gebhart/patrepeval huggingface dataset:
Deficiencies of vitamins E and A in the rat. Retinal damage and lipofuscin accumulation. (1980)

The interrelationships of vitamins E and A in maintaining various structural components of the retina were studied in four groups of weanling female rats fed purified diets adequate or deficient in each vitamin: +E, +A; -E, +A; +E, -A; and -E, -A. Groups deficient in retinol (-A) were supplemented with retinoic acid. After 14, 21, and 35 weeks, the retinas were examined histologically and ultrastructurally. At 35 weeks, the doubly deficient rats (-E, -A) had lost 92% of their rod nuclei, whereas rats deficient in vitamins A (+E, -A) or E (-E, +A) alone had lost only 34% and 20%, respectively. Vitamin E deficiency resulted in extensive lipofuscin deposits in the retinal pigment epithelium as early as 21 weeks, but the presence of vitamin A doubled the number of lipofuscin granules (-E, +A vs. -E, -A) and induced an even greater increase in their autofluorescence. Another clear influence of vitamin A was seen when +E, +A retinas autofluoresced not only much more than +E, -A retinas, which had similar numbers of granules, but also more than -E, -A retinas, which had about twice as many lipofuscin granules. In the retina, unlike the uterus, the lipofuscin-specific autofluorescence and lipofuscin granule number were not proportional. Moreover, the numbers of granules were influenced by both vitamins E and A, whereas the intensity of lipofuscin-specific autofluorescence was determined almost exclusively by vitamin A. Probably the accelerated loss of photoreceptor cells in -E, -A retinas resulted from both oxidation of membranes and oxidation of retinal vitamin A stores in the absence of vitamin E protection.
Purification of two forms of starch branching enzyme (Q‐enzyme) from developing rice endosperm (1992)

Two isoforms of starch branching enzyme (Q‐enzyme), QEI and QEII, have been purified to honlogeneity from developing rice endosperm. QEI and QEII, with molecular weights of about 80 and 85 kDa, respectively, could be fully separated by anion‐exchange or hydrophobic chromatography. The peptide maps obtained after V 8 proteinase digestion were quite different between the two enzymes. Antibodies prepared against QEI showed no immunological cross‐reaction with the QEII protein in Western blot experiments, and anti‐QEII serum did not react with the QEI protein. The data indicate that QEI and QEII are distinct proteins encoded by different genes in rice plants.
Assessment of the value of the vertebral heart scale in the radiographic diagnosis of cardiac disease in dogs (2000)

In order to assess the influence of the vertebral heart scale (VHS) on the accuracy of the radiographic diagnosis of cardiac disease, thoracic radiographs of 50 dogs with proven cardiac disease, 26 with other thoracic diseases, and 50 with no clinical signs of cardiovascular or respiratory disease were mixed and examined by three independent, blinded observers chosen to represent a range of radiographic abilities. They first examined all the radiographs without making measurements of VHS and made a diagnosis. They then re-examined the radiographs, and measured VHS on both lateral and dorsoventral or ventrodorsal radiographs before again recording a diagnosis without reference to their original diagnoses. For all the observers, the dogs with cardiac disease had a higher mean VHS than the normal dogs. A VHS over 10.7 on the lateral radiograph was a moderately accurate sign of cardiac disease. The observers' accuracy of diagnosis did not change significantly as a result of using VHS as an adjunct to a subjective assessment of the radiographs.
Noisy-light correlation functions by frequency resolved optical gating (1998)

A new technique for measuring the time- and frequency-dependent intensities and phases of correlation functions of broadband, non–transform-limited (noisy) light is presented. It is based on others’ successful previous efforts to measure the intensities and phases of short pulses by frequency-resolved optical gating. It is shown that a simplified algorithm based on the original algorithm for frequency-resolved optical gating is sufficient for the recovery of correlation functions. The first experimental realizations of this technique are presented, and the recovered noisy-light correlation functions are shown. By way of illustration, the dispersion of water is quantified. Applications to interferometrically time-resolved nonlinear optical spectroscopies are discussed.
PLASMA POLYMERASE CHAIN REACTION FOR CYTOMEGALOVIRUS DNA AFTER ALLOGENEIC MARROW TRANSPLANTATION (1997)

In a prospective longitudinal study, detection of cytomegalovirus (CMV) DNA in plasma (plasma polymerase chain reaction [PCR]) was compared with PCR of CMV DNA in peripheral blood leukocytes (PBL PCR), the CMV pp65 antigenemia assay, and viral cultures from blood, urine, and throat of 29 patients, 14 of whom received pp65 antigenemia-guided early ganciclovir treatment and 15 of whom received ganciclovir at engraftment. Among 328 blood samples tested by all methods, PBL PCR was the most sensitive test, followed by the pp65 antigenemia assay, plasma PCR, and viremia. In the 14 patients who received pp65 antigenemia-guided early treatment, the incidence of PBL PCR, pp65 antigenemia, plasma PCR, and viremia before day 100 was 79%, 79%, 71%, and 27%, respectively, with a median day of onset of day 32, 42, 45, and 51, respectively. Nine patients (64%) became positive by PBL PCR, pp65 antigenemia, and plasma PCR. Of 15 patients who were treated with ganciclovir at engraftment, 12 (80%) became positive by PBL PCR, plasma PCR, and/or pp65 antigenemia while receiving ganciclovir; 3 (20%) had breakthrough infection with all three methods, including 2 with high-grade antigenemia (more than three positive cells in duplicate staining); none of these patients subsequently developed positive CMV cultures or disease. In 49 specimens, PBL PCR and/or pp65 antigenemia assay could not be performed because of insufficient neutrophil counts. In conclusion, the sensitivity of plasma PCR is significantly lower than that of PBL PCR but similar to that of the pp65 antigenemia assay. Plasma PCR may be particularly useful in clinical situations in which a less sensitive and possibly more specific assay is warranted or in which leukocyte counts are inadequate to perform cell-based assays.
Gene Promoter Methylation in Plasma and Sputum Increases with Lung Cancer Risk (2005)

Concomitant methylation of multiple gene promoters in sputum is strongly associated with lung cancer risk.
Association between miR-125a rs12976445 and survival in breast cancer patients. (2014)

MicroRNAs (miRNAs) act as an oncogene or a tumor suppressor by negatively regulating target genes. Genetic variants in miRNA genes confer susceptibility to cancer and risk of death in cancer patients. The aim of this study was to investigate whether miRNA polymorphisms were associated with survival in breast cancer patients. Five miRNA polymorphisms (miR-26a1 rs7372209, miR-125a rs12976445, miR-218 rs11134527, miR-423 rs6505162, and miR-608 rs4919510) were genotyped in 196 breast cancer patients. We found that miR-125a rs12976445 was significantly associated with survival in codominant, recessive, and dominant models. However, only association under the codominant model remained significant after adjustment for lymph node metastasis, TNM stage, estrogen receptor, and progesterone receptor. Furthermore, this effect remained in stratification analysis. In conclusion, our results provide evidence that miR-125a rs12976445 may serve as a prognostic biomarker for breast cancer. Further large-scale studies are required to confirm these findings.
Controlled Ribonucleotide Tailing of cDNA ends (CRTC) by Terminal Deoxynucleotidyl Transferase: A New Approach in PCR-Mediated Analysis of mRNA Sequences (1996)

Controlled ribonucleotide tailing of cDNA ends (CRTC) by terminal deoxynucleotidyl transferase is a polymerase chain reaction (PCR)-mediated technique that was developed to facilitate cloning and direct sequence analysis of complete 5'-terminal unknown coding regions of rare RNA molecules. In contrast with standard tailing protocols using dNTPs as the substrate, ribo-tailing of cDNA ends is easily controllable, self-limited (from two to four rNMP incorporations) and highly efficient (>98%). By virtue of the homopolymeric ribo-tail, the modified cDNA is anchored to the 3' overhang of a double-stranded DNA-adaptor in a T4 DNA ligase-dependent ligation. PCR amplification, mediated by two sequence-specific primers, yields the desired unique product suitable for cloning and dideoxy-sequencing.
A Polymorphism in the Complement ComponentC1qACorrelates with Prolonged Response Following Rituximab Therapy of Follicular Lymphoma (2008)

Our findings indicate that polymorphisms in the C1qA gene may affect the clinical response and duration of response to rituximab therapy of follicular lymphoma. These results could have direct implications on designing antibodies with improved efficiency and enhance our understanding of the role of complement in monoclonal antibody therapy.
Intrusion detection using extraction of moving edges (2002)

In this article we present an image processing based method for intrusion detection. The algorithm is characterized by a low computational cost, a high sensitivity to the presence of objects, robustness to illumination changes and modest memory requirements. The suggested approach is to separate the moving object edges from the background.
Calbindin D28k blocks the proapoptotic actions of mutant presenilin 1: Reduced oxidative stress and preserved mitochondrial function (1998)

Mutations in the presenilin 1 (PS-1) gene account for many cases of early-onset autosomal dominant inherited forms of Alzheimer's disease. Recent findings suggest that PS-1 mutations may sensitize neurons to apoptosis induced by trophic factor withdrawal and exposure to amyloid beta-peptide (Abeta). We now report that overexpression of the calcium-binding protein calbindin D28k prevents apoptosis in cultured neural cells expressing mutant PS-1 (L286V and M146V missense mutations). Elevations of the intracellular Ca2+ concentration and generation of reactive oxygen species induced by Abeta, and potentiated by mutant PS-1, were suppressed in calbindin-overexpressing cells. Impairment of mitochondrial function by Abeta (which preceded apoptosis) was exacerbated by PS-1 mutations and was largely prevented by calbindin. These findings suggest that PS-1 mutations render neurons vulnerable to apoptosis by a mechanism involving destabilization of cellular calcium homeostasis, which leads to oxidative stress and mitochondrial dysfunction.
Complete Genome Structure of the Thermophilic Cyanobacterium Thermosynechococcus elongatus BP-1 (2002)

The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.
Novel antiplatelet therapies following percutaneous coronary interventions. (2009)

Drug-eluting stents effectively reduce the incidence of in-stent restenosis; however, the use of these stents has led to the requirement for more effective antiplatelet therapies than are currently available. This requirement primarily arises from the presence of the antiproliferative drug coating of the stents. These coatings cause the prolonged exposure of platelets to stent struts and denuded endothelium, resulting in an increased potential for prothrombotic clinical sequelae. New antiplatelet therapies are also required because of the inter-individual variability in responses to available antiplatelet drugs. Ideally, new drugs would selectively target distinct mechanisms of platelet activation, avoiding increases in bleeding risk. This review discusses novel antiplatelet therapies under clinical investigation.
Small molecule screening in zebrafish: swimming in potential drug therapies (2012)

Phenotype-driven chemical genetic screens in zebrafish have become a proven approach for both dissection of developmental mechanisms and discovery of potential therapeutics. A library of small molecules can be arrayed into multiwell plates containing zebrafish embryos. The embryo becomes a whole organism in vivo bioassay that can produce a phenotype upon treatment. Screens have been performed that are based simply on the morphology of the embryo. Other screens have scored complex phenotypes using whole mount in situ hybridization, fluorescent transgenic reporters, and even tracking of embryo movement. The availability of many well-characterized zebrafish mutants has also enabled the discovery of chemical suppressors of genetic phenotypes. Importantly, the application of chemical libraries that already contain FDA-approved drugs has allowed the rapid translation of hits from zebrafish chemical screens to clinical trials.
A windowed weighted approach for approximate cyclic string matching (2003)

A method for measuring dissimilarities between cyclic strings is introduced. It computes a weighted mean between two (lower and upper) bounds of the exact cyclic edit distance, which are founded on a window-constrained edit graph related to the strings involved. Weights are the ones which minimize the sum of squared relative errors of the weighted solution with respect to exact values, on a training set of string pairs. This method takes O(n/sup 2/) time. Experiments on both artificial and real data, show the highly accurate solutions achieved by this technique, which is clearly faster than the most efficient exact algorithms.
Transfer of drug resistance genes into hematopoietic progenitors to improve chemotherapy tolerance. (1996)

A number of drug resistance genes have been identified that may be useful in gene therapy approaches to ameliorate chemotherapy toxicity. Hematopoietic tissue is the most suitable target for drug resistance gene therapy because myelosuppression is the dose-limiting toxicity of the many chemotherapeutic agents. Recent studies have shown that murine and human hematopoietic progenitors can be transduced ex vivo using retroviral vectors to overexpress P-glycoprotein, dihydrofolate reductase, and O6-alkylguanine DNA alkyltransferase. In all instances, gene transfer results in significant drug resistance in hematopoietic progenitors both in vitro and in vivo. Clinical trials are underway to evaluate the role of MDR-1 gene therapy in amelioration of chemotherapy induced myelosuppression. Other genes being examined for their potential to transfer drug resistance to hematopoietic cells include genes encoding aldehyde dehydrogenase, nucleotide excision repair proteins, multidrug resistant protein, and superoxide dismutase. As a group these proteins could confer significant levels of chemotherapy drug resistance to bone marrow cells. When compared with other somatic gene therapy approaches, drug resistance gene therapy has the aim of protecting normal cells and preventing toxicity. In addition many of these genes could be used to select for cells carrying the drug resistance gene as well as cotransduced therapeutic gene. Thus, gene transfer of drug resistance genes will have broad applications in the field of gene therapy as well as in protecting hematopoietic cells from chemotherapy toxicity.
Sequence of the bacteriophage SP01 gene coding for transcription factor 1, a viral homologue of the bacterial type II DNA-binding proteins. (1984)

The Bacillus subtilis phage SP01, whose DNA contains 5-hydroxymethyluracil (hmUra) in place of thymine, codes for an abundant, small, basic protein called TF1. TF1 binds preferentially to hydroxymethyluracil-containing DNA and thereby selectively inhibits transcription of such DNA in vitro. The gene for TF1 has been sequenced. We find that this viral protein is a homologue of the ubiquitous bacterial type II DNA-binding proteins. The three-dimensional structure of one of these bacterial proteins has recently been determined. We are able to discern common as well as distinctive features in the amino acid sequence and the three-dimensional structure of the homologous viral protein.
The wonders of the Wanderer (2012)

Vagus is Latin for wandering, and the vagus nerve fully deserves this name due to its extensive distribution through the body. Indeed, one of the lines of the song that accompanied the 2012 G. L. Brown Prize Lecture exaggerates this diversity, 'My function's almost anythin', and vagus is my name'. Alteration of vagal activity was first investigated in the 1880s as a treatment for epilepsy, and vagus nerve stimulation is now an approved treatment for refractory epilepsy and depression in the USA, despite an incomplete understanding of the mechanisms involved. Vagus nerve stimulation could be beneficial in many other conditions, including heart failure, tinnitus, chronic hiccups, Alzheimer's disease and inflammatory diseases. Inhibition of vagal activity could also be beneficial in some conditions, e.g. reducing activation of vagal respiratory afferents to treat chronic cough. This review discusses evidence underlying some current and potential therapeutic applications of vagal modulation, illustrating the wonders of the Wanderer.
Slit lamp laser doppler interferometer (1993)

A slit lamp laser interferometer is described for clinical in vivo eye length measurements. The basic components are a laser Doppler interferometer, a slit lamp attachment, and a commercial slit lamp. First measurements of the axial length of the eye yielded a standard deviation of 0.04 mm and less.
Targeted Polymeric Micelles for siRNA Treatment of Experimental Cancer by Intravenous Injection (2012)

Small interfering ribonucleic acid (siRNA) cancer therapies administered by intravenous injection require a delivery system for transport from the bloodstream into the cytoplasm of diseased cells to perform the function of gene silencing. Here we describe nanosized polymeric micelles that deliver siRNA to solid tumors and elicit a therapeutic effect. Stable multifunctional micelle structures on the order of 45 nm in size formed by spontaneous self-assembly of block copolymers with siRNA. Block copolymers used for micelle formation were designed and synthesized to contain three main features: a siRNA binding segment containing thiols, a hydrophilic nonbinding segment, and a cell-surface binding peptide. Specifically, poly(ethylene glycol)-block-poly(L-lysine) (PEG-b-PLL) comprising lysine amines modified with 2-iminothiolane (2IT) and the cyclo-Arg-Gly-Asp (cRGD) peptide on the PEG terminus was used. Modification of PEG-b-PLL with 2IT led to improved control of micelle formation and also increased stability in the blood compartment, while installation of the cRGD peptide improved biological activity. Incorporation of siRNA into stable micelle structures containing the cRGD peptide resulted in increased gene silencing ability, improved cell uptake, and broader subcellular distribution in vitro and also improved accumulation in both the tumor mass and tumor-associated blood vessels following intravenous injection into mice. Furthermore, stable and targeted micelles inhibited the growth of subcutaneous HeLa tumor models and demonstrated gene silencing in the tumor mass following treatment with antiangiogenic siRNAs. This new micellar nanomedicine could potentially expand the utility of siRNA-based therapies for cancer treatments that require intravenous injection.
Effects of hydrophobicity and mat thickness on release from hydrogel-electrospun fiber mat composites (2013)

Poly(ethylene glycol) (PEG)-based hydrogel-electrospun fiber mat (EFM) composites are a promising new controlled release system for hydrophilic drugs, providing longer and more linear release characteristics accompanied by a smaller initial burst than traditional hydrogel systems. However, the effect of EFM properties on release characteristics has not yet been examined. Here, we investigated the influence of EFM thickness and hydrophobicity on swelling and release behavior using bovine serum albumin as a model hydrophilic protein. EFMs investigated were comprised of poly(ε-caprolactone) (PCL) at thicknesses of 300, 800, or 1100 μm. Hydrophobicity was adjusted through surface modification: fluorinated PCL, core/shell PCL/PEGPCL, and acrylic acid (AAc)-treated PCL EFMs were examined. EFMs comprised of the external composite surface, forming a sandwich around PEG-poly(lactic acid) (PEGPLA) hydrogels, and significantly restrained hydrogel swelling in the radial direction while increasing swelling in the axial direction. Incorporation of EFMs also reduced initial hydrophilic protein release rates and extended the duration of release. Increased EFM thickness and hydrophobicity were equally correlated with longer and more linear release profiles. Increased thickness most likely increases the diffusional path length, whereas increased hydrophobicity hinders hydrophilic drug diffusion. These composites form a promising new class of tunable release materials having properties superior to those of unmodified hydrogels.
Poly(vinyl butyral) based polymer networks with dual-responsive shape memory and self-healing properties (2014)

In this work, polymer networks are prepared by a simple cross-linked reaction of poly(vinyl butyral) (PVB) and hexamethylene diisocyanate. The cross-linked reaction was evaluated by Fourier transition infrared spectroscopy, degree of swelling and gel content. The polymer networks show high mechanical strength with tensile modulus and tensile strength over 1 GPa and 40 MPa, respectively, at rt. With PVB as switching domain, the polymer networks exhibit excellent thermal- and solvent-induced shape memory properties. Also, the influence of cross-linked density and solvents' properties on solvent-induced recovery speed were carefully investigated. Moreover, with the assistance of a shape memory effect, the polymer networks also show scratch self-healing behavior which was monitored using optical and scanning electron microscopy.