gebhart/patrepeval huggingface dataset:
Current Advances in Molecular Imaging: Noninvasive In Vivo Bioluminescent and Fluorescent Optical Imaging in Cancer Research (2003)

Recently, there has been tremendous interest in developing techniques such as MRI, micro-CT, micro-PET, and SPECT to image function and processes in small animals. These technologies offer deep tissue penetration and high spatial resolution, but compared with noninvasive small animal optical imaging, these techniques are very costly and time consuming to implement. Optical imaging is cost-effective, rapid, easy to use, and can be readily applied to studying disease processes and biology in vivo. In vivo optical imaging is the result of a coalescence of technologies from chemistry, physics, and biology. The development of highly sensitive light detection systems has allowed biologists to use imaging in studying physiological processes. Over the last few decades, biochemists have also worked to isolate and further develop optical reporters such as GFP, luciferase, and cyanine dyes. This article reviews the common types of fluorescent and bioluminescent optical imaging, the typical system platforms and configurations, and the applications in the investigation of cancer biology.
Extraordinary magnetoresistance effect in a microstructured metal–semiconductor hybrid structure (2002)

We have fabricated hybrid structures consisting of a metallic thin film and of a microstructured two-dimensional electron system in an InAs heterostructure. The devices are found to exhibit a huge magnetoresistance (MR) effect in magnetic fields ⩽1 T. At low temperature, a value of ΔR/R=[R(B=1 T)−R(B=0)]/R(B=0) as high as 115 000% is measured. The value of ΔR/R has been studied as a function of the electron mobility, the electron density and the lateral width of the semiconductor. We find that the MR effect can be tailored by these different parameters and technological relevant devices can be realized.
Smart video surveillance: exploring the concept of multiscale spatiotemporal tracking (2005)

Situation awareness is the key to security. Awareness requires information that spans multiple scales of space and time. Smart video surveillance systems are capable of enhancing situational awareness across multiple scales of space and time. However, at the present time, the component technologies are evolving in isolation. To provide comprehensive, nonintrusive situation awareness, it is imperative to address the challenge of multiscale, spatiotemporal tracking. This article explores the concepts of multiscale spatiotemporal tracking through the use of real-time video analysis, active cameras, multiple object models, and long-term pattern analysis to provide comprehensive situation awareness.
The M1 form of tumor-associated macrophages in non-small cell lung cancer is positively associated with survival time (2010)

The M1 macrophage density in the tumor islets is an independent predictor of survival time in NSCLC patients.
Screening and evaluation of probiotics as a biocontrol agent against pathogenic Vibrios in marine aquaculture (2007)

In vivo study reveals that the marine bacterial species can be used as probionts against pathogenic Vibrios in shrimp larval culture practices.
Continuous in vitro Evolution of Bacteriophage RNA Polymerase Promoters (1994)

Rapid in vitro evolution of bacteriophage T7, T3, and SP6 RNA polymerase promoters was achieved by a method that allows continuous enrichment of DNAs that contain functional promoter elements. This method exploits the ability of a special class of nucleic acid molecules to replicate continuously in the presence of both a reverse transcriptase and a DNA-dependent RNA polymerase. Replication involves the synthesis of both RNA and cDNA intermediates. The cDNA strand contains an embedded promoter sequence, which becomes converted to a functional double-stranded promoter element, leading to the production of RNA transcripts. Synthetic cDNAs, including those that contain randomized promoter sequences, can be used to initiate the amplification cycle. However, only those cDNAs that contain functional promoter sequences are able to produce RNA transcripts. Furthermore, each RNA transcript encodes the RNA polymerase promoter sequence that was responsible for initiation of its own transcription. Thus, the population of amplifying molecules quickly becomes enriched for those templates that encode functional promoters. Optimal promoter sequences for phage T7, T3, and SP6 RNA polymerase were identified after a 2-h amplification reaction, initiated in each case with a pool of synthetic cDNAs encoding greater than 10(10) promoter sequence variants.
Acute Enteritis Due to Related Vibrio: First Positive Stool Cultures (1972)

Strains of the related vibrio were isolated from two patients with acute enteritis. The vibrios were isolated from blood and stool of one patient and from the stool of the other. The isolation technique consists of diluting the stools in nutrient broth, letting them settle for 1 hr, centrifuging the supernatant, and passing the surface liquid through a 0.65-μ Millipore filter. This filtrate (0.3 ml) is plated on a blood-thioglycolate-agar medium containing 25 international units of bacitracin, 10 international units of polymyxin B sulfate, 0.005 mg of novobiocin, and 0.05 mg of actidione per ml. Colonies are well developed after incubation for three days at 37 C in an atmosphere from which two-thirds of the volume of air has been replaced by a mixture of 95% nitrogen and 5% carbon dioxide. The results suggest that in all cases of diarrhea where standard coprocultures remain negative, stools should be checked for the presence of vibrio.
Control of Carbon Flux to Acetate Excretion During Growth of Escherichia coli in Batch and Continuous Cultures (1989)

During growth of Escherichia coli ML308 on pyruvate in a continuous culture (turbidostat) or batch culture, flux of carbon into the cells exceeds the amphibolic capacity of the central pathways. This is balanced by diversion of carbon flux to acetate excretion which in turn diminishes the efficiency of carbon conversion to biomass [g] dry wt (mol substrate)-1]. However, restriction of carbon supply in a chemostat diminishes flux to acetate excretion and at a dilution rate (D = mu) of 0.35 h-1 or less, no flux to acetate excretion was sustained thus permitting perfect balance between carbon input on the one hand, and the output to biosynthesis and energy generation on the other. This, in turn, improves the efficiency of carbon conversion to biomass. Inclusion of 3-bromopyruvate (an inhibitor of pyruvate dehydrogenase) at a concentration which diminishes growth rate (mu) to 0.35 h-1 or less also prevented flux to acetate excretion. Furthermore, in a family of fluoroacetate-resistant strains, excessive flux of pyruvate was balanced by diversion of carbon flux to lactate excretion rather than acetate and a higher growth rate (mu = 0.63 h-1) was sustained.
Purification and Characterization of a Rat Liver Enzyme That Hydrolyzes Valaciclovir, the L-Valyl Ester Prodrug of Acyclovir (1995)

Valaciclovir is an oral prodrug of the antiherpetic agent acyclovir. An enzyme that hydrolyzes valaciclovir to acyclovir, valaciclovir hydrolase (VACVase), was purified from rat liver and characterized. VACVase was a basic (pI 9.4) protein associated with mitochondria. It was monomeric and had a molecular mass of 29 kDa. Amino acid sequences of six VACVase peptides, including its NH2 terminus (13 amino acids) and accounting for approximately 20% of its complete sequence, were not found in the SwissProt protein data base. VACVase hydrolyzed other amino acid esters of acyclovir in addition to valaciclovir (kcat/Km = 58 mM-1 s-1), with a preference for the L-alanyl (kcat/Km = 226 mM-1 s-1) and L-methionyl (kcat/Km = 200 mM-1 s-1) esters. It did not hydrolyze other types of esters or numerous di- and tripeptides and aminoacyl-beta-naphthylamides. Hydrolysis of valaciclovir by VACVase was not inhibited by amastatin, antipain, aprotinin, bestatin, chymostatin, E-64, EDTA, ebelactone A, ebelactone B, elastatinal, leupeptin, pepstatin, or phosphoramidon. It was neither inhibited nor activated by Ca2+, Co2+, Mg2+, Mn2+, or Zn2+. Therefore, this enzyme is not a typical esterase or peptidase and, to our knowledge, it has not been described previously. Its physiological function is not known; however, it may play a significant role in the biotransformation of valaciclovir to acyclovir.
Acne: a review of immunologic and microbiologic factors (1999)

Acne vulgaris is a self-limiting skin disorder seen primarily in adolescents, whose aetiology appears to be multifactorial. The four main aetiological factors are hypercornification of the pilosebaceous duct, increased sebum production, colonization with Propionibacterium acnes, and subsequently the production of inflammation. Considerable investigation has addressed the immunologic reaction to extracellular products produced by the acne-causing organism, P acnes. The immunologic response involves both humoral and cell-mediated pathways. Further research should clarify the role of complement, cytotoxins, and neutrophils in this acne-forming response.
Self-assembled Monolayers for Biosensors (1997)

The use of self-assembled monolayers (SAMs) in various fields of research is rapidly growing. In particular, many biomedical fields apply SAMs as an interface-layer between a metal surface and a solution or vapour. This review summarises methods for the formation of SAMs upon the most commonly used materials and techniques used for monolayer characterisation. Emphasis will lie on uniform, mixed and functionalised monolayers applied for immobilisation of biological components including (oligo-)nucleotides, proteins, antibodies and receptors as well as polymers. The application of SAMs in today's research, together with some applications will be discussed.
Decreased production of interleukin-12 and other Th1-type cytokines in patients with recent-onset systemic lupus erythematosus (1998)

This study suggests that even early in the course of SLE, monocyte production of IL-10 is increased and that of IL-12 is decreased. Decreased production of Th1-type cytokines in SLE may be secondary to this imbalance between IL-10 and IL-12. A contributory role of dysfunctional CD8+ cells is suggested.
Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a (1994)

We recently reported a novel genetic locus located in the sbcB-his region of the chromosomal map of Escherichia coli K-12 which directs the expression of group 6-positive phenotype in Shigella flexneri lipopolysaccharide, presumably due to the transfer of O-acetyl groups onto rhamnose residues of the S. flexneri O-specific polysaccharide (Z. Yao, H. Liu, and M. A. Valvano, J. Bacteriol. 174:7500-7508, 1992). In this study, we identified the genetic region encoding group 6 specificity as part of the rfb gene cluster of E. coli K-12 strain W3110 and established the DNA sequence of most of this cluster. The rfbBDACX block of genes, located in the upstream region of the rfb cluster, was found to be strongly conserved in comparison with the corresponding region in Shigella dysenteriae type 1 and Salmonella enterica. Six other genes, four of which were shown to be essential for the expression of group 6 reactivity in S. flexneri serotypes Y and 4a, were identified downstream of rfbX. One of the remaining two genes showed similarities with rfc (O-antigen polymerase) of S. enterica serovar typhimurium, whereas the other, located in the downstream end of the cluster next to gnd (gluconate-6-phosphate dehydrogenase), had an IS5 insertion. Recently, it has been reported that the IS5 insertion mutation (rfb-50) can be complemented, resulting in the formation of O16-specific polysaccharide by E. coli K-12 (D. Liu and P. R. Reeves, Microbiology 140:49-57, 1994). We present immunochemical evidence suggesting that S. flexneri rfb genes also complement the rfb-50 mutation; in the presence of rfb genes of E. coli K-12, S. flexneri isolates express O16-specific polysaccharide which is also acetylated in its rhamnose residues, thereby eliciting group 6 specificity.
Characterization of the EBV/C3d receptor on the human Jurkat T cell line: evidence for a novel transcript (1993)

EBV is a human herpes virus that causes mononucleosis and is associated with various tumors. EBV infects cells via the CR2 that was previously thought to be expressed only on the surface of B cells and certain epithelial cells. Recent findings in our laboratory and those of others, however, have shown that the EBV receptor is also present on T cells. Our study shows that Jurkat human T cells have a molecule that reacts with both anti-CR2 antibodies and the third component of complement, C3. Furthermore, the data indicate that this molecule binds EBV detected by incubation with biotin-conjugated virus and streptavidin phycoerythrin. Viral binding is specific, as it is inhibited by nonconjugated virus, with anti-CR2 antibodies, and with an antibody reactive with the glycoprotein (gp350) that EBV uses to bind CR2. In addition, EBV variably infects Jurkat cells as demonstrated by the presence of transcripts of Epstein Barr nuclear Ag (EBNA-1) using the polymerase chain reaction. Immunoprecipitation experiments with anti-CR2 antibodies and SDS-PAGE analysis reveal a protein with an apparent molecular mass of 155 kDa which is higher than the one seen in B cells. The size of this molecule is reduced to 119 kDa upon endoglycosidase F treatment. Northern blot analysis of Jurkat poly(A)+ RNA shows a transcript of 4.7 kb upon probing with the B cell CR2 cDNA. This size is consistent with that of B cell CR2 mRNA. Two cDNA clones were identified upon screening of a Jurkat cell cDNA library with the B cell CR2 cDNA. One of the clones possesses an identical nucleotide sequence to the one corresponding to B cell CR2, whereas the other represents a differentially spliced transcript which lacks the exon 8b of B cell CR2. Analysis of Jurkat and Raji mRNA by PCR demonstrated the presence of this novel splice variant in both cell lines.
A Note on Maximal Acceleration (1992)

It is found that the maximal acceleration of a quantum particle is directly related to the speed of transportation in the projective Hilbert space. The minimum space-time uncertainty is inversely proportional to the maximal acceleration of the particle. It is argued that the most accurate clocks are those which can be maximally accelerated.
Synthesis and application of cleavable photoactivatable heterobifunctional reagents (1981)

Three different cleavable photoactivable heterobifunctional reagents have been synthesized and characterized by proton NMR, 13C NMR, mass spectroscopy, infrared spectroscopy, and thin-layer chromatography. They are the N-hydroxysuccinimide ester of 3-[(4-azidophenyl)dithio]-propionic acid, methyl 3-[(4-azidophenyl)dithio]propionimidate, and N-[(4-azidophenyl)thio]phthalimide. Concanavalin A was coupled with one of the reagents, the N-hydroxysuccinimide ester of 3-[(4-azidophenyl)dithio]propionic acid, and radioiodinated. The [125I]lectin derivative and [125I]lectin showed similar specific binding to the receptors on the human erythrocyte membrane. Upon photolysis, subunits of the [125I]lectin derivative were cross-linked to produce dimer, trimer, and tetramer. These cross-linked complexes were readily cleaved by reducing the disulfide bond of the reagent.
Side-by-Side Comparison of Passive MEMS Strain Test Structures under Residual Compression (2001)

Knowledge and control of residual strain is critical for device design in MEMS, and therefore it is important to establish standards for residual strain measurement. In this study, pointer, microring, bent-beam, and fixed-fixed beam test structures are used to evaluate residual strain both theoretically and experimentally. An equation that enables easier evaluation of bent-beam structures is derived. Also, a finite difference model that incorporates the non-idealities of fixed-fixed beams and determines an optimum fit to the measured deflection curve is presented. The model allows accurate residual strain evaluation of each buckled fixed-fixed beam. Experimentally, pointer structures were found to be susceptible to adhesion. Microrings, intended for residual tension assessment, also could not be evaluated because the residual strain was compressive. Bent-beam and fixed-fixed beams could both be evaluated. The main criterion for test structure effectiveness was taken to be the repeatability of residual strain on structures in close proximity; each should exhibit the same value. Using optical microscopy, the residual strain of bent-beams was determined with ± 13 με repeatability based on standard deviation of adjacent structures of similar design. Using optical interferometry, the residual strain of fixed-fixed beams was determined with ± 2 με repeatability based on standard deviation for adjacent beams of different lengths. The strain values obtained from the two structures are in reasonably good agreement. Cantilevers were also evaluated to obtain film curvature values.
Physiology of the bacterial cell : a molecular approach (1990)

Composition and organization of the bacterial cell structure and function of bacterial cell parts assembly and polymerization - the bacterial interior assembly and polymerization - the bacterial envelope biosynthesis and fueling quest for food growth of cells and populations the effects of temperature, pressure and pH genetic adaptation - the genome and its plasticity genetic adaptation - genetic exchange and recombination co-ordination of metabolic reactions regulation of gene expression - individual operons regulation of gene expression - multigene systems and global regulation cell cycle growth rate as a variable cellular differentiation physiological ecology answers to study questions literature cited.
Temperature-insensitive long period grating sensors in photonic crystal fibre (2004)

A long period grating has been fabricated in endlessly singlemode photonic crystal fibre using a spatially-periodic electric arc discharge. The sensing characteristics of the grating have been studied and it was found to possess an insensitivity to temperature, a bend sensitivity of 3.7 nm · m and a strain sensitivity of −2.0 pm/µɛ
The size dependence of the melting point of small particles of tin (1967)

The size dependence of the melting point of tin has been studied by means of transmission electron diffraction and microscopy. In accordance with the observations of other workers, it has been found that the melting point of a spherical particle of tin decreases as the radius Rm of the particle decreases. However, the decrease does not depend linearly on 1/Rm. The experimental results are explained in terms of a thermodynamic treatment which allows for the fact that a liquid cannot be subdivided indefinitely. The theory ceases to give correct results for the melting point of particles with radii less than about 50 Å, the calculated temperatures being less than those observed. For particles to which the theory is applicable it is found that the surface tension at the interface between solid and liquid tin is σ1 = 62·2 ± 10 dyn cm-1.
A scalable coder designed for 10-kHz bandwidth speech (2003)

This paper presents a scalable speech coder with rate of 23.85-kbit/s to encode 10-kHz bandwidth speech signals. The perceptual quality of the 10-kHz bandwidth speech signals is much better than that of 7-kHz bandwidth ones, and it is close to that of 20-kHz bandwidth ones. The 10-kHz bandwidth is therefore promising for high-fidelity conversational applications. The scalable coder consists of two layers: a base-layer and an enhancement-layer. The adaptive multi-rate wideband speech coder (AMR-WB) at 15.85-kbit/s and a transform coding method at 8-kbit/s are utilized for the base-layer and the enhancement-layer, respectively. This hybrid structure ensures the efficient coding of the 10-kHz bandwidth speech. In enhancement-layer, the modified discrete cosine transform (MDCT) is exploited. Its analysis frame size is set to be short in order to minimize additional algorithmic delay. The total additional algorithmic delay of the enhancement-layer is 5-ms. Since it is difficult to quantize all the MDCT coefficients at 8-kbit/s, we have limited the region for quantization from 6-kHz to 9-kHz to improve the perceptual quality of decoded speech. Our subjective evaluation test results indicate the quality of the proposed coder clearly exceeds that of AMR-WB at 23.85-kbit/s under both clean and noise conditions.
Chymase-directed serine protease inhibitor that reacts with a single 30-kDa granzyme and blocks NK-mediated cytotoxicity. (1994)

Cytotoxic NK and T lymphocytes kill virally infected cells within minutes without causing damage to themselves or bystander cells. One mechanism of killing involves exocytosis of granules containing serine proteases and perforin. Serine protease inhibitors block killing of target cells mediated by the cytotoxic lymphocytes. There are at least five different serine protease activities in cytolytic granules. Ten different serine protease sequences have been identified with the use of cDNA-specific clones. It is not known whether only one or several of these serine proteases are essential for cytolytic activity. In this study we show that an irreversible serine protease inhibitor, biotinyl-Aca-Aca-Phe-Leu-PheP(OPh)2, selectively inhibits a chymotrypsin-like (chymase) serine protease activity of rat RNK-16 granule extracts. Under the same conditions, only one 30-kDa (reduced) band was detected on protein blots. Furthermore, only one of three chymase peaks separated by hydrophobic interaction chromatography was inhibited. When this granzyme was inhibited, granule-mediated lysis of erythrocytes was diminished. NK cell killing was completely blocked when biotinyl-Aca-Aca-Phe-Leu-PheP(OPh)2 was added to cytotoxicity assays at 200 microM with rat splenocytes as effectors. By confocal fluorescence microscopy, we show that this inhibitor localizes to distinct regions within RNK-16 cells and rat NK cells. Inhibitor treatment of intact cells inactivated the chymase activity and reduced lysis found in their dense organelles. Together these data indicate that biotinyl-Aca-Aca-Phe-Leu-PheP(OPh)2 inhibits a granule chymase that is essential to cytolytic activity of NK cells.
An Iron-Binding Exochelin Prevents Restenosis Due to Coronary Artery Balloon Injury in a Porcine Model (2001)

Background- Vascular smooth muscle cell (VSMC) proliferation is a critical factor in the neointima formation that causes restenosis after coronary angioplasty (PTCA). Desferri-exochelin 772SM (D-EXO), a highly diffusible, lipophilic iron chelator secreted by Mycobacterium tuberculosis, inhibits proliferation of VSMCs in culture. We hypothesized that treatment with D-EXO would inhibit neointima formation in balloon-injured vessels in vivo. Methods and Results- We subjected 24 pigs to overstretch coronary artery injury with standard PTCA balloons and then administered intramural injections of either D-EXO (n=14) or vehicle (n=10) through an Infiltrator catheter. Treatments were randomized, and the investigators were blinded with regard to treatment group until data analysis was completed. One month later, we euthanized the pigs, excised the injured coronary segments, made multiple sections of each segment, and identified the site of maximal neointima formation. An injury score based on the degree of disruption of the internal or external elastic lamina or media was assigned. D-EXO reduced stenosis index (neointima area divided by the area within the internal elastic lamina), adjusted for injury score, by 47%. Neointima thickness was also reduced. Conclusions- D-EXO, injected intramurally, substantially inhibited formation of neointima in a porcine vascular injury model.