gebhart/patrepeval huggingface dataset:
<title>Detection of ultrasonic vibrations on rough surfaces through the photorefractive effect</title> (1996)

We present and describe two techniques used for optical detection of ultrasonic signals based on the photorefractive effect. These techniques used the wavefront adaptation properties of the photorefractive effect. In the photorefractive beam combiner, a local oscillator matched to the signal wavefront is created, leading to an homodyne detection system having a large etendue. In the double phase conjugate heterodyne detection system the signal beam wavefront is cleaned by a double phase conjugate mirror and transformed in a plane wave that is sent on a classical heterodyne detection system. Both systems are characterized and used to detect ultrasound.
NADPH oxidase activity is higher in cerebral versus systemic arteries of four animal species: role of Nox2 (2008)

We previously reported that NADPH oxidase activity is greater in intracranial cerebral versus systemic arteries of the rat. Here, we first tested whether NADPH oxidase activity is also greater in intracranial cerebral than systemic arteries of three other animal species, i.e., mouse, rabbit, and pig. Second, using Nox2-deficient mice, we evaluated the involvement of Nox2-containing NADPH oxidases in any such regional differences. NADPH-stimulated superoxide (O(2)(-)) production by basilar, middle cerebral arteries (MCA), and common carotid arteries (CA) and thoracic aorta (AO) from rat, mouse, rabbit, and pig was measured using lucigenin-enhanced chemiluminescence. Basal production of O(2)(-) and hydrogen peroxide (H(2)O(2)) by cerebral arteries, AO, and CA from wild-type (WT) and Nox2(-/-) mice was measured using L-012-enhanced chemiluminescence and Amplex Red fluorescence, respectively. Western blotting was used to measure Nox2 and SOD1-3 protein expression, and immunofluorescence was used to localize Nox2, in mouse arteries. In rats, WT mice, rabbits, and pigs, NADPH-stimulated O(2)(-) production by cerebral arteries was up to 40-fold greater than that in AO and CA. In WT mice, basal O(2)(-) and H(2)O(2) production by cerebral arteries was ninefold and approximately 2.5-fold higher, respectively, than that in AO and CA and was associated with approximately 40% greater expression of Nox2 protein. Nox2 immunofluorescence was localized to the endothelium, and to a lesser extent the adventitia, in all mouse arteries and appeared to be more intense in endothelium of MCA than AO or CA. In Nox2(-/-) mice, NADPH-stimulated O(2)(-) production by cerebral arteries was approximately 35% lower than that in WT mice, whereas Nox2 deletion had no significant effect on O(2)(-) production by AO or CA. Thus NADPH oxidase activity is greater in intracranial cerebral versus systemic arteries of several animal species and is associated with higher cerebrovascular expression and activity of Nox2.
Nonsteroidal Anti-Inflammatory Drugs and Cancer Prevention (2000)

Nonsteroidal anti-inflammatory drugs (NSAIDs), including aspirin, appear to have clinically significant anticarcinogenic effects in the gastrointestinal tract. Epidemiological data indicate that use of these drugs is inversely associated with the risk of sporadic colorectal cancer, and clinical trials among patients with familial polyposis coli show that NSAIDs can lead to the regression of large bowel adenomas. Animal studies have reported a similar efficacy of NSAIDs against experimental carcinogenesis. A consistent pattern in this research is that continued long-term use of NSAIDs is required for an anticancer effect--up to 15 or 20 years before a reduced risk of colorectal cancer appears. Epidemiological data also suggest possible protective effects in the stomach and esophagus. The mechanisms underlying any chemopreventive effect of NSAIDs are not clear. Inhibition of cyclooxygenase is one possibility, but pathways independent of cyclooxygenase and prostaglandins are also possible.
Nano DCPA-Whisker Composites with High Strength and Ca and PO4 Release (2006)

The main challenges facing composite restorations are secondary caries and bulk fracture. The objective of this study was to develop nano DCPA (dicalcium phosphate anhydrous)-whisker composites with high strength and Ca and PO(4) ion release to combat caries. Flexural strength for the nano DCPA-whisker composites at a nano DCPA:whisker mass ratio of 1:2 ranged from (148 +/- 9) MPa to (167 +/- 23) MPa, significantly higher than the (103 +/- 32) MPa of an inlay/onlay commercial control composite without Ca-PO(4) release. The nano DCPA-whisker composite released PO(4) to a concentration of (1.95 +/- 0.13) mmol/L and Ca of (0.68 +/- 0.05) mmol/L. Compared with previous conventional Ca- and PO(4)-releasing composites, the nano DCPA-whisker composites had strengths two-fold higher, and released comparable or higher levels of Ca and PO(4). In conclusion, combining nano-DCPA with whiskers yielded novel composites that released high levels of Ca and PO(4) requisite for remineralization. These high-strength composites may provide a unique combination of stress-bearing and caries-inhibiting capabilities.
Major parietal cell antigen in autoimmune gastritis with pernicious anemia is the acid-producing H+,K+-adenosine triphosphatase of the stomach. (1988)

In autoimmune gastritis antibodies against a membrane-bound parietal cell antigen of previously unknown function are present in the sera of patients. In this study, a vesicular membrane preparation of porcine gastric mucosa cells was found to be a potent antigenic source. This preparation blocked greater than 90% of antibody binding to a lysate of gastric mucosa cells. The membrane fraction contained H+,K+-ATPase (EC 3.6.1.36) as the major protein, which in sodium dodecyl sulfate-polyacrylamide gel electrophoresis migrated with a weight of 92 kD. After reduction and alkylation, this component was resolved into two bands of similar staining intensity (92 and 88 kD). Immunoblotting analysis showed that sera of patients recognized antigen with pattern identical to the major protein of the vesicular membranes. Protein A-Sepharose beads preincubated with immunoglobulins of five individual patient (but not control) sera were all found to reduce both the H+,K+-ATPase activity and the amount of parietal cell antigen of a preparation of vesicular membranes solubilized in n-octylglucoside. Taken together, the results of this study indicate that the major parietal cell antigen is identical to the acid-producing enzyme, H+,K+-ATPase, of the parietal cell.
Laboratory production of Vouchered reference charcoal from small wood samples and non‐woody plant tissues (2005)

Abstract Taxonomic identification of small fragments of burned plant tissue in lake sediment profiles can enhance reconstructions of past vegetation, fire regimes, and climate. Vouchered reference collections of charcoal prepared from both soft and woody plant tissues, analogous to modern pollen reference collections, will be required for making rigorous identifications and for knowing the level of certainty achieved. Published methods of laboratory production of charcoal may only poorly mimic pyrolysis as it occurs in wildfires, and tend to require large volumes of plant material. We present a method for preparing reference charcoal from dried plant specimens that is simple, provides a high degree of control, yet requires only small tissue samples. Based on results of a series of experiments, we recommend placing dried samples in 25 cm3 perforated‐base porcelain Gooch filtering crucibles, surrounded by 250–500 μm sand; saturating the sand with water and draining; and placing for eight to nine minutes in a furnace heated to 550°C. The wet sand delays heating so that temperature rise is steep. Pyrolysis is brief and occurs under hypoxic conditions due to temporary oxygen flushing by water vapor. Using our method we achieved excellent results on both woody and soft tissues from a variety of plant taxa.
Postnatal development of synaptic transmission in local networks of L5A pyramidal neurons in rat somatosensory cortex (2007)

The probability of synaptic transmitter release determines the spread of excitation and the possible range of computations at unitary connections. To investigate whether synaptic properties between neocortical pyramidal neurons change during the assembly period of cortical circuits, whole-cell voltage recordings were made simultaneously from two layer 5A (L5A) pyramidal neurons within the cortical columns of rat barrel cortex. We found that synaptic transmission between L5A pyramidal neurons is very reliable between 2 and 3 weeks of postnatal development with a mean unitary EPSP amplitude of approximately 1.2 mV, but becomes less efficient and fails more frequently in the more mature cortex of approximately 4 weeks of age with a mean unitary EPSP amplitude of 0.65 mV. Coefficient of variation and failure rate increase as the unitary EPSP amplitude decreases during development. The paired-pulse ratio (PPR) of synaptic efficacy at 10 Hz changes from 0.7 to 1.04. Despite the overall increase in PPR, short-term plasticity displays a large variability at 4 weeks, ranging from strong depression to strong facilitation (PPR, range 0.6-2.1), suggesting the potential for use-dependent modifications at this intracortical synapse. In conclusion, the transmitter release probability at the L5A-L5A connection is developmentally regulated in such a way that in juvenile animals excitation by single action potentials is efficiently transmitted, whereas in the more mature cortex synapses might be endowed with a diversity of filtering characteristics.
Thermographic Selection of Effective Catalysts from an Encoded Polymer-Bound Library (1998)

A general method is introduced for the rapid and simultaneous evaluation of each member of large encoded catalyst libraries for the ability to catalyze a reaction in solution. The procedure was used to select active catalysts from a library of potential polymer-bound multifunctional catalysts. From approximately 7000 beads screened (3150 distinct catalysts), 23 beads were selected for catalysis of an acylation reaction. Kinetic experiments indicate that the most strongly selected beads are also the most efficient catalysts.
The Drosophila melanogaster dodo (dod) gene, conserved in humans, is functionally interchangeable with the ESS1 cell division gene of Saccharomyces cerevisiae. (1996)

We have sequenced the region of DNA adjacent to and including the flightless (fli) gene of Drosophila melanogaster and molecularly characterized four transcription units within it, which we have named tweety (twe), flightless (fli), dodo (dod), and penguin (pen). We have performed deletion and transgenic analysis to determine the consequences of the quadruple gene removal. Only the flightless gene is vital to the organism; the simultaneous absence of the other three allows the overriding majority of individuals to develop to adulthood and to fly normally. These gene deletion results are evaluated in the context of the redundancy and degeneracy inherent in many genetic networks. Our cDNA analyses and data-base searches reveal that the predicted dodo protein has homologs in other eukaryotes and that it is made up of two different domains. The first, designated WW, is involved in protein-protein interactions and is found in functionally diverse proteins including human dystrophin. The second is involved in accelerating protein folding and unfolding and is found in Escherichia coli in a new family of peptidylprolyl cis-trans isomerases (PPIases; EC 5.2.1.8). In eukaryotes, PPIases occur in the nucleus and the cytoplasm and can form stable associations with transcription factors, receptors, and kinases. Given this particular combination of domains, the dodo protein may well participate in a multisubunit complex involved in the folding and activation of signaling molecules. When we expressed the dodo gene product in Saccharomyces cerevisiae, it rescued the lethal phenotype of the ESS1 cell division gene.
An assessment of finite difference beam propagation method (1990)

A finite-difference beam propagation method (FD-BPM) is outlined and assessed in comparison with a conventional beam propagation method (FFT-BPM) which uses fast Fourier transformation. In the comparative study three straight waveguides with different index profiles that are frequently encountered in integrated optics are utilized. Using both methods normalized effective index values of the eigenmodes of these waveguides are calculated and compared with the exact values obtained from analytical expressions. As a further accuracy criterion, the power loss due to numerical errors when an eigenmode of a waveguide is excited is evaluated. Based on this comparison the accuracy, computational efficiency, and stability of the FD-BPM are assessed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Morphological Analysis of Human Embryonic Development Using Time-Lapse Cinematography (2006)

The dynamic observation of human gametes and the early stage of embryos is of paramount interest for clarifying the physiological events during the fertilization process. We present our morphological analysis of human embryonic development after both intracytoplasmic sperm injection (ICSI) and in vitro fertilization (IVF) using time-lapse cinematography. The results of this study indicate that non-invasive imaging, time-lapse cinematography, is useful not only for elucidating the morphological events of fertilization in humans, but also for evaluating the physiological importance of these events during the early stages of human embryonic development. In addition, analysis of cellular activity and quality during fertilization and embryogenesis using this system will contribute to the future improvement of the clinical results of assisted reproductive technology (ART).
Sampling Large Databases for Association Rules (1996)

Discovery of association rules.is an import-ant database mining problem. Current al-gorithms for finding association rules require several passes over the analyzed database, and obviously the role of I/O overhead is very sig-nificant for very large databases. We present new algorithms that reduce the database activ-ity considerably. The idea is to pick a Random sample, to find using this sample all associ-ation rules that probably hold in the whole database, and then to verify the results with the rest of the database. The algorithms thus produce exact association rules, not approx-imations based on a sample. The approach is, however, probabilistic, and in those rare cases where our sampling method does not produce all association rules, the missing rules can be found in a second pass. Our experiments show that the proposed algorithms can find associ-ation rules very efficiently in only one database Pa= 1
A High-Density Whole-Genome Association Study Reveals That APOE Is the Major Susceptibility Gene for Sporadic Late-Onset Alzheimer's Disease (2007)

This study provides empirical support for the suggestion that the APOE locus is the major susceptibility gene for late-onset AD in the human genome, with an OR significantly greater than any other locus in the human genome. It also supports the feasibility of the ultra-high-density whole-genome association approach to the study of AD and other heritable phenotypes. These whole-genome association studies show great promise to identify additional genes that contribute to the risk of AD.
Complications, Adverse Reactions, and Insights With the Use of Botulinum Toxin (2003)

In Brief Study Design. This study was an exploratory repeated measures design comparing patients undergoing two magnitudes of surgery in the lumbar spine: lumbar herniated disc repair and posterior lumbar fusion. Objective. The present study evaluated and compared the effect of perceived pain, perceived stress, anxiety, and mood on natural killer cell activity (NKCA) and IL-6 production among adult patients undergoing lumbar surgery. Summary of Background Data. Presurgical stress and anxiety can lead to detrimental patient outcomes after surgery, such as increased infection rates. It has been hypothesized that such outcomes are due to stress-immune alterations, which may be further exacerbated by the extent of surgery. However, psychologic stress, anxiety, and mood have not been previously characterized in patients undergoing spinal surgery. Methods. Pain, stress, anxiety, and mood were measured using self-report instruments at T1 (1 week before surgery), T2 (the day of surgery), T3 (the day after surgery), and T4 (6 weeks after surgery). Blood (30 mL) was collected for immune assessments at each time point. Results. Pain, stress, anxiety, and mood state were elevated at baseline in both surgical groups and were associated with significant reduction in NKCA compared with the nonsurgical control group. A further decrease in NKCA was observed 24 hours after surgery in both surgical groups with a significant rise in stimulated IL-6 production, regardless of the magnitude of surgery. In the recovery period, NKCA increased to or above baseline values, which correlated with decreased levels of reported pain, perceived stress, anxiety, and mood state. Conclusions. This study demonstrated that patients undergoing elective spinal surgery are highly stressed and anxious, regardless of the magnitude of surgery and that such psychologic factors may mediate a reduction in NKCA. The present study evaluated and compared the effect of perceived pain, stress, anxiety, and mood on natural killer cell activity (NKCA) and IL-6 production among adult patients undergoing lumbar surgery. The preoperative rise in pain, stress, anxiety, and mood was associated with a reduction in NKCA and a rise in IL-6 in the perioperative period.
Susceptibility of lamivudine-resistant hepatitis B virus to other reverse transcriptase inhibitors (1999)

The emergence of resistant hepatitis B virus (HBV), with mutations in the YMDD motif of the polymerase gene after treatment with lamivudine, is becoming an important clinical problem. In this study, susceptibility of wild-type and lamivudine-resistant HBV M552I, M552V, and L528M/M552V mutants to other reverse transcriptase inhibitors was investigated by transient transfection of full-length HBV DNA into human hepatoma cells. HBV DNA replication was monitored by Southern blot hybridization, which showed the presence of a single-stranded band (representative of the HBV replicative intermediates) in the drug-free, wild-type HBV-transfected cells. This band was diminished in the samples of wild-type HBV DNA treated with either lamivudine, adefovir, or lobucavir. The band intensities from the lamivudine-resistant mutants were not decreased by treatment with lamivudine, but were decreased by the treatments with adefovir or lobucavir. In contrast, penciclovir and nevirapine did not diminish the intensity of the single-stranded band of wild-type HBV or the lamivudine-resistant mutants. These results demonstrate that lamivudine-resistant HBV is susceptible to adefovir and lobucavir. Lamivudine-resistant HBV should be treated with adefovir or lobucavir, and combination therapy with lamivudine and adefovir/lobucavir may prevent the emergence of lamivudine-resistant HBV.
Recommendations on stent manufacture, implantation and utilization (1997)

The neologism 'stent' has irrevocably entered the English medical vocabulary as a noun as well as a verb' 1 '. It allegedly dates back to the English dentists Charles T. Stent (1807-1885) and his sons Charles R. Stent (1845-1901) and Arthur H. Stent (1859-1900) who used to support poorly aligned teeth with a special apparatus 1 ' 1 . Others have traced the word back to the 14th century. The first mention of the word stent in the (non-dentistry) medical literature can be found in a paper on reconstruction of the biliary duct in dogs in 1954 P1 . Charles Dotter employed the term stent for vascular implants in 1983 As a further development to heat-expandable stents, Maass published animal data in 1983 and 1984 on mechanically self-expanding stents for use in peripheral arteries' 5 ' 61 . In 1985, a spring-loaded self-expanding stent was described by Gianturco's group 171 , followed by the first balloonexpandable stent by Palmaz
Roles of Sall4 in the generation of pluripotent stem cells from blastocysts and fibroblasts (2009)

Pluripotency of embryonic stem (ES) cells is maintained by a network consisting of multiple transcription factors, including Oct3/4, Sox2, Nanog, Klf4 and Sall4. Among these factors, the forced expressions of Oct3/4, Sox2 and Klf4 are sufficient to reprogram fibroblasts into induced pluripotent stem (iPS) cells. The current study analyzed the role of Sall4 during the generation of ES cells and iPS cells. The mouse Sall4 gene was deleted by homologous recombination. Sall4-null embryos died shortly after implantation, as has been reported. ES-like cell lines can be established from Sall4-null blastocysts, albeit with a lower efficiency and a slower time course. The knockdown of Sall4 significantly decreased the efficiency of iPS cell generation from mouse fibroblasts. Furthermore, retroviral transduction of Sall4 significantly increased the efficiency of iPS cell generation in mouse and some human fibroblast lines. These results demonstrated that Sall4 plays positive roles in the generation of pluripotent stem cells from blastocysts and fibroblasts.
PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing (1997)

Fluorescence-based sequencing is playing an increasingly important role in efforts to identify DNA polymorphisms and mutations of biological and medical interest. The application of this technology in generating the reference sequence of simple and complex genomes is also driving the development of new computer programs to automate base calling (Phred), sequence assembly (Phrap) and sequence assembly editing (Consed) in high throughput settings. In this report we describe a new computer program known as PolyPhred that automatically detects the presence of heterozygous single nucleotide substitutions by fluorescencebased sequencing of PCR products. Its operations are integrated with the use of the Phred, Phrap and Consed programs and together these tools generate a high throughput system for detecting DNA polymorphisms and mutations by large scale fluorescence-based resequencing. Analysis of sequences containing known DNA variants demonstrates that the accuracy of PolyPhred with single pass data is >99% when the sequences are generated with fluorescent dye-labeled primers and approximately 90% for those prepared with dye-labeled terminators.
SPUR (2010)

Tracing just-in-time compilers (TJITs) determine frequently executed traces (hot paths and loops) in running programs and focus their optimization effort by emitting optimized machine code specialized to these traces. Prior work has established this strategy to be especially beneficial for dynamic languages such as JavaScript, where the TJIT interfaces with the interpreter and produces machine code from the JavaScript trace. This direct coupling with a JavaScript interpreter makes it difficult to harness the power of a TJIT for other components that are not written in JavaScript, e.g., the DOM implementation or the layout engine inside a browser. Furthermore, if a TJIT is tied to a particular high-level language interpreter, it is difficult to reuse it for other input languages as the optimizations are likely targeted at specific idioms of the source language. To address these issues, we designed and implemented a TJIT for Microsoft's Common Intermediate Language CIL (the target language of C#, VisualBasic, F#, and many other languages). Working on CIL enables TJIT optimizations for any program compiled to this platform. In addition, to validate that the performance gains of a TJIT for JavaScript do not depend on specific idioms of JavaScript that are lost in the translation to CIL, we provide a performance evaluation of our JavaScript runtime which translates JavaScript to CIL and then runs on top of our CIL TJIT.