gebhart/patrepeval huggingface dataset:
Ultrasound surgery: comparison of strategies using phased array systems (1996)

In this paper the possibility of using phased array generated multiple-focus patterns to reduce the overall treatment time in ultrasound surgery while restraining prefocal heating was investigated. This was done by comparing through computer simulation the performance of different possible schemes, i.e., single-focus scans, multiple-focus scans, and simultaneous multiple focusing without scanning, when used to "ablate" a 10/spl times/10/spl times/10 mm/sup 3/ tissue volume 100 mm deep. In all cases, 41 foci were used to cover the treatment volume. Multiple-focus scans were arranged into nine groups which were scanned in a raster fashion, as with single-focus scans. Keeping the treatment time constant, the maximum intensities, maximum thermal doses, dose distributions, and prefocal necrosis zones for the different schemes were compared. It was found that the nonscanned simultaneous multiple-focus case required the smallest maximum intensity and dose, and resulted in the most even dose distribution. Single-focus raster scanning of individual lesions, as currently used with fixed-focus transducers, gave the worst results. These results show that multiple-focus patterns help considerably in reducing the maximum intensity and dose, and in generating a more even dose distribution assuming the same treatment time and prefocal heating. Alternatively, multiple-focus patterns can be used to significantly reduce treatment time while keeping the maximum intensity and prefocal heating below predetermined limits.
Frequency domain equalization for single-carrier broadband wireless systems (2002)

Broadband wireless access systems deployed in residential and business environments are likely to face hostile radio propagation environments, with multipath delay spread extending over tens or hundreds of bit intervals. Orthogonal frequency-division multiplex (OFDM) is a recognized multicarrier solution to combat the effects of such multipath conditions. This article surveys frequency domain equalization (FDE) applied to single-carrier (SC) modulation solutions. SC radio modems with frequency domain equalization have similar performance, efficiency, and low signal processing complexity advantages as OFDM, and in addition are less sensitive than OFDM to RF impairments such as power amplifier nonlinearities. We discuss similarities and differences of SC and OFDM systems and coexistence possibilities, and present examples of SC-FDE performance capabilities.
Linkage of ATM to Cell Cycle Regulation by the Chk2 Protein Kinase (1998)

In response to DNA damage and replication blocks, cells prevent cell cycle progression through the control of critical cell cycle regulators. We identified Chk2, the mammalian homolog of the Saccharomyces cerevisiae Rad53 and Schizosaccharomyces pombe Cds1 protein kinases required for the DNA damage and replication checkpoints. Chk2 was rapidly phosphorylated and activated in response to replication blocks and DNA damage; the response to DNA damage occurred in an ataxia telangiectasia mutated (ATM)-dependent manner. In vitro, Chk2 phosphorylated Cdc25C on serine-216, a site known to be involved in negative regulation of Cdc25C. This is the same site phosphorylated by the protein kinase Chk1, which suggests that, in response to DNA damage and DNA replicational stress, Chk1 and Chk2 may phosphorylate Cdc25C to prevent entry into mitosis.
A General Discussion of Li Ion Battery Safety (2012)

Safety response of Li ion batteries is increasingly recognized as a critical performance requirement for commercial adoption of this chemistry, especially in large scale vehicular applications. The development of increasingly safe battery systems requires continued improvements in cell thermal stability as well as new pack and vehicle designs with rigorous and redundant safety controls. There are many advanced materials being developed and characterized in industry, universities, and national laboratories for Li ion batteries. These materials are often developed primarily for improved performance such as energy density, specific energy, power capability, low temperature response, cycle lifetime, and cost. Safety is often a property determined after the development phase. Safety and thermal stability should become a prime consideration in the initial development and material selection process. There is certainly no need for a "safe" battery that does not perform but also there is no need for a high performance battery that is unsafe.
Ribozymes: Structure, Function and Potential Therapy for Dominant Genetic Disorders (1996)

Some dominant genetic disorders, viral processes and neoplastic disorders base their pathogenicity on the production of protein or proteins that negatively affect cellular metabolism or environment. Thus, the inhibition of the synthesis of those proteins should prevent the biological damage. A promising approach to decreasing the level of the abnormal protein(s) is represented by specific interference with gene expression at the level of mRNA. The specific suppression of the expression of an mRNA can be achieved by using ribozymes. Ribozymes are RNA molecules able to break and form covalent bonds within a nucleic acid molecule. These molecules, with even greater potential advantages than antisense oligodeoxynucleotides, are able to bind specifically and cleave an mRNA substrate. There are advantages to using ribozymes instead of antisense oligodeoxynucleotides. Ribozymes can inactivate the target RNA without relying on the host cell's machinery and they have the capacity to cleave more than one copy of the target RNA by dissociating from the cleavage products and binding to another target molecule. Most of the studies performed to date have described the use of ribozymes as therapeutic agents for viral and cancer diseases. However, some dominant genetic disorders may also benefit from this approach. This is the case for some connective tissue disorders such as osteogenesis imperfecta, Marfan syndrome and the craniosynostotic syndromes.
Nanometer lithography on silicon and hydrogenated amorphous silicon with low energy electrons (1995)

The oxidation of a hydrogen terminated Si surface can locally be induced with a scanning tunnelling microscope (STM) operating in air or with a beam of free electrons in a controlled oxygen environment. The oxidation mechanism of both processes was studied and compared. The oxidation with the STM in air depends strongly on the applied tip-substrate voltage and writing speed, but is not proportional to the tunnelling current. This is in contrast to the process with a beam of free electrons. The thickness of the electron beam induced oxide is studied as a function of electron energy, electron dose, and oxygen pressure. Oxide thicknesses of 0.5–3 nm are measured using Auger spectroscopy. The initial step of the oxidation process is the electron beam induced removal of hydrogen from the surface. The electron dose requirement for this step was determined as a function of electron energy. The dose is found to be minimal for 100 eV electrons, and is ≊4 mC/cm2. Oxide lines made with the STM on Si(110) were used as a mask to wet etch the pattern into the Si(110). With tetramethyl ammonium hydroxide, a selective anisotropic etch liquid, trenches with a width of 35 nm and a depth of 300 nm were made. We show that it is also possible to locally oxidize hydrogenated amorphous silicon (a-Si:H) and use the oxide as an etching mask. Hydrogenated amorphous silicon has the advantage that it can be deposited in very thin layers on almost any substrate and therefore has great potential as STM and electron-beam resist.
Urodynamic and Immunohistochemical Evaluation of Intravesical Capsaicin Delivery Using Thermosensitive Hydrogel and Liposomes (2004)

In comparison with 30% ethanol liposomes are a superior vehicle for the intravesical administration of capsaicin, producing comparable efficacy with less tissue damage. Hydrogel can also serve as safe alternative option for capsaicin delivery.
A novel calcium-binding protein in amniotic fluid, CAAF1: its molecular cloning and tissue distribution (1996)

We found by using a 45Ca2+ overlay technique a large amount of Ca(2+)-binding activity in bovine amniotic fluid from which a novel calcium-binding protein (CaBP) was purified and is referred to as CAAF1 (calcium-binding protein in amniotic fluid-1), with an apparent molecular mass of 8 kDa determined by N-tris(hydroxymethyl)-methylglycine/ SDS-PAGE. It was structurally homologous with MRP/calgranulin proteins (MRP8/calgranulin A and MRP14/calgranulin B), members of the S100 protein family, which are abundantly found in the cytoplasm of granulocytes and macrophages. CAAF1 lacked the predicted signal peptide sequence, which is consistent with other CaBPs. The tissue and cellular distribution of CAAF1 was determined by monoclonal antibodies developed against this protein. Its immunoreactivity was found in squamous epithelial cells, neutrophils, and some macrophages throughout the fetal body. An especially characteristic staining pattern was obtained in the squamous epithelium, including that of the esophagus, skin and amnion: CAAF1 was detected in the suprabasal squamous epithelial cells undergoing differentiation, but not in the cells in the proliferating basal layer. Northern blot analysis also showed that CAAF1 mRNA was highly expressed in bovine fetal esophagus and skin. On the other hand, our ELISA studies showed that CAAF1 protein was present in amniotic fluid at a concentration of about 120 nM, which was over 30 times as high as that in the fetal serum. These results suggested that CAAF1 is one of the stage-specific proteins in the differentiation of squamous epithelial cells, and that CAAF1 is preferentially produced by fetal squamous epithelial cells, including epidermal keratinocytes and amniotic epithelial cells, and it is stored in the amniotic fluid during embryogenesis.
Protein phosphorylation in yeast mitochondria: cAMP‐Dependence, submitochondrial localization and substrates of mitochondrial protein kinases (1987)

We describe the identification and submitochondrial localization of four protein kinases and of their target proteins in derepressed yeast mitochondria. The activity of one of the kinases depends on the presence of cyclic AMP (cAMP). It is soluble and localized in the mitochondrial intermembrane space. Its natural target is a polypeptide of 40 kDa molecular mass, which is bound to the inner membrane. Besides this natural target this kinase phosphorylates acidic heterologous proteins, like casein, with high efficiency. The other protein kinases identified so far are cAMP-independent. At least one is localized in the matrix having its natural substrates (49 and 24 kDa) in the same compartment. Two others are firmly bound to the inner membrane phosphorylating target proteins in the inner membrane (52.5 kDa) and in the intermembrane space (17.5 kDa), respectively.
Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling (2006)

Pathogenic staphylococci can form biofilms in which they show a higher resistance to antibiotics and the immune defense system than their planktonic counterparts, which suggests that the cells in a biofilm have an altered metabolic activity. Here, 2-D PAGE was used to identify secreted, cell wall-associated and cytoplasmic proteins expressed in Staphylococcus aureus after 8 and 48 h of growth. The proteins were separated at pH ranges of 4-7 or 6-11. The protein patterns revealed significant differences in 427 protein spots; from these, 258 non-redundant proteins were identified using ESI-MS/MS. Biofilm cells expressed higher levels of proteins associated with cell attachment and peptidoglycan synthesis, and in particular fibrinogen-binding proteins. Enzymes involved in pyruvate and formate metabolism were upregulated. Furthermore, biofilm cells expressed more staphylococcal accessory regulator A protein (SarA), which corroborates the positive effect of SarA on the expression of the intercellular adhesion operon ica and biofilm growth. In contrast, proteins, such as proteases and particularly immunodominant antigen A (IsaA) and staphylococcal secretory antigen (SsaA), were found in lower amounts. The RNA expression profiling largely supports the proteomic data. The results were mapped onto KEGG pathways.
Water-enhanced solubility of carboxylic acids in organic solvents and its applications to extraction processes (1991)

The solubilities of carboxylic acids in certain organic solvents increase remarkably with an increasing amount of water in the organic phase. This phenomenon leads to a novel extract regeneration process in which the co-extracted water is selectively removed from an extract, and the carboxylic acid precipitates. This approach is potentially advantageous compared to other regeneration processes because it removes a minor component of the extract in order to achieve a large recovery of acid from the extract. Carboxylic acids of interest include adipic acid, fumaric acid, and succinic acid because of their low to moderate solubilities in organic solvents. Solvents were screened for an increase in acid solubility with increased water concentration in the organic phase. Most Lewis-base solvents were found to exhibit this increased solubility phenomena. Solvents that have a carbonyl functional group showed a very large increase in acid solubility. 71 refs., 52 figs., 38 tabs.
A Thorough Examination of the CNN/Daily Mail Reading Comprehension Task (2016)

Enabling a computer to understand a document so that it can answer comprehension questions is a central, yet unsolved goal of NLP. A key factor impeding its solution by machine learned systems is the limited availability of human-annotated data. Hermann et al. (2015) seek to solve this problem by creating over a million training examples by pairing CNN and Daily Mail news articles with their summarized bullet points, and show that a neural network can then be trained to give good performance on this task. In this paper, we conduct a thorough examination of this new reading comprehension task. Our primary aim is to understand what depth of language understanding is required to do well on this task. We approach this from one side by doing a careful hand-analysis of a small subset of the problems and from the other by showing that simple, carefully designed systems can obtain accuracies of 73.6% and 76.6% on these two datasets, exceeding current state-of-the-art results by 7-10% and approaching what we believe is the ceiling for performance on this task.
Study of alpha‐lipoic acid penetration in the human aqueous after topical administration (2010)

Our study demonstrates the presence of alpha-lipoic acid in the aqueous and indicates that its concentration increases after it is administered in the form of eye drops, reaching maximum values after around 93 min. The concentrations that are achieved in the anterior chamber allow us to theorize the possibility of exploiting the antioxidant properties of alpha-lipoic acid.
A direct comparison of approaches for increasing carbon flow to aromatic biosynthesis inEscherichia coli (1996)

Different approaches to increasing carbon commitment to aromatic amino acid biosynthesis were compared in isogenic strains of Escherichia coli. In a strain having a wild-type PEP:glucose phosphotransferase (PTS) system, inactivation of the genes encoding pyruvate kinase (pykA and pykF) resulted in a 3.4 fold increase in carbon flow to aromatic biosynthesis. In a strain already having increased carbon flow to aromatics by virtue of overexpression of the tktA gene (encoding transketolase), the pykA and/or pykf mutations had no effect. A PTS- glucose+ mutant showed a 1.6-fold increase in carbon flow to aromatics compared to the PTS+ control strain. In the PTS- glucose+ host background, overexpression of tktA caused a further 3.7-fold increase in carbon flow, while inactivation of pykA and pykF caused a 5.8-fold increase. When all of the variables tested (PTS-glucose+, pykA, pykF, and overexpressed tktA) were combined in a single strain, a 19.9-fold increase in carbon commitment to aromatic biosynthesis was achieved.
Chemokines Take Center Stage in Inflammatory Ills (1996)

The proteins known as chemokines achieved public fame late last year, as a result of work suggesting that they might help protect against AIDS. But the proteins have a much wider role than that. As magnets for white blood cells, they play a key role in in flammatory responses and thus in the body's defenses against a wide array of invading pathogens. What's more, chemokine effects can also backfire, and contribute to a wide range of inflammatory diseases, such as rheumatoid arthritis, asthma, and adult res piratory distress syndrome, a major killer characterized by fluid buildup in the lungs. As a result, the chemokines have become major targets of efforts to develop new anti-inflammatory therapies, and recent work is already producing some promising results.
Methicillin-Resistant Staphylococcus aureus in U.S. Hospitals, 1975–1991 (1992)

This study suggests that hospitals of all sizes are facing the problem of MRSA, the problem appears to be increasing regardless of hospital size, and control measures advocated for MRSA appear to require re-evaluation. Further study of MRSA in hospitals would benefit our understanding of this costly pathogen.
Adaptive routing for road traffic (2000)

The article reports on an integrated system which uses road congestion information to guide routing, both in advance and while in transit. It offers two novel features: historic information about congestion is collected and retained for use when planning routes; and GPS tracks vehicles while they undertake journeys, and the Global System for Mobile Communications (GSM) Short Message Service (SMS) maintains communications between a moving vehicle and a central planning service to suggest revised routes avoiding congestion.
Hyperthermophilic and salt-dependent formyltransferase from Methanopyrus kandleri (2004)

Methanopyrus kandleri is a hyperthermophilic methanogenic archaeon, which grows on H(2) and CO(2) as its sole energy source. Its growth temperature optimum is 98 degrees C. One of the interesting characteristics of this archaeon is its high intracellular salt content. The organism has been reported to contain the trianionic cDPG (cyclic 2,3-diphosphoglycerate) and K+ at concentrations of 1.1 and 3 M, respectively. Reflecting the high cellular salt concentration, the enzymes in this organism are adapted not only to high temperature but also to high salt concentrations. The formyltransferase from M. kandleri was characterized extensively with respect to thermo- and halophilicity. The crystal structure of the formyltransferase at 1.73 A shows the enzyme to be composed of four identical subunits of molecular mass 32 kDa. The formyltransferase is thermostable and active only at relatively high concentrations of potassium phosphate (1 M) or other salts with strongly hydrated anions (strong salting-out salts). Potassium phosphate and potassium cDPG were found to be equivalent in activating and stabilizing the enzyme. At low concentrations of these salts, the enzyme is inactive and thermolabile. It was shown by equilibrium sedimentation analysis that the enzyme is in a monomer/dimer/tetramer equilibrium, the equilibrium constant being dependent on the concentration of salts: the higher oligomeric species increase with increasing salt concentrations. Evidence was provided that the monomer is both inactive and thermolabile. Experiments using a mutation which is directed to break surface ion pairs between two dimers indicated that dimerization is required for activity and tetramerization leads to thermostability.
Programmed Death of T Cells in HIV-1 Infection (1992)

In human immunodeficiency virus (HIV) infection, functional defects and deletion of antigen-reactive T cells are more frequent than can be explained by direct viral infection. On culturing, both CD4+ and CD8+ T cells from asymptomatic HIV-infected individuals died as a result of programmed cell death (apoptosis). Apoptosis was enhanced by activation with CD3 antibodies. Programmed cell death, associated with impaired T cell reactivity, may thus be responsible for the deletion of reactive T cells that contributes to HIV-induced immunodeficiency.
A new easy-to-prepare homogeneous continuous electrochromatographic bed for enantiomer recognition (2000)

Completely homogeneous polyacrylamide-based gels were used for capillary electrochromatography (CEC) of drug enantiomers. Like continuous beds (also called continuous polymer rods, silica rods, monoliths) they do not require frits to support the bed because it is covalently linked to the capillary wall. A long lifetime is an important feature of the beds. The gel matrices can be prepared in any laboratory and for specific interactions they can be derivatized with appropriate ligands. The application range is, therefore, broad. For chiral electrochromatography, negatively and positively charged polyacrylamide gels copolymerized with 2-hydroxy-3-allyloxy-propyl-β-cyclodextrin (allyl-β-CD) were prepared. The latter monomer was synthesized from β-CD and allylglycidyl ether by a very simple one-step procedure. Eight acidic, neutral and basic drug compounds were resolved into their enantiomers, most of them with baseline separation. Interestingly, the resolution is independent of the electroendosmotic velocity, i.e., rapid analyses will not give low resolution. Upon increasing this velocity, the plate height for the fast enantiomer did not change (or decreased slightly), whereas that for the slow enantiomer increased. Only the last term in the van Deemter equation contributed significantly to the total plate height. The composition of the gel was chosen such that the „pores”︁ became large enough to guarantee a satisfactory electroendosmotic flow (EOF). This open gel structure explains why acetone diffused as in free solution, i.e., independently of the presence of the gel matrix. This finding also indicates that the separation of small molecules in polyacrylamide gels cannot be explained by „molecular-sieving”︁, but rather by some type of adsorption (”︁aromatic adsorption”︁?).
Preliminary Experiments on a Microbial Fuel Cell (1962)

Experiments were initiated to determine whether microbes using a hydrocarbon as food could generate electrical energy. Experiments with ethane were unsuccessful, but when microbes or glucose oxidase were added to a solution of glucose, electrical output was observed, confirming in part previous observations. As far as we know, no one had previously tested hydrocarbons in this manner, although the several effects of microbial activity on redox potential are well known. Failure of the microbes employed to dehydrogenate ethane in the absence of molecular oxygen is discussed in the light of recently published experimental evidence.