gebhart/patrepeval huggingface dataset:
Efficacy of fluorescence-based PCR-SSCP for detection of point mutations. (1993)

We assessed the efficiency of fluorescence-based PCR single-strand conformation polymorphism analysis (PCR-SSCP) using an automated DNA sequencer and analysis software. We evaluated 48 point mutations in a 191-bp stretch of mouse beta-globin. The mutations included 10 transversions and 38 transitions; and both types of mutation were compared at six different locations in the PCR fragment. Mobilities of the red dye-labeled internal standard fragments were non-proportional to size but highly reproducible and were used to normalize or correct minor differences in apparent electrophoretic mobility between lanes. Forty-six of forty-eight mutants (96%) were distinguished from wild type when run in separate lanes using one set of conditions. Co-electrophoresis of wild type and mutant in the same lane resolved 100% of 45 mutants from wild type. Under conditions of this study, the magnitude of mobility shifts resulting from the globin mutations were largely determined by position of the mutation, rather than by the nature of the substitution (transition vs. transversion). However, examination of paired mutations at the same position revealed that some substitutions cause greater mobility shifts than others.
Design and Fabrication of Soft Artificial Skin Using Embedded Microchannels and Liquid Conductors (2012)

We describe the design, fabrication, and calibration of a highly compliant artificial skin sensor. The sensor consists of multilayered mircochannels in an elastomer matrix filled with a conductive liquid, capable of detecting multiaxis strains and contact pressure. A novel manufacturing method comprised of layered molding and casting processes is demonstrated to fabricate the multilayered soft sensor circuit. Silicone rubber layers with channel patterns, cast with 3-D printed molds, are bonded to create embedded microchannels, and a conductive liquid is injected into the microchannels. The channel dimensions are 200 μm (width) × 300 μm (height). The size of the sensor is 25 mm × 25 mm, and the thickness is approximately 3.5 mm. The prototype is tested with a materials tester and showed linearity in strain sensing and nonlinearity in pressure sensing. The sensor signal is repeatable in both cases. The characteristic modulus of the skin prototype is approximately 63 kPa. The sensor is functional up to strains of approximately 250%.
New estimates of the prevalence of neurological and sensory sequelae and mortality associated with congenital cytomegalovirus infection (2007)

Congenital CMV is a major cause of neurological and sensory impairment in children. Reliable estimates of the prevalence of permanent sequelae and mortality associated with congenital CMV are needed to guide development of education and prevention programmes and to gauge the financial costs associated with this disease. To calculate such estimates, this review used data solely from studies in which children with congenital CMV were identified through universal screening. Based on 15 studies with a total of 117 986 infants screened, the overall CMV birth prevalence estimate was 0.7%. The percentage of infected children with CMV-specific symptoms at birth was 12.7%. The percentage of symptomatic children with permanent sequelae was 40-58%. The percentage of children without symptoms at birth who developed permanent sequelae was estimated to be 13.5%. The true burden of congenital CMV infection is unclear because data on important outcomes, such as visual impairment, are lacking and follow-up of infected children has been too short to fully identify late-onset sequelae. Therefore, the estimates of permanent sequelae associated with congenital CMV presented here are likely underestimates. Future studies should extend follow-up of CMV-infected children identified through universal screening and include the evaluation of visual impairment.
Problem Area Formation as an Element of Computer Aided Diagnosis: A Comparison of Two Strategies Within Quick Medical Reference (QMR) (1991)

INTERNIST-I's use of "partitioning" to group related diagnoses into problem areas (for competitive consideration and elimination during case analysis) is felt to be the source of many of its strengths as well as some of its weaknesses. QMR, INTERNIST-I's successor program, embodies a homology function which can act as an alternative to the partitioner for problem area formation. This study undertakes a comparison of the problem areas generated by the INTERNIST-I partitioning algorithm, the QMR homology function, and expert clinicians; it finds the correlation to be poor. The authors then discuss another method of problem area formation which might better mimic a human clinician and provide an alternative approach in diagnostic computer-aided decision making.
RAGE and Soluble RAGE: Potential Therapeutic Targets for Cardiovascular Diseases (2007)

Receptor for advanced glycation end-products (RAGE) is known to be involved in microvascular complications in diabetes. RAGE is also profoundly associated with macrovascular complications in diabetes through regulation of atherogenesis, angiogenic response, vascular injury, and inflammatory response. The potential significance of RAGE in the pathogenesis of cardiovascular disease appears not to be confined solely to nondiabetic rather than diabetic conditions. Numerous truncated forms of RAGE have recently been described, and the C-terminally truncated soluble form of RAGE has received much attention. Soluble RAGE consists of several forms, including endogenous secretory RAGE (esRAGE), which is a spliced variant of RAGE, and a shedded form derived from cell-surface RAGE. These heterogeneous forms of soluble RAGE, which carry all of the extracellular domains but are devoid of the transmembrane and intracytoplasmic domains, bind ligands including AGEs and can antagonize RAGE signaling in vitro and in vivo. ELISA systems have been developed to measure plasma esRAGE and total soluble RAGE, and the pathophysiological roles of soluble RAGE have begun to be unveiled clinically. In this review, we summarize recent findings regarding pathophysiological roles in cardiovascular disease of RAGE and soluble RAGE and discuss their potential usefulness as therapeutic targets and biomarkers for the disease.
A dynamic model of protein digestion in the small intestine of pigs. (2000)

A dynamic mathematical model of the digestion of proteins in the small intestine of pigs was developed. The model integrates current knowledge on the transit of digesta along the small intestine, endogenous secretions, digestion of proteins, and absorption of amino acids into a mechanistic representation of digestion. The main characteristics of the model are the following: the small intestine is divided into several segments of variable length but with equal digesta retention time; the rate of transfer of digesta between segments is based on the progression of myoelectric migration complexes; pancreatic and biliary secretions are poured into the first segment, whereas intestinal secretions enter all intestinal segments; protein hydrolysis is described by first-order equations; and an intestinal absorption capacity is used to estimate absorption of hydrolyzed protein. Simulation results are consistent with observed data, although more information is needed to represent reality more closely. The sensitivity analysis shows that parameters for protein hydrolysis largely determine protein digestibility. The absorption capacity of the small intestine limits the absorption of amino acids at the beginning of a meal and modulates the appearance of amino nitrogen in the portal vein. It also shows that amino acid absorption can be limiting to protein digestibility when large amounts of protein are eaten in a single daily meal. The model is useful in evaluating the dynamics of protein digestion and absorption of feedstuffs. The model can be used in evaluating protein digestion of different feedstuffs and feeding strategies.
Electron microscope studies of an alloyed Au/Ni/Au-Ge ohmic contact to GaAs (1983)

The interface structures resulting from the alloying reactions between a Au/Ni/Au-Ge composite film and a (100) GaAs substrate were studied by transmission electron microscopy and scanning transmission electron microscopy. Electron microscope examinations of the cross-sectional samples prepared in this study offered excellent lateral and depth resolution of local structures which are not available by other analytical techniques used previously in similar studies. The distributions and chemical compositions of various phases formed, and the morphologies of the interfaces between these phases were monitored and compared with the measured contact resistances at three different stages of alloying. A correlation between the interface structure and the contact resistance was found.
Sipuleucel-T Immunotherapy for Castration-Resistant Prostate Cancer (2010)

The use of sipuleucel-T prolonged overall survival among men with metastatic castration-resistant prostate cancer. No effect on the time to disease progression was observed. (Funded by Dendreon; ClinicalTrials.gov number, NCT00065442.)
Characterisation of the Sek‐1 receptor tyrosine kinase (1995)

We present an initial characterisation of the mouse Sek-1 protein, a member of the Eph subfamily of putative receptor tyrosine kinases, which has been proposed to play a role in the segmentation of both the hindbrain and the mesoderm. Antibodies raised against the protein have been used to confirm the early embryonic expression pattern previously established by mRNA in situ hybridisation. These antibodies, together with the expression of the Sek-1 gene in a baculovirus system, were instrumental in demonstrating that the protein carries a tyrosine kinase activity and that it is presented at the cell surface with its N-terminal (putative ligand-binding) domain outside of the cell. Therefore, as expected from its amino acid sequence, Sek-1 conforms to the general model of receptor-type tyrosine kinases.
Data flow analysis for software prefetching linked data structures in Java (2002)

Describes an effective compile-time analysis for software prefetching in Java. Previous work in software data prefetching for pointer-based codes asses simple compiler algorithms and does not investigate prefetching for object-oriented language features that male compile-time analysis difficult. We develop a new data flow analysis to detect regular accesses to linked data structures in Java programs. We use intra- and inter-procedural analysis to identify profitable prefetching opportunities for greedy and jump-pointer prefetching, and we implement these techniques in a compiler for Java. Our results show that both prefetching techniques improve four of our ten programs. The largest performance improvement is 48% with jump-pointers, but consistent improvements are difficult to obtain.
Therapeutic Antibodies (2005)

Since the time of the earliest jawed fish, some 400 million years ago, evolution has been honing the design of antibody molecules to function as specific markers, alerting immune defences to the presence of pathogenic antigens, and recruiting effector function in the form of complement and Fc receptor-bearing cells. For the last twenty-five years, the biopharmaceutical industry has been applying the versatility of antibodies to the treatment of disease, with roles ranging from the blocking of receptor/ligand interactions to the delivery of cytotoxic drugs. While the structures of antibody molecules are supremely tailored to carry out their natural roles, there is considerable scope for adapting the basic designs to match more closely the specific requirements now sought for antibodies as drugs. In this review, we chart the developments in antibody design, which have led to successful therapies, highlighting the key issues and challenges faced, and looking to a future in which antibody-based therapies will represent a significant proportion of newly registered products.
Dynamic Analysis of Non-Symmetric Cracks Extension (2000)

ABSTRACT This paper applies the method of self-similar potentials to analyze the dynamic behaviors of the problems of mode-I, mode-II, and mode-III cracks propagating along the x -axis with constant speed, while the constant speeds of both crack tips are not the same, called nonsymmetric crack expansion. It is assumed that an unbound homogeneous isotropic elastic material is at rest for time t &lt; 0. However, for time t ≥ 0, a central crack starts to extend from zero length along the x -axis. On the crack surfaces of x ≥ 0, there exists uniform distributed load such that the rightmost crack tip propagates with speed ms , while the leftmost crack tip with speed s , where m &gt; 1 and is constant. First, the complete solutions of the mode-I, mode-II, and mode-III problems are obtained. After the complete solutions are found, attention is focused on the crack surface displacements and dynamic stress intensity factors. The results of this study show that the DSIF is equal to the static SIF when the crack-tip speed is zero, and DSIF is zero as the crack-tip speed approaches the Rayleigh-wave speed. Moreover, for the special case m = 1 which indicates that the velocities of both crack tips are the same, the DSIFs of this three modes in this study is the same as those of Ref. [15].
Cloning and expression of cDNA encoding a neural calcium-dependent cell adhesion molecule: its identity in the cadherin gene family. (1988)

The neural cadherin (N-cadherin) is a Ca2+-dependent cell-cell adhesion molecule detected in neural tissues as well as in non-neural tissues. We report here the nucleotide sequence of the chicken N-cadherin cDNA and the deduced amino acid sequence. The sequence data suggest that N-cadherin has one transmembrane domain which divides the molecule into an extracellular and a cytoplasmic domain; the extracellular domain contains internal repeats of characteristic sequences. When the N-cadherin cDNA connected with virus promoters was transfected into L cells which have no endogenous N-cadherin, the transformants acquired the N-cadherin-mediated aggregating property, indicating that the cloned cDNA contained all information necessary for the cell-cell binding action of this molecule. We then compared the primary structure of N-cadherin with that of other molecules defined as cadherin subclasses. The results showed that these molecules contain common amino acid sequences throughout their entire length, which confirms our hypothesis that cadherins make a gene family.
Influence of a perturbation in a double phase-encoding system (1998)

We consider the recently proposed double phase-encoding system [Opt. Lett.20, 767 (1995)]. We study the robustness of the decoding process, that is, the way in which a perturbation of the coded image modifies the decoded image. We demonstrate that the amplitude signal-to-noise ratio (SNR) in the decoded image is strictly (and not only statistically) equal to the SNR in the coded image for different kinds of coded-image perturbations. In optical implementations the intensity of the decoded image is measured at the output of the decoding system. We show that there exists a simple relation between the intensity SNR of the decoded image and the amplitude SNR of the coded image and that this relation is quasi-independent of the nature of the coded-image perturbation. The results presented could provide a simple and efficient way of determining the precision level of the components of the optical decoding system necessary to reach a predefined quality level of the decoded image.
Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA (1996)

Genetic analysis of limiting quantities of genomic DNA play an important role in DNA forensics, paleoarcheology, genetic disease diagnosis, genetic linkage analysis, and genetic diversity studies. We have tested the ability of degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) to amplify picogram quantities of human genomic DNA for the purpose of increasing the amount of template for genotyping with microsatellite repeat markers. DNA was uniformly amplified at a large number of typable loci throughout the human genome with starting template DNAs from as little as 15 pg to as much as 400 ng. A much greater-fold enrichment was seen for the smaller genomic DOP-PCRs. All markers tested were amplified from starting genomic DNAs in the range of 0.6-40 ng with amplifications of 200- to 600-fold. The DOP-PCR-amplified genomic DNA was an excellent and reliable template for genotyping with microsatellites, which give distinct bands with no increase in stutter artifact on di-, tri-, and tetranucleotide repeats. There appears to be equal amplification of genomic DNA from 55 of 55 tested discrete microsatellites implying near complete coverage of the human genome. Thus, DOP-PCR appears to allow unbiased, hundreds-fold whole genome amplification of human genomic DNA for genotypic analysis.
Reverse Micelle Based Formation of BaCO3 Nanowires (1997)

A reverse micelle based approach is reported for the synthesis of BaCO3 nanowires with lengths up to 100 μm and diameters as small as 10−30 nm, each of which is a continuous single crystal with the c-axis along the wire length axis. The synthesis is achieved by the reaction of barium and carbonate ions solubilized in the polar cores of nonionic reverse micelles of C12E4 (tetraethylene glycol monododecyl ether) in cyclohexane. The crystal growth of BaCO3 nanowires has been examined by electron microscopy observations, and a directional aggregation process is proposed for the nanowire formation.
A New Photosensitive Polymeric Material for WORM Optical Data Storage Using Multichannel Two-Photon Fluorescence Readout (2002)

We report image formation via photoinduced fluorescence changes in a polymeric medium with nondestructive two-photon fluorescence readout of a multilayer structure. A two-photon absorbing fluorescent dye possessing functional groups with differential basicity, (7-benzothiazolyl-9,9-didecyl-2,2-(N,N-diphenylamino)fluorene) (1), underwent protonation in the presence of a photoinduced acid generator upon exposure to a broadband UV light source or femtosecond near-IR laser irradiation. Solution studies demonstrated formation of monoprotonated and diprotonated species upon irradiation, each resulting in distinctly different absorption and fluorescence properties. The fluorescence of the original, neutral fluorophore was reduced upon monoprotonation, leading to a concomitant increase in fluorescence at longer wavelengths due to the monoprotonated form. Experiments in polymer films demonstrate the changes in fluorescence properties of the fluorophores can be employed for a write-once read-many (WORM) data storage medium with a two-photon fluorescence readout. Two-channel, two-photon fluorescence imaging provided both "positive" and "negative" image readout capability.
How to turn the page (2003)

Can digital libraries provide a reading experience that more closely resembles a real book than a scrolled or paginated electronic display? This paper describes a prototype page-turning system that realistically animates full three-dimensional page-turns. The dynamic behavior is generated by a mass-spring model defined on a rectangular grid of particles. The prototype takes a PDF or E-book file, renders it into a sequence of PNG images representing individual pages, and animates the pageturns under user control. The simulation behaves fairly naturally, although more computer graphics work is required to perfect it.
A pilot study on the liver protective effect of silybin-phosphatidylcholine complex (IdB1016) in chronic active hepatitis. (1993)

In order to assess the liver protective activity and the antioxidant properties of a new silybin complex (IdB1016), we carried out a short-term pilot study on 20 patients with chronic active hepatitis (CAH), randomly assigned to 240 mg of silybin b.i.d. (10 patients, 4 m/6 f, mean age: 50 years) or placebo (10 patients, 2 m/8 f, mean age: 55 years). Blood samples were collected before and after 7 days of treatment for liver function tests (LFTs), malonaldehyde (MDA) as an index of lipid peroxidation, and copper (Cu) and zinc (Zn), two trace elements involved in protecting cells against free radical-mediated lipid peroxidation. In the treated group, there was a statistically significant reduction of mean (+/- SEM) serum concentrations of aspartate aminotransferase (AST) from 88.0 (+/- 13.3) to 65.9 (+/- 7.5) u/l, (p < 0.01), of alanine aminotransferase (ALT) from 115.9 (+/- 12.9) to 82.5 (+/- 10.6) u/l (p < 0.01), of gamma-glutamyltranspeptidase (gamma-GT) from 51.4 (+/- 9.3) to 41.3 (+/- 4.2) u/l (p < 0.02) and of total bilirubin (TB) from 0.76 (+/- 0.08) to 0.53 (+/- 0.04) mg/dl (p < 0.05). Alkaline phosphatase (AP) fell slightly from 143.4 (+/- 6.4) to 137.5 (+/- 7.8) u/l. There were no significant changes in MDA, Cu or Zn serum concentrations. These results show that IdB1016 may improve LFTs related to hepatocellular necrosis and/or increases membrane permeability in patients affected by CAH.
Transition from semiorder to disorder in the aggregation of dense colloidal solutions (1993)

By using low-angle static light scattering we study the aggregation of dense colloidal solutions under diffusion limited (DLCA) and reaction limited cluster aggregation (RLCA) conditions. While it has been recently shown that DLCA surprisingly leads to a semiordered state, we show here that any order is lost under RLCA conditions. While in the first case a scattering peak at finite wave vector q is observed, in the second the scattered peak always occurs at q=0.
The amino acid sequence of an active site peptide from the H,K-ATPase of gastric mucosa. (1985)

The gastric H,K-ATPase is an active transport protein that is responsible for the maintenance of a large pH gradient across the secretory canaliculus of the mammalian parietal cell. Acid secretion across these epithelial cell membranes is coupled to the potassium-stimulated hydrolysis of ATP catalyzed by H,K-ATPase, but the mechanism of coupling between ion transport and ATP hydrolysis is unknown. In order to investigate the enzymatic mechanism of this coupling, a peptide derived from the ATP binding site of H,K-ATPase has been purified and its amino acid sequence has been determined. The peptide was identified by the incorporation of a fluorescent probe, fluorescein 5'-isothiocyanate (FITC), into the active site before trypsin digestion of the protein. The labeling of the enzyme by FITC was associated with the irreversible inhibition of enzymatic activity, and both the labeling of the tryptic peptide and inhibition of activity were prevented when the reaction was performed in the presence of ATP. At 100% inhibition of activity, 3.5 +/- 1.6 nmol of FITC were incorporated per mg of protein. The amino acid sequence of the active site peptide is His-Val-Leu-Val-Met-Lys-Gly-Ala-Pro-Glu-Gln-Leu-Ser-Ile-Arg, and FITC reacts with the lysine. This sequence is very similar to sequences of fluorescein-labeled peptides from the ATP binding sites of Na,K-ATPase and Ca2+-ATPase, and suggests that the active site structures of these ion transport ATPases are similar.
Nanoscale solid-state quantum computing (2003)

Most experts agree that it is too early to say how quantum computers will eventually be built, and several nanoscale solid-state schemes are being implemented in a range of materials. Nanofabricated quantum dots can be made in designer configurations, with established technology for controlling interactions and for reading out results. Epitaxial quantum dots can be grown in vertical arrays in semiconductors, and ultrafast optical techniques are available for controlling and measuring their excitations. Single-walled carbon nanotubes can be used for molecular self-assembly of endohedral fullerenes, which can embody quantum information in the electron spin. The challenges of individual addressing in such tiny structures could rapidly become intractable with increasing numbers of qubits, but these schemes are amenable to global addressing methods for computation.