gebhart/patrepeval huggingface dataset:
Linkage strategies for genetically complex traits. II. The power of affected relative pairs. (1990)

The power to detect disease-susceptibility loci through linkage analysis using pairs of affected relatives and affected-unaffected pairs is examined. Allelic identity by descent (ibd) for a completely polymorphic marker for sibling, uncle-nephew, grandparent-grandchild, half-sib, and first-cousin pairs is considered. Affected-unaffected pairs generally represent a poor strategy. For single-locus models, ibd depends on lambda R, the risk ratio for type R relatives compared with population prevalence, and the recombination fraction theta. The ibd for grandparent-grandchild pairs is least affected by recombination, followed by sibs, half-sib, uncle-nephew, and first-cousin pairs. For diseases with large lambda values and for small theta values, distant relatives offer greater power. For larger theta values, grandparent-grandchild pairs are best; for small lambda values, sibs are best. Additive and multiplicative multilocus models are considered. For the multiplicative model, the same formulas as in the single-locus model apply, except that lambda iR (for the ith contributing locus) is substituted for lambda R. For the additive model, the deviation from null expectation for ibd is divided among all contributing loci. Compared with the multiplicative model, for an additive model there is usually greater advantage in distant relationships. Multipoint analysis using linked marker loci for affected relative pairs is described. Simultaneous use of multiple markers diminishes the effect of recombination and allows for localization of the disease-susceptibility locus.
Survival Outcome of Squamous Cell Carcinoma Arising from Sinonasal Inverted Papilloma (2015)

Patients with SCC/IP had low overall survival outcomes. Advanced age, stage, and metachronous tumors are the main factors affecting prognosis. Treatment planning should consider high-risk factors to improve survival outcome.
Biomethane from Dairy Waste, a Sourcebook for the Production and Use of Renewable Natural Gas (2005)

This report examines the feasibility of producing biomethane from dairy manure.We investigated a number of possible technologies for producing renewable forms of energy and fuel from dairy wastes as well as applications and markets for these products. Although some of the applications proved to be technically or economically infeasible at this time, we believe that the information gathered could prove useful for other investigators or future studies. With this in mind, we designed this sourcebook for readers and investigators interested in exploring alternate uses of biogas created from dairy wastes.
Space Object Imaging Through The Turbulent Atmosphere (1979)

For telescopes operating at optical wavelengths, the turbulence of the atmosphere limits the resolution of space objects to about one second of arc, although the diffraction limit of the largest telescopes is many times as fine. We discuss an image processing technique that uses interferometer data (the modulus of the Fourier transform) to reconstruct diffraction limited images. Data from a stellar speckle interferometer or from an amplitude interferometer can be used. The processing technique is an iterative method that finds a real, non-negative object that agrees with the Fourier modulus data. For complicated two-dimensional objects, the solutions found by this technique are surprisingly unique. New results are shown for simulated speckle interferometer data having realistic noise present.
Climate and Satellite Indicators to Forecast Rift Valley Fever Epidemics in Kenya (1999)

All known Rift Valley fever virus outbreaks in East Africa from 1950 to May 1998, and probably earlier, followed periods of abnormally high rainfall. Analysis of this record and Pacific and Indian Ocean sea surface temperature anomalies, coupled with satellite normalized difference vegetation index data, shows that prediction of Rift Valley fever outbreaks may be made up to 5 months in advance of outbreaks in East Africa. Concurrent near-real-time monitoring with satellite normalized difference vegetation data may identify actual affected areas.
Diagonal low-density parity-check code for simplified routing in decoder (2006)

We propose a novel low-density parity-check (LDPC) decoder design methodology by introducing a special code named diagonal-LDPC (DLDPC) code. An LPDC code, defined by a parity check matrix H, can be represented by a bipartite graph. To address the complex routing problem in the LDPC decoder implementation, a partitioned bipartite-graph code is proposed and generalized to a DLDPC code having constraint of positioning 1's near the diagonal area. This structured code simplifies the routing problem [Y. Kou et al, 2001] [R.M. Tanner et al, 2001] [H. Zhang et al, 2003] and enables cell-based highly regular fully-parallel decoder design without compromising the code performance.
Three-dimensional dosimetry for intralesional radionuclide therapy using mathematical modeling and multimodality imaging. (1997)

Initial results suggest that this method offers a means of determining the absorbed dose distribution within a tumor resulting from intralesional infusion. This method extends the Medical Internal Radiation Dose computation, which, in these circumstances, would make erroneous assumptions. Furthermore, it will enable individual patient treatment planning and optimization of the parameters that are within the clinician's control.
Calcium Entry through Cyclic Nucleotide-Gated Channels in Individual Cilia of Olfactory Receptor Cells: Spatiotemporal Dynamics (1997)

Transient elevations of intracellular Ca2+ play an important role in regulating the sensitivity of olfactory transduction, but such elevations have not been demonstrated in the olfactory cilia, which are the site of primary odor transduction. To begin to understand Ca2+ signaling in olfactory cilia, we used high-resolution imaging techniques to study the Ca2+ transients that occur in salamander olfactory receptor neurons (ORNs) as a result of cyclic nucleotide-gated (CNG) channel activation. To visualize ciliary Ca2+ signals, we loaded ORNs with the Ca2+ indicator dye Fluo-3 AM and measured fluorescence with a laser scanning confocal microscope. Application of the phosphodiesterase inhibitor IBMX increased fluorescence in the cilia and other neuronal compartments; the ciliary signal occurred first and was more transient. This signal could be abolished by lowering external Ca2+ or by applying LY83583, a potent blocker of CNG channels, indicating that Ca2+ entry through CNG channels was the primary source of fluorescence increases. Direct activation of CNG channels with low levels of 8-Br-cGMP (1 microM) led to tonic Ca2+ signals that were restricted locally to the cilia and the dendritic knob. Elevated external K+, which depolarizes cell membranes, increased fluorescence signals in the cell body and dendrite but failed to increase ciliary Ca2+ fluorescence. The results demonstrate the existence and spatiotemporal properties of Ca2+ transients in individual olfactory cilia and implicate CNG channels as a major pathway for Ca2+ entry into ORN cilia during odor transduction.
Optical font recognition using typographical features (1998)

A new statistical approach based on global typographical features is proposed to the widely neglected problem of font recognition. It aims at the identification of the typeface, weight, slope and size of the text from an image block without any knowledge of the content of that text. The recognition is based on a multivariate Bayesian classifier and operates on a given set of known fonts. The effectiveness of the adopted approach has been experimented on a set of 280 fonts. Font recognition accuracies of about 97 percent were reached on high-quality images. In addition, rates higher than 99.9 percent were obtained for weight and slope detection. Experiments have also shown the system robustness to document language and text content and its sensitivity to text length.
Numerical dispersion compensation for Partial Coherence Interferometry and Optical Coherence Tomography (2001)

Dispersive samples introduce a wavelength dependent phase distortion to the probe beam. This leads to a noticeable loss of depth resolution in high resolution OCT using broadband light sources. The standard technique to avoid this consequence is to balance the dispersion of the sample byarrangingadispersive materialinthereference arm. However, the impact of dispersion is depth dependent. A corresponding depth dependent dispersion balancing technique is diffcult to implement. Here we present a numerical dispersion compensation technique for Partial Coherence Interferometry (PCI) and Optical Coherence Tomography (OCT) based on numerical correlation of the depth scan signal with a depth variant kernel. It can be used a posteriori and provides depth dependent dispersion compensation. Examples of dispersion compensated depth scan signals obtained from microscope cover glasses are presented.
Simultaneous synthesis of peptide libraries on single resin and continuous cellulose membrane supports: examples for the identification of protein, metal and DNA binding peptide mixtures. (1994)

Peptide libraries were simultaneously synthesized on single supports by double coupling 0.8 equivalents of an equimolar acylating amino acid mixture consisting of 19 amino acids (cysteine omitted) at randomized sites, thus compensating for the different coupling rates of the amino acids. Peptide epitope mixtures, as well as very complex mixtures such as a completely randomized hexapeptide, were prepared and analyzed by HPLC and amino acid analysis. The results obtained indicate that this method can be applied to the synthesis of peptide libraries. Parts of a simultaneously synthesized solution phase combinatorial library XXB1B2XX were successfully used for the detection of the linear epitope HFND of transforming growth factor-alpha (TGF alpha) recognized by the monoclonal antibody Tab2. Furthermore, novel combinatorial peptide libraries XXB1B2XX were prepared on continuous cellulose membrane supports, also allowing the identification of TGF alpha epitope sequences. In addition, peptide mixtures that bound to a double-stranded DNA (15mer) and silver were identified. These preliminary results indicate that cellulose-bound combinatorial peptide libraries can be used for the rapid and inexpensive screening of millions of peptides to identify single molecules that bind any given ligand such as proteins, nucleic acids and metals.
Inhibitory effect of a selective cyclooxygenase‐2 inhibitor on liver metastasis of colon cancer (2002)

COX-2 overexpression is recognized in various cancers, but the role of COX-2 in the progression of cancer, including the liver metastasis of colon cancer, is not clearly understood. We examined the role of COX-2 in the mechanism of liver metastasis of colon cancer, using a highly metastasizable colon carcinoma cell line, LM-H3. A COX-2 inhibitor, JTE-522, inhibited cell proliferation and invasion of LM-H3 in vitro and clearly reduced the number of metastatic nodules on the surface of nude mouse livers in vivo. We also examined the effects of JTE-522 on the production of growth factors and MMPs through the use of ELISA and gelatin zymography, respectively. JTE-522 downregulated PDGF production by LM-H3 but had no influence on VEGF production. JTE-522 also inhibited MMP-2 secretion by LM-H3. JTE-522 downregulated PGE(2) production, but the associated changes in PGE(2) did not affect PDGF and VEGF production by LM-H3. We conclude that JTE-522 downregulated the cell proliferation and invasive potential of LM-H3 by reducing the production of PDGF and MMP-2 and hypothesize that these inhibitory effects on the production of PDGF and MMP-2 can lead to inhibition of liver metastasis of colon cancer. These data indicate that the COX-2 inhibitor JTE-522 has a high potential for use as a clinical agent for the treatment of liver metastasis of colon cancer.
Evolution of Mouse T-box Genes by Tandem Duplication and Cluster Dispersion (1996)

The T-box genes comprise an ancient family of putative transcription factors conserved across species as divergent as Mus musculus and Caenorhabditis elegans. All T-box gene products are characterized by a novel 174-186-amino acid DNA binding domain called the T-box that was first discovered in the polypeptide products of the mouse T locus and the Drosophila melanogaster optomotor-blind gene. Earlier studies allowed the identification of five mouse T-box genes, T, Tbx1-3, and Tbr1, that all map to different chromosomal locations and are expressed in unique temporal and spatial patterns during embryogenesis. Here, we report the discovery of three new members of the mouse T-box gene family, named Tbx4, Tbx5, and Tbx6. Two of these newly discovered genes, Tbx4 and Tbx5, were found to be tightly linked to previously identified T-box genes. Combined results from phylogenetic, linkage, and physical mapping studies provide a picture for the evolution of a T-box subfamily by unequal crossing over to form a two-gene cluster that was duplicated and dispersed to two chromosomal locations. This analysis suggests that Tbx4 and Tbx5 are cognate genes that diverged apart from a common ancestral gene during early vertebrate evolution.
Efficient Multisite Unnatural Amino Acid Incorporation in Mammalian Cells via Optimized Pyrrolysyl tRNA Synthetase/tRNA Expression and Engineered eRF1 (2014)

The efficient, site-specific introduction of unnatural amino acids into proteins in mammalian cells is an outstanding challenge in realizing the potential of genetic code expansion approaches. Addressing this challenge will allow the synthesis of modified recombinant proteins and augment emerging strategies that introduce new chemical functionalities into proteins to control and image their function with high spatial and temporal precision in cells. The efficiency of unnatural amino acid incorporation in response to the amber stop codon (UAG) in mammalian cells is commonly considered to be low. Here we demonstrate that tRNA levels can be limiting for unnatural amino acid incorporation efficiency, and we develop an optimized pyrrolysyl-tRNA synthetase/tRNACUA expression system, with optimized tRNA expression for mammalian cells. In addition, we engineer eRF1, that normally terminates translation on all three stop codons, to provide a substantial increase in unnatural amino acid incorporation in response to the UAG codon without increasing readthrough of other stop codons. By combining the optimized pyrrolysyl-tRNA synthetase/tRNACUA expression system and an engineered eRF1, we increase the yield of protein bearing unnatural amino acids at a single site 17- to 20-fold. Using the optimized system, we produce proteins containing unnatural amino acids with comparable yields to a protein produced from a gene that does not contain a UAG stop codon. Moreover, the optimized system increases the yield of protein, incorporating an unnatural amino acid at three sites, from unmeasurably low levels up to 43% of a no amber stop control. Our approach may enable the efficient production of site-specifically modified therapeutic proteins, and the quantitative replacement of targeted cellular proteins with versions bearing unnatural amino acids that allow imaging or synthetic regulation of protein function.
Population heterogeneity among cells of the megakaryocyte lineage (1993)

Understanding the developmental steps in megakaryocyte differentiation requires information regarding the microenvironmental influences which direct or permit the growth and differentiation of these cells. The megakaryocyte microenvironment, like other lineages, is a complex structure comprised of the various megakaryocytic cells, the extracellular matrix (ECM) surrounding them, and the hematopoietic stromal cells which elaborate both growth factors and ECM. As a result, definition of the minimal essential requirements for megakaryocyte development is difficult. The intricacies of megakaryocyte development are further complicated by the cellular heterogeneity of both mature megakaryocytes and their precursors, as well as a differential responsiveness of these cells to hematopoietic growth factors. This review focuses on defining the various subpopulations of megakaryocytic cells and examining their functional distinctions and in vitro responsiveness to various stimuli.
Co-culture of early cattle embryos to the blastocyst stage with oviducal tissue or in conditioned medium (1989)

In Exp. 1, 5-8-cell embryos from superovulated cattle were co-cultured with oviducal tissue suspended in Ham's F10 + 10% fetal calf serum (F10FCS) or in F10FCS alone. After 4 days, the proportion of embryos developing into compact morulae or blastocysts was greater (P less than 0.005) in co-culture (38/82; 46%) than in F10FCS (1/27; 4%). In Exp. 2, a solution of collagenase, trypsin, DNAse and EDTA was used to disperse oviducal tissue, which was then cultured in TCM199 + 10% fetal calf serum (M199FCS) to obtain monolayers. Embryos (1-8 cells) were then co-cultured with monolayers or in M199FCS alone. The proportion of embryos developing into compact morulae and blastocysts after 4-5 days was higher (P less than 0.005) in co-culture (15/34; 43%) than in M199FCS (1/37; 3%); mean numbers of cells/embryo were also higher (P less than 0.001) (27.70; range 2-82 in co-culture; 8.83; range 2-18 in M199FCS). In Exp. 3, embryos obtained from in-vitro maturation and fertilization were used to compare development between co-culture and medium conditioned by oviducal tissue. Initial cleavage rate (no. embryos greater than 1 cell/total) was 76% (611/807) and did not differ among treatments. After 5 days, the proportion cleaving to greater than 16 cells was higher (P less than 0.005) in co-culture (71/203; 35%) and conditioned medium (48/205; 23%) compared to M199FCS (14/203; 7%). Similarly, the proportion developing into compact morulae and blastocysts was greater (P less than 0.005) in co-culture (44/203; 22%) and conditioned medium (46/205; 22%) than in M199FCS (7/203; 3%).(ABSTRACT TRUNCATED AT 250 WORDS)
Therapeutic Angiogenesis Induced by Human Hepatocyte Growth Factor Gene in Rat Diabetic Hind Limb Ischemia Model (2001)

Overall, intramuscular injection of human HGF plasmid induced therapeutic angiogenesis in a rat diabetic ischemic hindlimb model as a potential therapy for peripheral arterial disease. The delay of angiogenesis in diabetes might be due to downregulation of MMP-1 and ets-1 through a decrease in HGF by high D-glucose.
Simultaneous inhibition of the receptor kinase activity of vascular endothelial, fibroblast, and platelet-derived growth factors suppresses tumor growth and enhances tumor radiation response. (2002)

We have investigated the effect of simultaneous inhibition of multiple angiogenic growth factor signaling pathways on tumor growth, tumor blood perfusion, and radiation-induced tumor-growth delay using SU6668, an inhibitor of the receptor-tyrosine kinase activity of vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF), and platelet-derived growth factor (PDGF). The SCK mammary carcinoma, FSaII fibrosarcoma, and CFPAC human pancreatic carcinoma were grown s.c. in the hind leg of A/J mice, C3H mice, and Balb/cAnNCrl-nuBr nude mice, respectively. Daily i.p. injection of 100 mg/kg of SU6668 markedly suppressed the growth of these three tumor types. SU6668 also markedly prolonged the survival time of host mice bearing SCK tumors, which appeared to be caused by a reduction of metastatic tumor growth in the lung. There was little or no change in normal tissue blood perfusion, whereas in SCK tumors the perfusion decreased by 50% at 1 h after a single i.p. injection of SU6668, slightly recovered at 4 h, and completely recovered by 8 h. Interestingly, the tumor blood flow was significantly increased above the baseline level 24 h after SU6668 injection. After extended daily i.p. injections of SU6668, the tumor blood flow in all of the three tumor types studied was markedly decreased compared with control. The observed effects of this drug on tumor blood perfusion may partially explain the effectiveness of the compound in suppressing tumor growth and extending survival of tumor-bearing mice. We also observed that daily SU6668 administration and a single dose of 15 Gy of X-irradiation was significantly more effective than either treatment alone in suppressing tumor growth. Our results suggest that SU6668 increased the radiosensitivity of tumor blood vessels. We conclude that SU6668 is a potent therapeutic agent potentially useful to suppress tumor growth and enhance the response of tumors to radiotherapy.
Bringing VR and Spatial 3D Interaction to the Masses through Video Games (2008)

This article examines why innovations such as the Sony EyeToy and Nintendo Wii have been so successful and discusses the research opportunities presented by the latest commercial push for spatial 3D interaction in games.
Strength evaluation of composite laminate under biaxial loading: Configuration and stress distribution of a crossed specimen. (1991)

As a basic investigation of the static or fatigue strength of the composite laminates under the combined loading, the configuration and the stress distribution of the specimen to be used in the investigation are examined. The stress distribution of the crossed specimen with a stacking sequence of a laminate is analysed by the finite element method, and the effects of the root radius of the crossed portion, width and stiffened plates of the specimen under various kinds of the biaxial loading on the stress distribution are discussed. From the numerical results, the recommended informations to design the crossed specimen are obtained.
Mesoscale organization of metal nanocrystals (2002)

Abstract Nanocrystals of metals covered by alkanethiols organize themselves in two-dimensional arrays. We discuss such arrays of metal nanocrystals at length, with focus on the dependence of the structure and the stability of the arrays on the particle diameter and the distance between the particles. Three-dimensional superstructures of metal nanocrystals obtained by the use of alkanedithiols are examined. These ordered two- and three-dimensional structures of thiolized metal nanocrystals are good examples of mesoscale self-assembly. The association of metal nanocrystals to give rise to giant clusters with magic nuclearity provides an even more graphic demonstration of mesoscale self-assembly.
Cuff-less and Noninvasive Measurements of Arterial Blood Pressure by Pulse Transit Time (2005)

The current blood pressure (BP) measurement devices are mostly built on the principle of auscultation, oscillometry or tonometry, all of which use an inflatable cuff to occlude or unload the artery. The need of a cuff in these devices limits the further reduction in size and power consumption, and restricts the frequency and ease of their usage. Therefore, this study aims to develop a cuff-less and noninvasive technique for measuring BP by pulse transit time. The technique was evaluated on 85 subjects, aged 57+/-29 yrs., including 36 males and 39 hypertensives, over an average period of 6.4 wks. A total of 999 pairs of systolic BP (SBP) and diastolic BP (DBP) estimations were made. The average of BP readings reported by an experienced registered nurse and those obtained from a clinically approved automatic BP meter was used as reference. It is found that the estimated SBP and DBP differed from the reference BP by 0.6+/-9.8mmHg and 0.9+/-5.6mmHg respectively. When compared to the AAMI requirement (5+/-8mmHg for both SBP and DBP estimation), the results suggest that the cuff-less technology has great potential to be developed into wearable devices that are useful in self BP monitoring for home healthcare and eventually in clinical diagnosis.