gebhart/patrepeval huggingface dataset:
Evaluation of Different Amplification Protocols for Use in Primer-Extension Preamplification (1996)

Different amplification protocols were evaluated for use with primer-extension preamplification (PEP). We hypothesized that a protocol known to improve amplification of long DNA fragments would improve efficacy of PEP. Eight DNA samples were preamplified by PCR using different protocols. Treatments consisted of the use of Taq DNA polymerase (T), Taq plus a second polymerase obtained from Pyrococcus furiosus (E) or Stoffel fragment (S) in PEP. After preamplification, six genetic markers were genotyped, and the number of scorable genotypes was recorded. A control reaction (C) consisted of amplification using genomic DNA as template. A second experiment was performed to evaluate preamplification efficiency using Taq DNA polymerase (5 units) and exponential dilutions of Pfu DNA polymerase. After preamplification, the same procedure was used to obtain a number of scorable genotypes. In the first experiment, treatment E was the most reliable approach for amplifying genomic DNA in PEP. Treatments T and S produced fewer scorable genotypes than treatments E or C. In the second experiment, low concentrations of Pfu DNA polymerase produced a similar percentage of scorable genotypes as higher concentrations. Low concentrations of Pfu DNA polymerase combined with Taq DNA polymerase is the most cost-effective procedure to maximize amplification of limited DNA samples in PEP.
Training the brain: Practical applications of neural plasticity from the intersection of cognitive neuroscience, developmental psychology, and prevention science. (2011)

Prior researchers have shown that the brain has a remarkable ability for adapting to environmental changes. The positive effects of such neural plasticity include enhanced functioning in specific cognitive domains and shifts in cortical representation following naturally occurring cases of sensory deprivation; however, maladaptive changes in brain function and development owing to early developmental adversity and stress have also been well documented. Researchers examining enriched rearing environments in animals have revealed the potential for inducing positive brain plasticity effects and have helped to popularize methods for training the brain to reverse early brain deficits or to boost normal cognitive functioning. In this article, two classes of empirically based methods of brain training in children are reviewed and critiqued: laboratory-based, mental process training paradigms and ecological interventions based upon neurocognitive conceptual models. Given the susceptibility of executive function disruption, special attention is paid to training programs that emphasize executive function enhancement. In addition, a third approach to brain training, aimed at tapping into compensatory processes, is postulated. Study results showing the effectiveness of this strategy in the field of neurorehabilitation and in terms of naturally occurring compensatory processing in human aging lend credence to the potential of this approach. (PsycINFO Database Record (c) 2012 APA, all rights reserved).
Modulation of the biologic activities of IgE-binding factor. V. The role of glycosylation-enhancing factor and glycosylation-inhibiting factor in determining the nature of IgE-binding factors. (1984)

Glycosylation-enhancing factor (GEF) and IgE-potentiating factor were detected in culture supernatants of rat mesenteric lymph nodes (MLN) cells obtained 14 days after infection with Nippostrongylus brasiliensis (Nb), but not in supernatants of MLN cells of 8-day Nb-infected rats. Both factors were also released from T cells upon antigenic stimulation of KLH + alum-primed spleen cells. The GEF from the Nb-infected rats and KLH + alum-primed spleen cells had affinity for p-aminobenzamidine agarose and were inactivated by phenylmethylsulfonylfluoride, an inhibitor of serine proteases. These results indicate that the GEF obtained in the two systems is a serine protease and is identical to that obtained by stimulation of normal T cells with lymphocytosis-promoting factor (LPF) from Bordetella pertussis. The concomitant formation of IgE-potentiating factor and GEF by Nb infection, by antigenic simulation of KLH + alum-primed spleen cells, and by treatment of rats with Bordetella pertussis vaccine suggests that the serine protease is involved in a common pathway leading to the selective formation of IgE-potentiating factor. In contrast, glycosylation-inhibiting factor (GIF) is always found during the selective formation of IgE-suppressive factor. IgE-suppressive factor and GIF were formed by MLN cells of 8-day Nb-infected rats and KLH-CFA-primed spleen cells. GIF was detected in culture supernatants of T cell hybridomas 23A4 and 23B6, which form unglycosylated IgE-binding factors upon incubation with IgE. GIF obtained from all of these sources bound to monoclonal anti-lipomodulin. These findings indicate that GIF or lipomodulin is involved in all systems, which leads to the selective formation of IgE-suppressive factor. However, the formation of GIF was not restricted to those conditions in which IgE-suppressive factor was selectively formed. The culture supernatants of MLN cells of 14-day Nb-infected rats and antigen-stimulated KLH + alum-primed spleen cells contained a small amount of GIF, which could be detected after inactivation of GEF. It appears that T cells from these sources formed GEF and GIF, but that GEF overcame the effect of GIF on glycosylation of IgE-binding factors. The results indicate that the nature and biologic activities of IgE-binding factors are decided by the balance between GEF and GIF formed by T cells.
Electric current sensors employing spun highly birefringent optical fibers (1989)

The theory of highly elliptically birefringent fibers fabricated by spinning a linearly birefringent fiber during the draw is described. These fibers are particularly interesting for application as Faraday-effect fiber current monitors, since, in contrast to conventional fibers, they can be wound in small multiturn coils while retaining their sensitivity. The fiber and its application in three optical schemes are modeled using Jone calculus and are also experimentally investigated. A simple optical configuration is proposed, combining the elliptically birefringent fiber and a broad-spectrum light source. An accurate, compact, and robust current monitor is obtained. The sensor is characterized by a measurement repeatability of +or-0.5%, a temperature drift of 0.05%/ degrees C and a sensitivity of 1 mA RMS/Hz/sup 1/2/. Further, the performance of this sensor with optimized fiber length for a given measurement bandwidth is predicted.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An ab initio and MNDO-d SCF-MO computational study of stereoelectronic control in extrusion reactions of R2I–F iodine(III) intermediates† (1999)

MNDO-d and ab initio RHF, B3LYP and MP2 energies and geometries are reported for reactant ground and transition states for F–R′ and R–R′ extrusion and R/R′ interconversion reactions of substituted RR′I–F iodine(III) reactive intermediates. The RR′I–F reactant is predicted to form a stable asymmetric bridged dimer involving a square planar iodine centre, hitherto unconsidered as a factor in the chemistry of hypervalent iodine species. Evidence in support of this hypothesis obtained from previously reported crystal structures is discussed. The reactions of both monomer and bridged dimer are found to exhibit unusually large stereoelectronic effects at the iodine centre, deriving from electron donating and withdrawing substituents on the R groups. They are also unusual in showing transition state substituent effects which are opposite to those controlling the ground state stabilities, for which an NBO analysis is presented. Both these effects are manifest in the transition states for reaction of the dimeric species, which is stabilised by electron withdrawing groups present in the pseudo equatorial R′ group of the reacting centre and in the pseudo axial position of the unreacting R component of the dimer.
Pair-Wise Privilege Control for Cross-Domain Private Data Sharing (2010)

Enterprise-scale organizations have large numbers of internal and external users, with different privilege requirements spanning across many resources. The dynamic nature of modern organizations demands that they efficiently and securely provision and deactivate data privileges to reflect rapidly changing user responsibilities. Previous approaches to consolidated user provisioning have focused on constructing and maintaining a formal model of user privileges, in order to predict what role/roles should be assigned to any given user, based on user classification and other user attributes. In real-world deployments, formal models have not scaled well, because many users are unique and consequently there is no leverage to be gained by grouping them into roles. This paper proposes a scheme for dual control of user granular privilege and dynamic granular data access. The framework includes a correlated privilege control model and a label-based dynamic access level process. The method supports user activity control over cross-domain objects with variable data access granularity. It encompasses the advantages of existing role based and label based control, while reducing computation complexity and storage requirements. The proposed method has been formally verified and implemented in JAVA.
Diagnostic Errors—The Next Frontier for Patient Safety (2009)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Direct selection procedure for the isolation of functional centromeric DNA. (1981)

Several plasmids, each containing a segment of DNA capable of conferring mitotic stability on the ars1 vector YRp7 replicating in yeast (Saccharomyces cerevisiae), have been isolated from a yeast genomic library by direct selection for stable plasmid maintenance. The mitotic-stabilizing sequences fall into two classes: (i) segments of the yeast "2-micrometers" plasmid and (ii) DNA segments containing yeast centromeric DNA. Plasmids of the first class segregate 4+:0- through meiosis whereas the centromere plasmids segregate predominantly 2+:2-, as typical chromosomes. Previously identified centromeres from chromosomes II (CEN3) and XI (CEN11), along with the CEN11-linked gene MET14, can be isolated by this direct selection procedure. In addition, several other unidentified centromere DNAs were obtained. There are no detectable sequence homologies between CEN3 and CEN11 DNAs nor do these DNAs hybridize to the other yeast centromere regions.
Catastrophic Antiphospholipid Syndrome: Clinical and Laboratory Features of 50 Patients (1998)

We analyzed the clinical and laboratory characteristics of 50 patients with catastrophic antiphospholipid syndrome (APS) (5 from our clinics and 45 from a MEDLINE computer-assisted review of the literature from 1992 through 1996). Thirty-three (66%) patients were female and 17 (34%) were male. Twenty-eight (56%) patients had primary APS, 15 (30%) had defined systemic lupus erythematosus (SLE), 6 (12%) had "lupus-like" syndrome, and 1 (2%) had rheumatoid arthritis. Mean age of patients in this series was 38 +/- 14 years (range, 11-74 yr). Three (6%) patients developed the clinical picture of catastrophic APS under the age of 15 years, and 11 (22%) were 50 years old or more. In 11 (22%) patients, precipitating factors contributed to the development of catastrophic APS (infections in 3, drugs in 3, minor surgical procedures in 3, anticoagulation withdrawal in 2, and hysterectomy in 1). The presentation of the acute multi-organ failure was usually complex, involving multiple organs simultaneously or in a very short period of time. The majority of patients manifested microangiopathy--that is, occlusive vascular disease affecting predominantly small vessels of organs, particularly kidney, lungs, brain, heart, and liver--with a minority of patients experiencing only large vessel occlusions. Thrombocytopenia was reported in 34 (68%) patients, hemolytic anemia in 13 (26%), disseminated intravascular coagulation in 14 (28%), and schistocytes in 7 (14%). The following antibodies were detected: lupus anticoagulant (94%), anticardiolipin antibodies (94%), anti-dsDNA (87% of patients with SLE), antinuclear antibodies (58%), anti-Ro/SS-A (8%), anti-RNP (8%), and anti-La/SS-B (2%). Anticoagulation was used in 70% of the patients, steroids in 70%, plasmapheresis in 40%, cyclophosphamide in 34%, intravenous gammaglobulins in 16%, and splenectomy in 4%. Most patients, however, received a combination of nonsurgical therapies. Death occurred in 25 of the 50 (50%) patients. In most, cardiac problems seemed to be the major cause of death. In several of these, respiratory failure was also present, usually due to acute respiratory distress syndrome and diffuse alveolar hemorrhage. Among the 20 patients who received the combination of anticoagulation, steroids, and plasmapheresis or intravenous gammaglobulins, recovery occurred in 14 (70%) patients. The use of ancrod and defibrotide appeared to be effective in the 2 respective patients in whom they were used.
Proprotein convertase subtilisin/kexin type 9: A new target molecule for gene therapy (2012)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) has emerged as a novel target for controlling plasma levels of low-density lipoprotein cholesterol (LDL-C) and decreasing the risk of cardiovascular diseases. At present it is clear that the major classes of commonly prescribed lipid-lowering medications increase serum PCSK9 levels and fail to protect a significant percentage of patients from cardiovascular events. Therefore development of new LDL-C lowering medications that either do not increase circulating PCSK9 levels or work through inhibition of PCSK9 expression and protease activity is a highly desirable approach to overcome hypercholesterolemia. Since there are several agents which are being evaluated in human preclinical and clinical trials, this review summarizes current therapeutic strategies targeting PCSK9, including specific antibodies, antisense oligonucleotides, small interfering RNAs (siRNAs) and other small-molecule inhibitors.
[Experimental study of repairing peripheral nerve damage with conduit made of human hair keratin]. (2002)

As an ideal material for nerve injury repair, HHK conduits can guide tibial nerve elongation across a 10-mm gap.
Ge abundances in the lunar mantle and implications for the origin of the Moon (1984)

Regardless of the origin of the Moon, metal segregation must have occurred within the moon in order to account for its low siderophile element abundances relative to the Earth or chondrites. Germanium is a strongly siderophile element whose bulk distribution coefficient indicates that it is not fractionated during igneous processes on the Moon. The variability in absolute Ge abundances in mare basalts and pristine highland rocks, rather than elemental ratios, can be used to infer lunar mantle abundances and processes. Literature data have been compiled for Ge abundances in mare basalts and pristine highland rocks. For some landing sites, samples with 12 ppb Ge were considered to be extreme outliers and are not included. The Apollo 15 samples are enriched in Ge by a factor of 2.5 over the Apollo 12, 16 and 17 samples. Other siderophile element variations have been found in the Moon. Based on this data, best estimate of the average Ge abundance in the silicate portion of the Moon is 3.52 ppb. The Moon is depleted, relative to chondritic abundances, by a factor of 38,000 normalized to Si. Two possible explanations for the observed variations in Ge abundance in the Moon are: (1) more metal may have segregated from some regions of the Moon than from others; or Ge-bearing material may been been added later in the evolution of the Moon.
Inertial microfluidics for continuous particle separation in spiral microchannels (2009)

In this work we report on a simple inertial microfluidic device that achieves continuous multi-particle separation using the principle of Dean-coupled inertial migration in spiral microchannels. The dominant inertial forces coupled with the Dean rotational force due to the curvilinear microchannel geometry cause particles to occupy a single equilibrium position near the inner microchannel wall. The position at which particles equilibrate is dependent on the ratio of the inertial lift to Dean drag forces. Using this concept, we demonstrate, for the first time, a spiral lab-on-a-chip (LOC) for size-dependent focusing of particles at distinct equilibrium positions across the microchannel cross-section from a multi-particle mixture. The individual particle streams can be collected with an appropriately designed outlet system. To demonstrate this principle, a 5-loop Archimedean spiral microchannel with a fixed width of 500 microm and a height of 130 microm was used to simultaneously and continuously separate 10 microm, 15 microm, and 20 microm polystyrene particles. The device exhibited 90% separation efficiency. The versatility of the device was demonstrated by separating neuroblastoma and glioma cells with 80% efficiency and high relative viability (>90%). The achieved throughput of approximately 1 million cells/min is substantially higher than the sorting rates reported by other microscale sorting methods and is comparable to the rates obtained with commercial macroscale flow cytometry techniques. The simple planar structure and high throughput offered by this passive microfluidic approach make it attractive for LOC devices in biomedical and environmental applications.
Localization of the major heparin-binding site in fibronectin. (1991)

We have identified the major site required for the interaction of fibronectin (FN) with heparin. Affinity chromatography was used to test the binding ability of a library of truncated, monomeric forms of fibronectin (deminectins) containing deletions or two point mutations in the heparin-binding domain. This domain consists of type III repeats 12, 13, and 14. Deletions of individual repeats showed that both III13 and III14 are required for complete binding. Small deletions within these repeats localized a major site of heparin interaction to the amino-terminal half of III13. Site-directed mutagenesis of adjacent arginines within this sequence to uncharged residues reduced heparin binding by 98%, identifying these positively charged amino acids as essential for the interaction. A significant role for the flanking alternatively spliced regions and for repeat III12 was not found. We conclude that, while both repeats III13 and III14 participate in heparin binding, there is a major site of interaction in repeat III13 that accounts for nearly all of the activity. The significance of multiple heparin-binding sites within this domain is discussed and a model is proposed to account for how these sites may function in vivo.
Detection of a virus disease on white button mushroom (Agaricus bisporus) in Ankara, Turkey (1991)

Critically ill trauma patients were entered in a prospective, randomized trial to determine the role of gastric colonization in the development of pneumonia. Trauma patients admitted to the SICU were randomized to receive antacids (n = 27), continuous IV cimetidine (n = 32), or sucralfate (n = 30). Quantitative nasogastric tube (NGT) cultures were obtained biweekly and correlated with gastric pH, the incidence of pneumonia, and the incidence of pneumonia caused by an organism previously isolated from the stomach (percentage of gastric source of pneumonia--% GSP). Patients receiving antacids had a significantly greater pH than those receiving cimetidine (5.6 +/- 1.03 vs. 4.7 +/- 1.03; p = 0.006). However, there was no significant difference between the overall incidence of pneumonia, the percentage of NGT isolates greater than 10(6)/ml, or the % GSP. The gastric bacteriology of the three subgroups was nearly identical, with Candida albicans, Enterococci, and beta-hemolytic Streptococci being the most frequently isolated organisms. Gastric growth of organisms preceding their appearance in the blood occurred in 5 of 89 (5.6%) patients. These results suggest that 1) in trauma patients, the incidence of pneumonia is not increased by the use of stress ulcer prophylactic agents that elevate gastric pH; 2) increases in gastric pH progressively increased the number of intragastric bacteria but this did not correlate with an increased incidence of % GSP; and 3) while organisms in the upper intestinal tract may be pathogens for pneumonia, they are uncommonly a source of bacteremia in seriously injured patients.
Magnetic Evaluation of Microstructures and Strength of Eutectoid Steel (2003)

Microstructures and strength of variously heat treated eutectoid steel were evaluated by magnetic property measurements. Isothermal transformation, continuous cooling or spheroidization heat treatment was performed to produce various microstructures. Microstructural parameters (phase, pearlite interlamellar spacing), mechanical properties (fracture strength) and magnetic parameters (coercivity, remanence, hysteresis loss, saturation magnetization) were measured to investigate the relationships among these parameters. Coercivity and remanence were observed to be high in order of martensite, pearlite and ferrite phase. The linear decrease of coercivity and remanence with the interlamellar spacing and the linear increase of those with fracture strength of pearlitic eutectoid steel were found. Coercivity and remanence were suggested as potential magnetic parameters for discriminating phases and quantitatively assessing the pearlite interlamellar spacing as well as strength of eutectoid steel.