gebhart/patrepeval huggingface dataset:
A Simple, Valveless Microfluidic Sample Preparation Device for Extraction and Amplification of DNA from Nanoliter-Volume Samples (2006)

A glass microdevice has been constructed for the on-line integration of solid-phase extraction (SPE) of DNA and polymerase chain reaction (PCR) on a single chip. The chromatography required for SPE in the microfluidic sample preparation device (muSPD) was carried out in a silica bead/sol-gel SPE bed, where the purified DNA was eluted directly into a downstream chamber where conventional thermocycling allowed for PCR amplification of specific DNA target sequences. Through rapid, simple passivation of the PCR chamber with a silanizing reagent, reproducible DNA extraction and amplification was demonstrated from complex biological matrixes in a manner amenable to any research laboratory, using only a syringe pump and a conventional thermocycler. The muSPD allowed for SPE concentration of DNA from 600 nL of blood coupled to subsequent on-chip amplification that yielded a detectable amplicon; this simple device can be applied to a variety of routine genetic analyses without the need for sophisticated instrumentation. In addition, the applicability of these developments to nonconventional thermocycling was demonstrated through the use of noncontact, IR-mediated heating. This was exemplified with the isolation of DNA from an anthrax spore-spiked nasal swab and the subsequent on-chip amplification of target DNA sequences in a total processing time of only 25 min.
Screening and Characterization of Protease Inhibitors from Marine Bacteria Associated with Sponge Jaspis sp. (2010)

Three isolates among 138 sponge-associated bacteria were isolated from Waigeo Island, Raja Ampat West Papua Province, Indonesia, have been shown protease inhibitory activity against subtilisin (serine protease), thermolysin (metalloprotease), and crude extract from pathogenic bacteria (Eschericia coli enteropathogenic/EPEC K.1.1, Staphylococcus aureus, and Pseudomonas aeruginosa). Those three isolates were designated as sponge associated bacteria SAB S-12, SAB S-21, and SAB S-17. A simple casein and Sea Water Complete (SWC) double layer agar method was used to screen the bacteria against pathogenic bacteria producing protease, i.e. EPEC K.1.1, S. aureus, and P. aeruginosa. Among them, SAB S-12 isolate showed no inhibitory zone indicated. The isolate had the highest inhibitory activity against subtilisin and crude extract enzyme of pathogenic bacteria, the inhibitory activity was 91.6 and 98.9%, respectively. In addition, the SAB S-21 isolate had the highest inhibitory activity against thermolysin, it was 70.4%. The optimum pH and temperature for protease inhibition of the three isolates was at pH 7.0-8.0 and 40-50 °C respectively. Based on 16S rRNA gene sequence, the closest related with SAB S-12, SAB-17, and SAB-21 isolates was Providencia sp. (92% identity), Paracoccus sp. (86% identity), and Bacillus sp. (100% identity), respectively.
The effects of mutation of the anr gene on the aerobic respiratory chain of Pseudomonas aeruginosa (1997)

The anr gene of Pseudomonas aeruginosa encodes a transcriptional regulator of anaerobic gene expression, homologous to the Fnr protein of Escherichia coli. We report here that Anr has a role in regulating the activity of the aerobic respiratory chain of P. aeruginosa. Strains with internal deletions in their anr gene had lowered levels of membrane bound cytochromes whilst the activity of the cytochrome c oxidase, cytochrome co (likely to be a cytochrome cbb3-type oxidase), and the cyanide-insensitive respiratory pathway was markedly higher than in the wild-type strains. These data, and the finding that provision of multiple copies of the anr gene led to severe repression of these respiratory activities, suggest that Anr is a repressor of aerobic respiratory pathways and possibly the terminal oxidases themselves. In contrast, Anr activated cytochrome c peroxidase, a respiratory chain linked enzyme induced under low oxygen conditions.
Twenty years of document image analysis in PAMI (2000)

The contributions to document image analysis of 99 papers published in the IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI) are clustered, summarized, interpolated, interpreted, and evaluated.
Flow cytometry (1984)

Flow cytometry instrumentation developed from early efforts to count cells and particles in liquid suspension as they passed through a sensing device. Since the mid-1960’s sophisticated instruments have been designed for analyzing cells based on various cytological, biochemical, and functional properties. These instruments have revolutionized automated cell analysis methods in that measurements are made at high speed, multiparameter data is correlated on each cell, statistical precision is high, and cells are separated in high purity from heterogeneous mixtures for identification and functional analysis. Advanced instruments capable of measuring cell volume, surface area, multicolor fluorescence, fluorescence polarization, light scatter within various angular regions, and axial light loss (extinction) at different wavelengths are being used in biomedical research for analyzing and sorting normal and abnormal cell populations. This article reviews the development of flow cytometers, the conceptual basis of flow measurements, and discusses some of the numerous applications of the technology in biology and medicine.
Cancer's Molecular Sweet Tooth and the Warburg Effect (2006)

More than 80 years ago, the renowned biochemist Otto Warburg described how cancer cells avidly consume glucose and produce lactic acid under aerobic conditions. Recent studies arguing that cancer cells benefit from this phenomenon, termed the Warburg effect, have renewed discussions about its exact role as cause, correlate, or facilitator of cancer. Molecular advances in this area may reveal tactics to exploit the cancer cell's "sweet tooth" for cancer therapy.
Inhibitory properties of double-helix-forming circular oligonucleotides (1997)

Several circular oligonucleotides were synthesized and characterized by electrospray ionization mass spectrometry. Experiments on termination of primer extension catalysed by DNA polymerases, Klenow fragment and Tth have demonstrated that a double helix forming circular 2'-deoxyribooligomer containing a 25mer sequence complementary to the target single-stranded DNA along with a 34mer random mismatching stretch appears to be a potent inhibitor of replication in vitro. Studies on inhibition of luciferase gene expression in a cell-free transcription-translation system have shown that a duplex forming circular 2'-deoxyribooligonucleotide containing a 25mer sequence complementary to the target mRNA and a 14mer random mismatching stretch can serve as an effective antisense compound as a standard linear complementary oligomer. Features of double helix forming circular oligonucleotides composed of 2'-deoxyribonucleosides seem to be useful for the design of new antigene and antisense agents.
Resonance Absorption by Nuclear Magnetic Moments in a Solid (1946)

The suggestion is also made that Co& may be strongly dissociated by the metastable Xe atoms (and H~O some- what less strongly), thus producing oxygen atoms which combine to form the O~molecules; (D(CO~) =5.5 v, D{HgO) =5.0 v). If so, the fact that CO did not yield the bands would indicate that the dissociation energy of CO is greater than the energy of the upper metastable state of Xe, namely 9.4 volts. (Energy of lower metastable state equals 8.3 v. ) This appears to be direct evidence in favor of the 9.6-volt value of D(CO) as determined by Hagstrum and Tate from appearance potentials in the mass spectro- graph, or for the 11.11 v-value obtained in a recent spectral analysis by Gaydon and Penney/ but against the 9.14-volt value determined from certain predissociation data. ' The higher value appears to be more in accord also with thermochemical data as brought out by Hagstrum and Tate, ' a.nd also by Asundi and Samuel. '
Covalently Attached Saccharides on Silicon Surfaces (2003)

This paper presents the first functionalization of silicon surfaces with well-defined, covalently attached monolayers containing saccharides. Two methods were used to this aim: a thermal method (refluxing in mesitylene) and a recently developed, extremely mild photochemical method (irradiation with 447 nm at room temperature). The results were analyzed by FT-IR and angle-resolved X-ray photoelectron spectroscopy. The use of a two-dimensional detector in ARXPS allows for unparalleled, subnanometer resolution in the determination of the elemental composition of monolayers. Even for monolayers with a total thickness of only approximately 1.5 nm, a clear elemental depth profile can be obtained. Such analyses display for sialic acid-containing monolayers that the mild photochemical attachment does not destroy the (rather fragile) sialic acid moiety and that the sugar is present at the top of the monolayer and thus available for biological interactions.
Duration of Infection-Derived Immunity to Cholera (1981)

Four volunteers were rechallenged with Vibrio cholerae (10(6) classical Ogawa 395 organisms) 33-36 months after their initial induced cholera infection; none of the four veterans and four of five control volunteers developed diarrhea (P = 0.04). All control subjects, but only one veteran, had positive coprocultures. Three of the four veterans had significant levels of serum IgG antitoxin before challenge, but none had measurable intestinal levels of secretory IgA antitoxin. Significant rises in levels of serum vibriocidal and antitoxic antibody occurred in all control subjects and in two veterans, who also manifested rises in levels of intestinal secretory IgA antitoxin. The impressive duration of infection-derived immunity suggests that the most promising approach to development of cholera vaccines may be to mimic natural immunity with orally administered, attenuated strains of V. cholerae.
Identification of a common antigen of herpes simplex virus bovine herpes mammillitis virus, and B virus (1978)

In immunoelectrophoretic analyses one common antigen was demonstrated in antigen preparations from herpes simplex virus types 1- and 2- (HSV-1 and HSV-2), bovine herpes mammillitis (BHM) virus-, and B virus-infected cells solubilized by Triton X-100. The antigen was also demonstrated in solubilized purified HSV-1 and BHM virus. The common antigen was identified as antigen 11 of HSV-1 or HSV-2. Differences were found in the polypeptide composition of the related antigens when isolated from the four different herpesviruses, but a glycopolypeptide with a molecular weight of 125,000 was present in each of the four different antigen preparations, indicating that this polypeptide carried the common antigenic determinants.
Alkaline Unfolding and Salt-Induced Folding ofAminoacylase at High pH (1994)

The conformational changes of aminoacylase during unfolding at alkaline pH have been followed by fluorescence emission, circular dichroism (CD) and ultraviolet difference spectra. The results of comparison of inactivation and conformation show that much lower values of alkaline pH are required to bring about inactivation than significant conformational change of the enzyme molecule. At pH above 12, although the enzyme has been inactivated, the apparently fully unfolded enzyme retains some ordered secondary structure. At pH 12 by adding KCl, the relatively unfolded state of denatured enzyme changes into a compact conformational state by hydrophobic collapsing, but no new secondary structure is formed. On decreasing the pH from pH 12 to approximate neutrality, the unfolded enzyme also undertakes the similar conformational transition. It can be suggested that hydrophobic collapsed intermediate may be a general intermediate conformational state from alkaline unfolded state to native state.
Sharp Bending of On-Chip Silicon Bragg Cladding Waveguide With Light Guiding in Low Index Core Materials (2006)

A novel on-chip Bragg cladding waveguide is designed and fabricated using conventional CMOS techniques. This optical waveguide has a low refractive index core surrounded by high index-contrast cladding bilayers. Polysilicon (n=3.5) and silicon nitride (n=2.0) are used for high index-contrast Bragg layers, where index difference is as high as 1.5. Our simulation shows that sharp bending in low index core materials can be achieved, which is not possible using index guiding mechanism. Within our approach, various on-chip applications are expected such as optical integration, high power transmission, biosensor/microelectromechanical system and so on
Fc receptor mediated endocytosis of small soluble immunoglobulin G immune complexes in Kupffer and endothelial cells from rat liver (2000)

Soluble circulating immunoglobulin G immune complexes are mainly eliminated by the liver, predominantly by uptake in the Kupffer cells, but also the liver endothelial cells seem to be of importance. In the present study we have followed the intracellular turnover of immune complexes after Fc(gamma) receptor mediated endocytosis in cultured rat liver endothelial cells and Kupffer cells by means of isopycnic centrifugation, DAB cross-linking and morphological techniques. For the biochemical experiments the antigen, dinitrophenylated bovine serum albumin (BSA), was labeled with radioiodinated tyramine cellobiose that cannot cross biological membranes and therefore traps labeled degradation products at the site of formation. The endocytic pathway followed by immune complexes was compared with that followed by scavenger receptor ligands, such as formaldehyde treated BSA and dinitrophenylated BSA, and the mannose receptor ligand ovalbumin. Both Kupffer cells and liver endothelial cells took up and degraded the immune complexes, but there was a clear delay in the degradation of immune complexes as compared to degradation of ligands taken up via scavenger receptors. The kinetics of the endocytosis of scavenger receptor ligand was unaffected by simultaneous uptake of immune complexes. Experiments using both biochemical and morphological techniques indicated that the delayed degradation was due to a late arrival of the immune complexes at the lysosomes, which partly was explained by retroendocytosis of immune complexes. Electron microscopy studies revealed that the immune complexes were retained in the early endosomes that remained accessible to other endocytic markers such as ovalbumin. In addition, the immune complexes were seen in multivesicular compartments apparently devoid of other endocytic markers. Finally, the immune complexes were degraded in the same lysosomes as the ligands of scavenger receptors. Thus, immune complexes seem to follow an endocytic pathway that is kinetically or maybe morphologically different from that followed by scavenger and mannose receptor ligands.
Developing live vaccines against plague (2011)

Three great plague pandemics caused by the gram-negative bacterium Yersinia pestis have killed nearly 200 million people and it has been linked to biowarfare in the past. Plague is endemic in many parts of the world. In addition, the risk of plague as a bioweapon has prompted increased research to develop plague vaccines against this disease. Injectable subunit vaccines are being developed in the United States and United Kingdom. However, the live attenuated Y. pestis-EV NIIEG strain has been used as a vaccine for more than 70 years in the former Soviet Union and in some parts of Asia and provides a high degree of efficacy against plague. This vaccine has not gained general acceptance because of safety concerns. In recent years, modern molecular biological techniques have been applied to Y. pestis to construct strains with specific defined mutations designed to create safe, immunogenic vaccines with potential for use in humans and as bait vaccines to reduce the load of Y. pestis in the environment. In addition, a number of live, vectored vaccines have been reported using attenuated viral vectors or attenuated Salmonella strains to deliver plague antigens. Here we summarize the progress of live attenuated vaccines against plagu.
Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. (1992)

Historical Introduction. Classification and Nomenclature of Enzymes. Enzyme List: Oxidoreductases. Transferases. Hydrolases. Lyases. Isomerases. Ligases. Nomenclature of Electron-Transport Proteins: General Introduction. Flavoproteins. Proteins Containing Reducible Disulfide. Cytochromes. Non-Heme Iron Proteins Copper Proteins Molybdenum Proteins Nickel Proteins Vanadium Proteins Quinoproteins Metal-Substituted Metalloproteins References. Nomenclature of Multienzymes. Glossary of Chemical Names. Abbreviations Used in the Enzyme List. Index of Enzyme Names.
Simulation of laser-generated ultrasonic waves in layered plates (2001)

A model is presented for the pulsed laser generation of ultrasound in isotropic layered plates. The stresses and displacements of the plate have been formulated in the Hankel and Laplace transform domains using the Thompson transfer matrix approach. The time domain response has been obtained by numerically inverting the transforms. Several numerical results are presented showing the normal surface displacement in the following configurations: single-layer film on a semi-infinite substrate, two layers on a semi-infinite substrate, and three-layer plates. The model provides a useful tool for the determination of which modes are generated by a laser source in a layered system. It can also be used to determine how sensitive the modes are to small changes in density, thickness, or elastic properties of the layers and to help in the selection of experimental parameters (laser spot size, pulse length, and source to receiver distance) for optimal sensitivity.
An Octahedral Coordination Complex of Iron(VI) (2006)

The hexavalent state, considered to be the highest oxidation level accessible for iron, has previously been found only in the tetrahedral ferrate dianion, FeO4(2-). We report the photochemical synthesis of another Fe(VI) compound, an octahedrally coordinated dication bearing a terminal nitrido ligand. Mössbauer and x-ray absorption spectra, supported by density functional theory, are consistent with the octahedral structure having an FeN triple bond of 1.57 angstroms and a singlet d2(xy) ground electronic configuration. The compound is stable at 77 kelvin and yields a high-spin Fe(III) species upon warming.
COX-2: an in vivo evidence of its participation in heat stress-induced myocardial preconditioning (2003)

This study provides the first evidence of an implication of COX-2 as a mediator of HS-induced cardioprotection. This suggests that prostaglandins are involved in this type of cardioprotective preconditioning.
Type IV collagen, laminin, and fibronectin promote the adhesion and migration of rabbit lens epithelial cells in vitro. (1993)

The results of these studies indicate that adhesion and migration of lens epithelial cells occurs in response to the lens capsule proteins type IV collagen and laminin and in response to fibronectin, a protein found in the lens during embryologic development. Because fibronectin plays a role in the embryologic development of the lens but is not normally present in the adult lens, the possible introduction of fibronectin into the eye after surgery may play a critical role in the posterior migration of lens epithelial cells and the development of posterior capsular opacification or secondary cataract.
Signalling through CD28 T-cell activation pathway involves an inositol phospholipid-specific phospholipase C activity (1993)

Stimulation of the human T-cell line, Jurkat, by a monoclonal antibody (mAb) directed against the CD28 molecule leads to sustained increases in intracellular levels of Ca2+ ([Ca2+]i); the initial rise in Ca2+ comes from internal stores, followed by Ca2+ entry into the cells. The CD28 molecule also appears to activate polyphosphoinositide (InsPL)-specific phospholipase C (PLC) activity in Jurkat cells, as demonstrated by PtdInsP2 breakdown, InsP3 and 1,2-diacylglycerol generation and PtdIns resynthesis. We also observed that interleukin-2 (IL2) production induced via CD28 triggering was sensitive to a selective protein kinase C inhibitor. Of the four other anti-CD28 mAbs (CD28.2, CD28.4, CD28.5, CD28.6) tested, only one (CD28.5) was unable to generate any InsPL-specific PLC or IL2 secretion. However, the cross-linking of cell-bound CD28.5 with anti-mouse Ig antibodies led to an increase in [Ca2+]i. CD28-molecule clustering in itself appears to be a sufficient signal for induction of PLC activity.
Potent Tetracyclic Guanine Inhibitors of PDE1 and PDE5 Cyclic Guanosine Monophosphate Phosphodiesterases with Oral Antihypertensive Activity (1997)

Tetracyclic guanines have been shown to be potent and selective inhibitors of the cGMP-hydrolyzing enzymes PDE1 and PDE5. In general, these compounds are inactive or only weakly active as inhibitors of PDE3, which is a major isozyme involved in cAMP hydrolysis. Structure-activity relationships are developed at N-1, C-2, N-3, and N-5 on the core nucleus. Compound 31, with an IC50 of 70 pM, is the most potent inhibitor of PDE1, while 50, with an IC50 of 4 nM, is the most potent inhibitor of PDE5. Compounds 20, 22, 30, and 50 are potent dual inhibitors with IC50 values below 30 nM for both PDE1 and PDE5. Compounds 12, 20, and 28 reduced blood pressure by more than 45 mmHg when administered orally at 10 mg/kg to the spontaneously hypertensive rat (SHR).
Posttranslational signal peptidase cleavage at the flavivirus C-prM junction in vitro (1995)

We have investigated the cleavages at the flavivirus capsid-prM protein junction in vitro. When expressed in the absence of the flavivirus proteinase, capsid and prM, which are separated by an internal signal sequence, exist as a membrane-spanning precursor protein. Here we show the induction of posttranslational signal peptidase cleavage of prM by trypsin cleavage of a cytoplasmic region of this precursor protein.
Caspase activity and expression of cell death genes during development of human preimplantation embryos (2002)

It has been observed that apoptosis occurs in human blastocysts. In other types of cell, the characteristic morphological changes seen in apoptotic cells are executed by caspases, which are regulated by the BCL-2 family of proteins. This study investigated whether these components of the apoptotic cascade are present throughout human preimplantation development. Developing and arrested two pronucleate embryos at all stages were incubated with a fluorescently tagged caspase inhibitor that binds only to active caspases, fixed, counterstained with 4,6-diamidino-2-phenylindole (DAPI) to assess nuclear morphology and examined using confocal microscopy. Active caspases were detected only after compaction, at the morula and blastocyst stages, and were frequently associated with apoptotic nuclei. Occasional labelling was seen in arrested embryos. Expression of proapoptotic BAX and BAD and anti-apoptotic BCL-2 was examined in single embryos using RT-PCR and immunohistochemistry. BAX and BCL-2 mRNAs were expressed throughout development, whereas BAD mRNA was expressed mainly after compaction. Simultaneous expression of BAX and BCL-2 proteins within individual embryos was confirmed using immunohistochemistry. The onset of caspase activity and BAD expression after compaction correlates with the previously reported appearance of apoptotic nuclei. As in other types of cell, human embryos express common molecular components of the apoptotic cascade, although apoptosis appears to be suppressed before compaction and differentiation.