gebhart/patrepeval huggingface dataset:
Chemical structure of the lipid A component of the lipopolysaccharide from a <i>Proteus mirabilis</i> Re‐mutant (1983)

The chemical structure of the lipid A component from the lipopolysaccharide of a Proteus mirabilis Re-mutant (strain R45) was analysed. It consists of a beta(1-6)-linked D-glucosamine disaccharide which carries two phosphate groups, one being ester-linked to position 4' of the nonreducing glucosaminyl residue and the other being bound to the glycosidic hydroxyl group of the reducing glucosaminyl residue. The ester-bound phosphate group is quantitatively substituted by a 4-amino-4-deoxy-L-arabinopyranosyl residue, the glycosidic phosphoryl group appears to be unsubstituted. Two available hydroxyl groups of the disaccharadide (probably at positions 3 and 3') are acylated by approximately 1 mol each of (R)-3-tetradecanoyloxytetradecanoic and (R)-3-hydroxytetradecanoic acid/mol. The amino group of the nonreducing glucosaminyl residue carries (R)-3-tetradecanoyloxytetradecanoic and that of the reducing residue (R)-3-hydroxytetradecanoic acid. In addition smaller amounts of (R)-3-hexadecanoyloxytetradecanoic acid are present in amide linkage. The attachment site of the oligosaccharide portion to lipid A was also investigated. It was found that the hydroxyl group at position 6' of the nonreducing glucosaminyl residue carries 3-deoxy-D-manno-octulosonic acid. This indicates that the saccharide portion in this Proteus lipopolysaccharide is linked to lipid A via the primary hydroxyl group in position 6'.
EXPERIMENTAL DEMYELINATION BY MEANS OF ENZYMES, ESPECIALLY THE ALPHA TOXIN OF CLOSTRIDIUM WELCHII (1950)

DEMYELINATING diseases still constitute one of the major problems of neurology, and the lack of knowledge concerning their etiology is a constant handicap to rational therapy. The various manifestations of myelin degradation, as observed in the different demyelinating diseases, have been explained by divers causes: mechanical, chemical, infectious, immunologic and hereditary. The variety of mechanisms underlying the breakdown of myelin apparently is so great that one wonders with Hurst 1 whether is not a type of response of the nervous system to noxious stimuli of multiple causation. On the other hand, it may be that demyelination itself is not always precisely the same thing. The order of events and the extent of degradation may not always be identical in the demyelinating process, and the implications of these variations may be significant. It was shown in 1931 2 that experimental venous thrombosis might act as a contributory cause of demyelination.
Pilot-Scale Lactic Acid Production via Batch Culturing of Lactobacillus sp. RKY2 Using Corn Steep Liquor As a Nitrogen Source (2006)

In this study, the determination of the efficiency of a pilot-scale fermentation process using corn steep liquor as a nitrogen source was attempted in order to produce lactic acid via batch culturing of Lactobacillus sp. RKY2. Using pure glucose, fermentation efficiency characteristics, such as final lactic acid, cell growth, yield, and productivity were not substantially influenced by the scale-up of the laboratory-scale fermentation from 2.5- to 30- and 300-litre scale fermentations. In all experiments, the content of lactic acid produced increased in a linear fashion with increases in the initial glucose concentration. In the experiments using wood hydrolyzate, both lactic acid productivity and cell growth were decreased as a result of the scaling-up of the fermentation. This might be attributed to the toxic chemicals contained in the wood hydrolyzates. However, in all experiments, lactic acid yields remained higher than 90 % with regard to the amount of glucose consumed. Therefore, lactic acid was successfully produced by the pilot-scale bioreactor scheme adopted in this study.
Lactobacillus fermentum CECT 5716 prevents and reverts intestinal damage on TNBS-induced colitis in mice (2009)

Pretreatment with L. fermentum CECT 5716 attenuates TNBS colitis, an effect that seems to be due to its antioxidant abilities. When administered after TNBS, this probiotic is also effective in accelerating colitis recovery, and this is associated with an enhanced Toll-like receptor function.
Randomized Trial of Trimethoprim-Sulfamethoxazole versus Pyrimethamine-Sulfadiazine for Therapy of Toxoplasmic Encephalitis in Patients with AIDS (1998)

The aim of the present pilot study was to compare the efficacy and safety of trimethoprim (TMP) and sulfamethoxazole (SMX) with those of the standard therapy pyrimethamine (P)-sulfadiazine (S) for the treatment of toxoplasmic encephalitis in patients with AIDS. This was a pilot, multicenter, randomized, and prospective study. Patients were randomly assigned to receive TMP (10 mg/kg of body weight/day) and SMX (50 mg/kg/day) or P (50 mg daily) and S (60 mg/kg/day) as acute therapy (for 4 weeks) and then as maintenance therapy for 3 months at half of the original dosage. Seventy-seven patients were enrolled and randomized to the study: 40 patients were treated with TMP-SMX and 37 were treated with P-S. There was no statistically significant difference in clinical efficacy during acute therapy. In contrast, patients randomized to TMP-SMX appeared more likely to achieve a complete radiologic response after acute therapy. Adverse reactions were significantly more frequent in patients treated with P-S, and skin rash was the most common adverse event noted in these patients. In conclusion, the results of the study suggest that TMP-SMX appears to be a valuable alternative to P-S, in particular in patients with opportunistic bacterial infections.
DNA Polymerase e - More Than a Polymerase (2003)

This paper presents a comprehensive review of the structure and function of DNA polymerase epsilon. Together with DNA polymerases alpha and delta, this enzyme replicates the nuclear DNA in the eukaryotic cell. During this process, DNA polymerase alpha lays down RNA-DNA primers that are utilized by DNA polymerases delta and epsilon for the bulk DNA synthesis. Attempts have been made to assign these two enzymes specifically to the synthesis of the leading and the lagging strand. Alternatively, the two DNA polymerases may be needed to replicate distinct regions depending on chromatin structure. Surprisingly, the essential function of DNA polymerase epsilon does not depend on its catalytic activity, but resides in the nonenzymatic carboxy-terminal domain. This domain not only mediates the interaction of the catalytic subunit with the three smaller regulatory subunits, but also links the replication machinery to the S phase checkpoint. In addition to its role in DNA replication, DNA polymerase epsilon fulfils roles in the DNA synthesis step of nucleotide excision and base excision repair, and has been implicated in recombinational processes in the cell.
Analytical design of magnetic loop induction systems (1965)

The method of orthogonal fields, presented in the companion article, permits the design of a loop system with little spreading out of the resultant magnetic field. This article describes the mathematical basis of the design. Good approximation and ease of handling are obtained by the use of complex function theory and conformal mapping. Two solutions for the problem emerge, one based on the properties of hyperbolic functions, the other on those of elliptic functions. In the first solution, the field decays monotonically to zero outside the primary area of communication. In the second solution, the field exhibits equiripple character in the region where communication is to be prevented. The ultimate design was chosen from the second category, after elaborate computation with the help of an electronic computer.
Waste in the US Health Care System (2019)

In this review based on 6 previously identified domains of health care waste, the estimated cost of waste in the US health care system ranged from $760 billion to $935 billion, accounting for approximately 25% of total health care spending, and the projected potential savings from interventions that reduce waste, excluding savings from administrative complexity, ranged from $191 billion to $286 billion, representing a potential 25% reduction in the total cost of waste. Implementation of effective measures to eliminate waste represents an opportunity reduce the continued increases in US health care expenditures.
Differences in the regulation of messenger RNA for housekeeping and specialized-cell ferritin. A comparison of three distinct ferritin complementary DNAs, the corresponding subunits, and identification of the first processed in amphibia. (1987)

The ferritin family is a widespread group of proteins that maintain iron in a soluble form and also protect against the toxic effects of excess iron. The structure and sequence of the proteins are highly conserved. However, the cell-specific features of structure which occur within the same organism indicate cell specificity of gene expression and may be related to variations in types of iron storage, i.e. specialized-cell ferritin (stored iron is for other cell types) versus housekeeping ferritin (stored iron is for intracellular purposes related to normal or stress metabolism); the protein structure may also affect rates of iron turnover. Iron induces ferritin synthesis and accumulation by recruiting stored ferritin mRNA that is efficiently translated in cells specialized for iron storage. For the first time we show the occurrence of three different cDNAs from bullfrog tadpoles, corresponding to three subunits of the protein: H, M, and L. Thus, ferritin can be encoded by at least three different mRNAs and probably three different genes, in contrast to the older idea of two, H and L; the subunits maintain the conserved sequences of known ferritins and have similar predicted masses, 20.5, 20.6, and 19.9 kDa, but have distinct mobilities in denaturing gels. Ferritin subunit expression is cell specific; more of the H and L chain mRNAs are expressed in red cells than in liver. Ferritin expression is regulated by transcription (or mRNA stability) in adult red cells; cellular levels of ferritin mRNA were 20% that of embryonic red cells, and L subunit mRNA increased 2.5 times with excess iron. Ferritin expression is also regulated during translation in adult red cells; iron recruits stored ferritin mRNA, but only during certain stages of red cell maturation, in contrast to embryonic red cells. The developmental differences in ferritin expression are discussed in relation to the shift from specialized-cell ferritin to housekeeping ferritin in red cells of the embryonic versus adult lines.
Bioengineered Norovirus S<sub>60</sub> Nanoparticles as a Multifunctional Vaccine Platform (2018)

Homotypic interactions of viral capsid proteins are common, driving viral capsid self-formation. By taking advantage of such interactions of the norovirus shell (S) domain that naturally builds the interior shells of norovirus capsids, we have developed a technology to produce 60-valent, icosahedral S<sub>60</sub> nanoparticles through the E. coli system. This has been achieved by several modifications to the S domain, including an R<sub>69</sub>A mutation to destruct an exposed proteinase cleavage site and triple cysteine mutations (V<sub>57</sub>C/Q<sub>58</sub>C/S<sub>136</sub>C) to establish inter-S domain disulfide bonds for enhanced inter-S domain interactions. The polyvalent S<sub>60</sub> nanoparticle with 60 exposed S domain C-termini offers an ideal platform for antigen presentation, leading to enhanced immunogenicity to the surface-displayed antigens for vaccine development. This was proven by constructing a chimeric S<sub>60</sub> nanoparticle displaying 60 rotavirus (RV) VP8* proteins, the major RV-neutralizing antigen. These S<sub>60</sub>-VP8* particles are easily produced and elicited high IgG response in mice toward the displayed VP8* antigens. The mouse antisera after immunization with the S<sub>60</sub>-VP8* particles exhibited high blockades against RV VP8* binding to its glycan ligands and high neutralizing activities against RV infection in culture cells. The three-dimensional structures of the S<sub>60</sub> and S<sub>60</sub>-VP8* particles were studied. Furthermore, the S<sub>60</sub> nanoparticle can display other antigens, supporting the notion that the S<sub>60</sub> nanoparticle is a multifunctional vaccine platform. Finally, the intermolecular disulfide bond approach may be used to stabilize other viral-like particles to display foreign antigens for vaccine development.
Outcome After Partial Medial Meniscus Substitution With the Collagen Meniscal Implant at a Minimum of 10 Years' Follow‐up (2011)

Purpose The aim of the study was to evaluate the clinical outcome of a collagen meniscus graft implanted in an injured medial meniscus after a minimum of 10 years' follow‐up. Methods Twenty‐five patients underwent arthroscopic implantation of the collagen meniscus device. They had either persistent compartmental joint line pain due to a previous medial meniscus resection (5 cases) or a large irreparable meniscus tear at arthroscopy (20 cases). Implant failure was defined as infection due to the implant or mechanical failure of the device. Twenty‐two patients returned for clinical, functional, and radiographic evaluation. Magnetic resonance imaging was also performed and was analyzed with the criteria of Genovese et al. (where type 3 indicates normal and type 1 indicates completely abnormal). All the aforementioned evaluations were carried out at a minimum of 10 years (range, 10.1 to 12.5 years) after the procedure. Results The mean Lysholm score improved from 59.9 preoperatively to 89.6 at 1 year ( P < .001), and it was 87.5 at final follow‐up ( P < .001). The results were good or excellent in 83% of the population. No differences were observed when we compared the Lysholm score at 1 year of follow‐up with the score at final follow‐up ( P > .05). The mean pain score on a visual analog scale improved by 3.5 points at final follow‐up. Patient satisfaction with the procedure was 3.4 of 4 points. Radiographic evaluation showed either minimal or no narrowing of the joint line. Magnetic resonance imaging showed type 2 in 64% of cases and type 3 in 21%. All cases showed less volume than expected (size type 2 in 89%). The failure rate in the patient population was 8% (2 of 25). There were no complications related to the device. Conclusions Although there were several different types of patients and acute and chronic tears were treated in a limited number of patients, meniscal substitution with the collagen meniscal implant provides significant pain relief and functional improvement after a minimum of 10 years' follow‐up. The implant generally diminished in size, but the procedure proved to be safe and had a low rate of implant failure on a long‐term basis. No development or progression of degenerative knee joint disease was observed in most cases. Level of Evidence Level IV, therapeutic case series.
Experimental Validation of an Efficient Fan-Beam Calibration Procedure for <formula formulatype="inline"><tex Notation="TeX">$k$</tex></formula>-Nearest Neighbor Position Estimation in Monolithic Scintillator Detectors (2015)

Monolithic scintillator detectors can achieve excellent spatial resolution and coincidence resolving time. However, their practical use for positron emission tomography (PET) and other applications in the medical imaging field is still limited due to drawbacks of the different methods used to estimate the position of interaction. Common statistical methods for example require the collection of an extensive dataset of reference events with a narrow pencil beam aimed at a fine grid of reference positions. Such procedures are time consuming and not straightforwardly implemented in systems composed of many detectors. Here, we experimentally demonstrate for the first time a new calibration procedure for k-nearest neighbor ( k-NN) position estimation that utilizes reference data acquired with a fan beam. The procedure is tested on two detectors consisting of 16 mm ×16 mm ×10 mm and 16 mm ×16 mm ×20 mm monolithic, Ca-codoped LSO:Ce crystals and digital photon counter (DPC) arrays. For both detectors, the spatial resolution and the bias obtained with the new method are found to be practically the same as those obtained with the previously used method based on pencil-beam irradiation, while the calibration time is reduced by a factor of ~ 20. Specifically, a FWHM of ~ 1.1 mm and a FWTM of ~ 2.7 mm were obtained using the fan-beam method with the 10 mm crystal, whereas a FWHM of ~ 1.5 mm and a FWTM of ~ 6 mm were achieved with the 20 mm crystal. Using a fan beam made with a ~ 4.5 MBq <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">22</sup> Na point-source and a tungsten slit collimator with 0.5 mm aperture, the total measurement time needed to acquire the reference dataset was ~ 3 hours for the thinner crystal and ~ 2 hours for the thicker one.
Experimental Study of Acoustic Resonances in the Side Cavities of a High-Pressure Centrifugal Compressor Excited by Rotor/Stator Interaction (2010)

Under unfavorable conditions aerodynamic and aeroacoustic excitation mechanisms may lead to fatigue failures of centrifugal compressor impellers. The mechanisms for consideration are, for example, the arising pressure patterns due to rotor/stator interactions, the so-called Tyler/Sofrin modes, or acoustic resonances in the compressor housing. In a research program, a high-pressure radial compressor has been equipped with a multiplicity of sensors to investigate the excitation and interaction mechanisms in a complete centrifugal compressor stage. The current paper deals with the experimental detection of acoustic resonances in the compressor side cavities and the excitation of these acoustic eigenmodes due to Tyler/Sofrin modes. In this context the test rig and the installed instrumentation are briefly described. The methods of measuring as well as the analyzing techniques for detecting acoustic resonances and evaluating the measurements are presented. In addition, acoustic eigenmodes have been calculated by the finite-element method for the representative numerical test rig parameters. Results are presented and compared to the experimental findings. The accomplished experiments are the first available in open literature showing that the fluid core rotation in the compressor side cavities plays a crucial role for the prediction of the acoustic eigenfrequencies with respect to the rotor frame of reference. Without taking into account the effect of fluid rotation, large deviations between predicted (simulated) and measured acoustic eigenfrequencies would be the result.
Quarantine Treatments of Imported Nursery Plants and Exported Cut Flowers by Phosphine Gas (PH<sub>3</sub>) as Methyl Bromide Alternative (2016)

Quarantine treatments by phosphine (PH<sub>3</sub>) gas have been performed to replace methyl bromide (MeBr) for export cut flowers and imported nursery plant in Korea. In this preliminary study, two dominant insect pests of cut flowers, Tetranychus urticae Koch and Frankliniella occidentalis Pergande, and the dominant insect pest of nursery plants, Planococcus citri Risso, were used to certify optimum concentration and fumigation time, along with evaluation of phytotoxic damages. To validate the results of preliminary tests, quarantine treatments for export cut flowers was performed in a 58-m<sup>3</sup> reefer container. When 14 species of cut flowers were fumigated with 2 g m<sup>-3</sup> PH<sub>3</sub> for 24 h (Ct product was 30.9 g h m<sup>-3</sup>) at 5 °C, all pests were effectively controlled and no phytotoxic damage were observed on roses and chrysanthemums. On quarantine trials for imported nursery trees, which was performed at 10 m<sup>3</sup> scale covered with a PVC-tarpaulin tent, 2 g m<sup>-3</sup> of PH<sub>3</sub> for 24 h (Ct product was 30.0 g h m<sup>-3</sup>) at 15 °C was enough to kill all pests and no damage was observed on seven species of nursery plants. Phosphine gas shows the promise as MeBr alternative to perishable commodities in terms of efficacy to certain quarantine pest and maintenance of its quality as well as being a more environmentally safe fumigant.
EEG source localization in focal epilepsy: Where are we now? (2007)

Electroencephalographic source localization (ESL) by noninvasive means is an area of renewed interest in clinical epileptology. This has been driven by innovations in the computer-assisted modeling of dipolar and distributed sources for the investigation of focal epilepsy; a process fueled by the ever-increasing computational power available to researchers for the analysis of scalp EEG recordings. However, demonstration of the validity and clinical utility of these mathematically derived source modeling techniques has struggled to keep pace. This review evaluates the current clinical "fitness' of ESL as applied to the focal epilepsies by examining some of the key studies performed in the field, with emphasis given to clinical work published in the last five years. In doing so, we discuss why ESL techniques have not made an impact on routine epilepsy practice, underlining some of the current problems and controversies in the field. We conclude by examining where ESL currently sits alongside magnetoencephalography and combined EEG-functional magnetic resonance imaging in the investigation of focal epilepsy.
Interplay of heritage and habitat in the distribution of bacterial signal transduction systems (2010)

Comparative analysis of the complete genome sequences from a variety of poorly studied organisms aims at predicting ecological and behavioral properties of these organisms and helping in characterizing their habitats. This task requires finding appropriate descriptors that could be correlated with the core traits of each system and would allow meaningful comparisons. Using the relatively simple bacterial models, first attempts have been made to introduce suitable metrics to describe the complexity of organism's signaling machinery, which included introducing the "bacterial IQ" score. Here, we use an updated census of prokaryotic signal transduction systems to improve this parameter and evaluate its consistency within selected bacterial phyla. We also introduce a more elaborate descriptor, a set of profiles of relative abundance of members of each family of signal transduction proteins encoded in each genome. We show that these family profiles are well conserved within each genus and are often consistent within families of bacteria. Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche.
Joint sparsity-based optimization of a set of orthonormal 2-D separable block transforms (2009)

We propose an iterative method for the optimization of a set of 2-D separable transforms for a given training data set. The method outputs orthornormal transforms, each one being optimal for a subset of the data with respect to a sparsity-based objective function. The vertical and horizontal directions of the transform may be different, thus allowing directional-adapted transforms (in contrast to the usual DCT). Additionally, we relate the reconstruction error and the sparsity cost terms through the quantization step. To prove the validity of our approach, experimental results concerning coding applications are provided.
MPLS Tunnel Support for Proxy Mobile IPv6 (2008)

The Proxy Mobile IPv6 allows a mobile node's IPv4 and IPv6 traffic
between a Local Mobility Anchor(LMA) and a Mobile Access Gateway (MAG)
to be tunneled using IPv6, IPv4 or IPv4-UDP encapsulation headers. In
this document, Multiprotocol Label Switching (MPLS) tunneling is
proposed as an alternative tunnel technology which is used between a
MAG and a LMA. MPLS is now become more and more popular, and MPLS
support is an important function for edge and core routers.
Integrating MPLS and Proxy IP Mobility can leverage Proxy IP Mobility
deployment in the industry.