considerable yield in a bulk polymer specimen.
Spontaneous and evoked synaptic rewiring in the neonatal neocortex (2006)

The local microcircuitry of the neocortex is structurally a tabula rasa, with the axon of each pyramidal neuron having numerous submicrometer appositions with the dendrites of all neighboring pyramidal neurons, but is functionally highly selective, with synapses formed onto only a small proportion of these targets. This design leaves a vast potential for the microcircuit to rewire without extensive axonal or dendritic growth. To examine whether rewiring does take place, we used multineuron patch-clamp recordings on 12- to 14-day-old rat neocortical slices and studied long-term changes in synaptic connectivity within clusters of neurons. We found pyramidal neurons spontaneously connecting and disconnecting from each other and that exciting the slice with glutamate greatly increases the number of new connections established. Evoked emergence of new synaptic connections requires action potential activity and activation of metabotropic glutamate receptor 5, but not NMDA receptor or group II or group III metabotropic glutamate receptor activation. We also found that it is the weaker connections that are selectively eliminated. These results provide direct evidence for spontaneous and evoked rewiring of the neocortical microcircuitry involving entire functional multisynaptic connections. We speculate that this form of microcircuit plasticity enables an evolution of the microcircuit connectivity by natural selection as a function of experience.
Emerging drugs for the treatment of anxiety (2015)

In the face of an ever-growing understanding of fear-related behavior, the field awaits the translation of this research into mechanistically novel treatments. Obstacles will be overcome through close collaboration between basic and clinical researchers with the goal of aligning valid endophenotypes of human anxiety disorders with improved animal models. Novel approaches are needed to move basic discoveries into new, more effective treatments for our patients.
Effect of protein and cell behavior on pattern-grafted thermoresponsive polymer (1998)

A thermoresponsive copolymer, poly(Nisopropylacrylamide-co-acrylic acid), was coupled with azidoaniline. The azidophenyl-derivatized copolymer was grafted in a specific pattern on a polystyrene matrix by photolithography. The surface micropattern appeared and disappeared interchangeably, as observed under a phase-contrast microscope, by varying the temperature between 10 degrees C and 37 degrees C. The copolymer-grafted polystyrene surface was hydrophobic at 37 degrees C and hydrophilic at 10 degrees C. Albumin and fibronectin adsorption on the matrix was investigated using the fluorescent-labeling method. Fibronectin adsorbed onto both the grafted and nongrafted regions, while albumin adsorbed more onto the nongrafted regions than the grafted regions. Protein adsorption did not affect surface wettability. Mouse fibroblast STO cells were cultured on tissue culture plates pattern-grafted with the thermoresponsive copolymer. Fibronectin adsorption enhanced cell spreading, while albumin reduced it. When the temperature was lowered, the cells selectively detached from the surface areas grafted with the thermoresponsive copolymer when cultured in serum-free medium; the cells partially detached from these areas when cultured in serum-containing medium. The effect of serum proteins on cell detachment was similar to that caused by a mixture of albumin and fibronectin. Albumin adsorption did not affect the detachment of cells, while fibronectin adsorption inhibited it. The results of the present study indicate that a pattern-grafted, thermoresponsive, azidophenyl-derivatized copolymer can effectively facilitate selective cell detachment under some conditions such as serum-free culture or preadsorption of albumin. The pattern-grafting technique will be useful for qualitative microscopic comparison of surfaces prepared differently on one chip under the same conditions.
An Introduction to Common Music (1997)

Common Music is an object-oriented music composition environment. It treats musical composition as an experimental process involving the description of sound and its higher-order structural relationships. Common Music provides an extensive compositional toolbox and a public interface through which a composer may modify and extend the system. Sound is rendered on demand, by traversing high-level structure, producing sound descriptions, and transforming these into a variety of control protocols for sound synthesis and display. Realization targets currently include MIDI, Csound, Common Lisp Music, Music Kit, C Mix, C Music, M4C, RT, Mix, and Common Music Notation.
Infliximab for Induction and Maintenance Therapy for Ulcerative Colitis (2005)

Patients with moderate-to-severe active ulcerative colitis treated with infliximab at weeks 0, 2, and 6 and every eight weeks thereafter were more likely to have a clinical response at weeks 8, 30, and 54 than were those receiving placebo. (ClinicalTrials.gov numbers, NCT00036439 and NCT00096655.)