gebhart/patrepeval huggingface dataset:
Estimation of the Frequency-Dependent Average Dielectric Properties of Breast Tissue Using a Time-Domain Inverse Scattering Technique (2006)

Ultrawideband (UWB) microwave radar imaging techniques for breast cancer detection typically require estimates of the spatially averaged dielectric properties of breast tissue. We propose an algorithm for estimating patient-specific, frequency-dependent average dielectric properties from scattered UWB microwave signals. The algorithm is a variation of an iterative finite-difference time-domain (FDTD) technique for solving the time-domain inverse scattering problem. The assumption is made that the breast consists of two homogeneous regions: skin and underlying tissue. This two-medium geometry results in an inverse scattering problem that is not as ill-posed as those typically encountered in microwave tomography because the number of unknowns being sought is very small. We test the performance of the algorithm on data simulated using anatomically realistic 2-D numerical breast phantoms
Proliferation of mouse embryonic stem cell progeny and the spontaneous contractile activity of cardiomyocytes are affected by microtopography (2009)

The niche in which stem cells reside and differentiate is a complex physicochemical microenvironment that regulates cell function. The role played by three-dimensional physical contours was studied on cell progeny derived from mouse embryonic stem cells using microtopographies created on PDMS (poly-dimethyl-siloxane) membranes. While markers of differentiation were not affected, the proliferation of heterogeneous mouse embryonic stem cell-derived progeny was attenuated by 15 microm-, but not 5 microm-high microprojections. This reduction was reversed by Rho kinase and myosin light chain kinase inhibition, which diminishes the tension generating ability of stress fibers. Purified cardiomyocytes derived from embryonic stem cells also showed significant blunting of proliferation and increased beating rates compared with cells grown on flat substrates. Thus, proliferation of stem cell-derived progeny appears to be regulated by microtopography through tension-generation of contractility in the third-dimension. These results emphasize the importance of topographic cues in the modulation of stem cell progeny behavior.
Detection of point mutations by solid-phase methods (1994)

Several techniques exist that permit the efficient distinction among characterized DNA sequence variants. In this review we discuss a number of such analytic procedures. These techniques all take advantage of a variety solid supports to prepare and analyze reaction products. The described diagnostic principles are now being applied for the development of miniaturized assay formats, suitable for automated detection of large sets of sequences in clinical samples.
Visual Acuity as Measured with Various Orientations of a Parallel-Line Test Object* (1948)

Visual acuity has been measured in terms of the reciprocal of the angle in minutes subtended by the individual lines in a parallel-line test object at the limit of perception of the lines. Both clear and opaque lines in this test object were of equal width. It was found that the limit of perception of the lines in such a test object depends upon the orientation of the lines. Visual acuity, measured with the lines passing diagonally through the visual field at an angle of 45 degrees to the horizontal, is between 10 and 20 percent lower than that measured with the parallel lines passing vertically or horizontally through the visual field.
Production of Hybridization Probes by the PCR Utilizing Digoxigenin-Modified Nucleotides (2003)

The polymerase chain reaction (PCR) (1) is an efficient method for copying a fragment of DNA when primers exist that flank the target sequence. We have found that since most cloning vectors utilize the lacZ gene with a synthetic multiple cloning site (2), a single pair of primers will amplify sequences inserted into many common phage and plasmid vectors, such as the pUC plasmid and Lambda Zap phage series and their derivatives. We have had little difficulty amplifying inserts up to 3000 bp in length and now consider this as a preferred alternative to growth of bacterial cultures with subsequent nucleic acid purification to produce DNA fragments of this length for both mapping and sequencing.
Osteoprotegerin, trail and osteoprotegerin/trail ratio in patients at early phase of acute pancreatitis. (2014)

Determination of serum OPG concentrations may help in early prediction of severity of AP. However, diagnostic utility of the measurements seems too low to use OPG as a single clinically reliable predictor. Serum TRAIL is not useful in the differentiation between mild and severe form of AP.
AVPGEN-A test generator for architecture verification (1995)

This paper describes a system (AVPGEN) for generating tests (called architecture verification programs or AVP's) to check the conformance of processor designs to the specified architecture. To generate effective tests, AVPGEN uses novel concepts like symbolic execution and constraint solving, along with various biasing techniques. Unlike many earlier systems that make biased random choices, AVPGEN often chooses intermediate or final values and then solves for initial values that can lead to the desired values. A language called SIGL (symbolic instruction graph language) is provided in AVPGEN for the user to specify templates with symbolic constraints. The combination of user-specified constraints and the biasing functions is used to focus the tests on conditions that are interesting in that they are likely to activate various kinds of bugs. The system has been used successfully to debug many S/390 processors and is an integral part of the design process for these processors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Overview of MAC layer enhancements for IEEE 802.15.4a (2009)

Ultra wideband impulse radio (IR-UWB) based on the IEEE 802.15.4a PHY standard offers unique features which are exploitable in MAC designs for wireless personal area networks (WPANs) and wireless sensor networks (WSNs) to improve performance and robustness. To achieve this, different strategies of cross-layer optimizations to the IEEE 802.15.4 MAC using features of UWB have been proposed. This paper compares current approaches and exposes individual advantages and disadvantages regarding energy efficiency and positioning.
The molecular gas toward Cassiopeia A. (1993)

Fully sampled 20″ resolution maps of Cassiopeia A in the J = 1 − 0 line of 13 CO, and additional observations of the J = 1 − 0 and J = 2 − 1 lines of 12 CO and 13 CO are presented. From the peak 12 CO line intensity, the kinetic temperature of the molecular gas reaches 20K. The warmest clouds are in the SE part of the region mapped. From the 13 CO data, there are at least eleven molecular clouds. Ten clouds are in the Perseus spiral arm, ∼ 3 kpc from the sun; one is in the solar neighborhood. For the Perseus arm clouds, a Large Velocity Gradient analysis of J = 2 − 1 and J = 1 − 0 lines of 13 CO gives H 2 densities <4000 CM −3 . For these clouds, masses from CO data are significantly smaller than obtained from the virial theorem if only gravity is important; the clouds toward the SE of Cas A are closest to being bound
Techniques patents for SNP genotyping (2003)

Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation in the human genome, accounting for more than 90% of all differences between individuals. Many complex phenotypes in humans have a significant genetic component and most of the variability is therefore likely to stem from differences in patterns of SNPs. Association studies involving the large-scale analysis of SNPs can help to identify genes affecting many human phenotype variations, including complex diseases and drug responses. SNPs therefore play a major role in all stages of the drug development process, from target identification through to clinical trials. SNPs are also the basis of pharmacogenomics, the tailoring of medicines to suit an individual's genome. Given the potential impact of SNPs on healthcare, the biotechnology industry has focussed urgently on the development of high-throughput methods for SNP genotyping. All genotyping methods are a mix and match of different allele discrimination and signal detection technologies and as such may represent the intellectual property of several individuals or organizations. In this review, we explore the patent issues surrounding SNP genotyping and how this is influencing large scale, commercially valuable projects involving SNPs.
Activities of the RNAI and RNAII promoters of plasmid pBR322 (1987)

The synthesis rates of the replication control RNAs of plasmid pBR322, RNAI, an inhibitor of replication, and RNAII, the preprimer, have been determined by hybridizing in vivo pulse-labeled RNA to specific, single-stranded DNA probes for RNAI and RNAII. In Escherichia coli growing in glycerol minimal medium, RNAI transcripts were made at a rate of one molecule per 30 s per plasmid; RNAII was transcribed fivefold less, at a rate of one molecule per 3 min per plasmid. It is estimated that only 1 in 20 prepriming events leads to replication.
Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration (2008)

Serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so-called "classical" catalytic Ser/His/Asp triad. Although the classical serine proteases are the most widespread in nature, there exist a variety of "nonclassical" serine proteases where variations to the catalytic triad are observed. Such variations include the triads Ser/His/Glu, Ser/His/His, and Ser/Glu/Asp, and include the dyads Ser/Lys and Ser/His. Other variations are seen with certain serine and threonine peptidases of the Ntn hydrolase superfamily that carry out catalysis with a single active site residue. This work discusses the structure and function of these novel serine proteases and threonine proteases and how their catalytic machinery differs from the prototypic serine protease class.
Effects of retinoids on induction of differentiation of cultured mouse myeloid leukemia cells. (1980)

Retinoic acid, retinol, retinyl acetate, and retinal induced activities of lysosomal enzymes, such as lysozyme, acid protease, and acid phosphatase, in mouse myeloid leukemia cells (M1), while the pyridyl analog of retinoic acid had no effect. Retinoic acid was the most potent inducer of lysosomal enzyme activities. The induction of lysozyme activity by retinoic acid was inhibited by treatment with puromycin. The retinoids did not induce phagocytic and locomotive activities or morphological changes in M1 cells, and they inhibited the induction of these differentiation-associated properties by various inducers without inhibiting cell growth. Retinoic acid was the most potent inhibitor of induction of these differentiation-associated properties. The inhibitory effect of retinoic acid was found to be reversible. These results suggest that distinct mechanisms exist for control of induction of lysosomal enzyme activities and of other differentiation-associated properties of M1 cells, such as phagocytosis, morphological changes, and migration.
Coenzyme A-acylating aldehyde dehydrogenase from Clostridium beijerinckii NRRL B592 (1990)

Acetaldehyde and butyraldehyde are substrates for alcohol dehydrogenase in the production of ethanol and 1-butanol by solvent-producing clostridia. A coenzyme A (CoA)-acylating aldehyde dehydrogenase (ALDH), which also converts acyl-CoA to aldehyde and CoA, has been purified under anaerobic conditions from Clostridium beijerinckii NRRL B592. The ALDH showed a native molecular weight (Mr) of 100,000 and a subunit Mr of 55,000, suggesting that ALDH is dimeric. Purified ALDH contained no alcohol dehydrogenase activity. Activities measured with acetaldehyde and butyraldehyde as alternative substrates were copurified, indicating that the same ALDH can catalyze the formation of both aldehydes for ethanol and butanol production. Based on the Km and Vmax values for acetyl-CoA and butyryl-CoA, ALDH was more effective for the production of butyraldehyde than for acetaldehyde. ALDH could use either NAD(H) or NADP(H) as the coenzyme, but the Km for NAD(H) was much lower than that for NADP(H). Kinetic data suggest a ping-pong mechanism for the reaction. ALDH was more stable in Tris buffer than in phosphate buffer. The apparent optimum pH was between 6.5 and 7 for the forward reaction (the physiological direction; aldehyde forming), and it was 9.5 or higher for the reverse reaction (acyl-CoA forming). The ratio of NAD(H)/NADP(H)-linked activities increased with decreasing pH. ALDH was O2 sensitive, but it could be protected against O2 inactivation by dithiothreitol. The O2-inactivated enzyme could be reactivated by incubating the enzyme with CoA in the presence or absence of dithiothreitol prior to assay.
Efficient crawling through URL ordering (1998)

In this paper we study in what order a crawler should visit the URLs it has seen, in order to obtain more “important” pages first. Obtaining important pages rapidly can be very useful when a crawler cannot visit the entire Web in a reasonable amount of time. We define several importance metrics, ordering schemes, and performance evaluation measures for this problem. We also experimentally evaluate the ordering schemes on the Stanford University Web. Our results show that a crawler with a good ordering scheme can obtain important pages significantly faster than one without.
Serine phosphorylation by SYK is critical for nuclear localization and transcription factor function of Ikaros (2012)

Ikaros is a zinc finger-containing DNA-binding protein that plays a pivotal role in immune homeostasis through transcriptional regulation of the earliest stages of lymphocyte ontogeny and differentiation. Functional deficiency of Ikaros has been implicated in the pathogenesis of acute lymphoblastic leukemia, the most common form of childhood cancer. Therefore, a stringent regulation of Ikaros activity is considered of paramount importance, but the operative molecular mechanisms responsible for its regulation remain largely unknown. Here we provide multifaceted genetic and biochemical evidence for a previously unknown function of spleen tyrosine kinase (SYK) as a partner and posttranslational regulator of Ikaros. We demonstrate that SYK phoshorylates Ikaros at unique C-terminal serine phosphorylation sites S358 and S361, thereby augmenting its nuclear localization and sequence-specific DNA binding activity. Mechanistically, we establish that SYK-induced Ikaros activation is essential for its nuclear localization and optimal transcription factor function.
Periodic Transfusions for Sickle Cell Anemia and CNS Infarction (1979)

Recurrences of CNS infarction often lead to progressive neurologic disability in sickle cell anemia. To prevent such reccurrence, a periodic blood transfusion program was begun in 1969. Currently, 27 patients are on this regimen. Before inclusion in the program, 12 patients had had one to nine CNS recurrences each. Since the program was started, two patients have had transient CNS ischemia. There were no other recurrences and none of the patients have shown progression of neurologic abnormalities. In addition, there was a striking decrease in bacterial infection and pain. We conclude that periodic transfusions are effective in preventing recurrent CNS infarction in sickle cell anemia. The benefits must be weighed against the potentially serious problem of iron overload, as evidenced by moderately elevated serum ferritin values.
The Abolition of the Death Penalty: Does "Abolition" Really Mean What You Think it Means? (1999)

Human rights, in all that the phrase embodies, represent a massive and constantly growing body of law. The protection of human rights is constantly expanding, and though obviously of local and national concern, protection of these rights is of paramount importance in the international and global spheres. Human rights law focuses upon a wide spectrum of issues and crises; it encompasses economic, political, cultural, moral, religious, and social topics, and is motivated by crime, race, age, and gender. For example, past human rights instruments have dealt with the use of poison or bacteriological methods of warfare;1 the granting of civil and political rights to women;2 suppression of person-trafficking and exploitation of prostitution;3 territorial asylum;4 the rights of children;5 the rights of deaf-blind persons;6 and safety of civil aviation.7
Diet, Physical Activity, and Colorectal Cancer Among Chinese in North America and China (1990)

In a population-based case-control study of colorectal cancer among Chinese men and women in western North America and the People's Republic of China, a common protocol was used to assess past life-style characteristics of 905 cases diagnosed during 1981-1986 and 2,488 controls. Risks for cancers of both the colon and rectum increased with increased food energy from fat, protein, carbohydrate, and all energy sources combined, for both sexes and on both continents. Yet, in multivariate analysis, colorectal cancer risk was significantly associated only with saturated fat; no relationships were seen with other dietary sources of energy. Colon cancer risk was elevated among men employed in sedentary occupations. On both continents and in both sexes, risks for cancers of both the colon and rectum increased with increasing time spent sitting. Further, the association between colorectal cancer risk and saturated fat was stronger among the sedentary than among the active. Risk among sedentary Chinese Americans of either sex increased more than fourfold from the lowest to the highest category of saturated fat intake. Among migrants to North America, risk increased with increasing years lived in North America. These observations suggest (a) that colorectal cancer risk increases with duration of exposure to a sedentary life-style and a diet rich in saturated fat; (b) that higher incidence among Chinese-American men relative to women is due to longer duration of these habits among men, who have lived longer in North America; and (c) that higher risk among Chinese Americans of both sexes relative to risk among the general population in China is due to differences in such habits. Attributable risk calculations suggest that, if these associations are causal, saturated fat intakes exceeding 10 g/day, particularly in combination with physical inactivity, could account for 60% of colorectal cancer incidence among Chinese-American men and 40% among Chinese-American women.
Design strategies for the identification of MMP-13 and Tace inhibitors. (2003)

Inhibitors of matrix metalloprotease (MMP)-13 and tumor necrosis factor-alpha converting enzyme (TACE) have been highly sought as potential therapeutic agents for the treatment of osteoarthritis and rheumatoid arthritis, respectively. This review focuses on the published literature on these inhibitors from 2001 to mid-2003. Significant advances have been reported in the design and synthesis of potent and selective inhibitors of MMP-13 using hydroxamic acid and non-hydroxamate zinc chelators on a variety of scaffolds. TACE inhibitors based on variations of known MMP inhibitors scaffolds and novel designs have been reported. Selectivity profiles for these inhibitors range from broad-spectrum to TACE-specific. Future clinical studies on these and other inhibitors will determine which MMP, or set of MMPs, must be inhibited for efficacy and long-term safety.
The Chemistry of Heterocycles: Structure, Reactions, Syntheses, and Applications (1995)

Abbreviations and Symbols.1. The Structures of Heterocyclic Compounds.2. Systematic Nomenclature of Heterocyclic Compounds.3. Three-Membered Heterocycles.4. Four-Membered Heterocycles.5. Five-Membered Heterocycles.6. Six-Membered Heterocycles.7. Seven-Membered Heterocycles.8. Larger Rings Heterocycles.9. Problems and their Solutions.Indices.
In VivoPositron Emission Tomographic Imaging of Glial Responses to Amyloid-β and Tau Pathologies in Mouse Models of Alzheimer's Disease and Related Disorders (2011)

Core pathologies of Alzheimer's disease (AD) are aggregated amyloid-β peptides (Aβ) and tau, and the latter is also characteristic of diverse neurodegenerative tauopathies. These amyloid lesions provoke microglial activation, and recent neuroimaging technologies have enabled visualization of this response in living brains using radioligands for the peripheral benzodiazepine receptor also known as the 18 kDa translocator protein (TSPO). Here, we elucidated contributions of Aβ and tau deposits to in vivo TSPO signals in pursuit of mechanistic and diagnostic significance of TSPO imaging in AD and other tauopathies. A new antibody to human TSPO revealed induction of TSPO-positive microgliosis by tau fibrils in tauopathy brains. Emergence of TSPO signals before occurrence of brain atrophy and thioflavin-S-positive tau amyloidosis was also demonstrated in living mice transgenic for mutant tau by positron emission tomography (PET) with two classes of TSPO radioligands, [(11)C]AC-5216 and [(18)F]fluoroethoxy-DAA1106. Meanwhile, only modest TSPO elevation was observed in aged mice modeling Aβ plaque deposition, despite the notably enhanced in vivo binding of amyloid radiotracer, [(11)C]Pittsburgh Compound-B, to plaques. In these animals, [(11)C]AC-5216 yielded better TSPO contrasts than [(18)F]fluoroethoxy-DAA1106, supporting the possibility of capturing early neurotoxicity with high-performance TSPO probes. Furthermore, an additional line of mice modeling intraneuronal Aβ accumulation displayed elevated TSPO signals following noticeable neuronal loss, unlike TSPO upregulation heralding massive neuronal death in tauopathy model mice. Our data corroborate the utility of TSPO-PET imaging as a biomarker for tau-triggered toxicity, and as a complement to amyloid scans for diagnostic assessment of tauopathies with and without Aβ pathologies.
Tandem triple-pass Fabry–Perot interferometer for applications in the near infrared (1997)

A standard tandem triple-pass scanning Fabry-Perot interferometer of the Vernier type for applications in the near infrared is described. The Fabry-Perot etalons have been coated with a specially designed dielectric multilayer stack with low loss factors and a uniform reflectivity of (92.5 +/- 1.0)% between 730 and 860 nm. The performances of the instrument, such as resolution, total transmission, and contrast, are equivalent to conventional tandem Fabry-Perot spectrometers but over the whole near-infrared wavelength range. Applications of the system to Brillouin scattering on semiconductors in the transparent wavelength regime and high-resolution spectroscopy of vertical cavity surface-emitting lasers are given.