gebhart/patrepeval huggingface dataset:
Quantitation of fetal DNA in maternal serum during the first trimester of pregnancy by the use of a DAZ repetitive probe (2006)

Cell-free fetal DNA in maternal plasma or serum is at present widely investigated as a source of fetal genetic material, both in studies of pregnancy-related disorders and in planning strategies for non-invasive prenatal diagnosis. Despite the number of trials already performed on the quantitation of fetal DNA, data about the amount of DNA at the beginning of pregnancy, in particular in the first trimester, remain limited. A new probe mapping on the deleted in azoospermia (DAZ) repetitive region of the Yq chromosome was designed for an early assessment of fetal DNA concentration in maternal serum. Among 57 pregnant women prospectively studied in their first trimester, fetal DNA was detected already by the 5th gestational week, with the analysis becoming reliable by the 8th week of gestation when a 100% accuracy in fetal sex determination was achieved. Moreover, in the three cases of pregnancy ending in fetal loss, the amount of fetal DNA apparently decreased before the abortion was diagnosed, whereas it consistently showed an increasing trend in normal pregnancies. Real-time PCR with the use of DAZ multilocus probe can efficiently quantitate free fetal DNA in the maternal serum at the beginning of pregnancy.
Construction and In Vitro Properties of SIV mac Mutants with Deletions in "Nonessential" Genes (1994)

The so-called "nonessential" genes of primate lentiviruses can be deleted without abrogating the ability of virus to replicate under at least some cell culture conditions. In SIVmac, these genes are vif, vpx, vpr, and nef. Sequences in the upstream region of U3 in the LTR have also been shown to be dispensable for replication in cell culture. We report here the construction and characterization of a panel of 40 single and combination deletion mutants derived from the pathogenic molecular clone SIVmac239. Deletion of the vpr gene caused little or no change in the growth properties of SIVmac239 in CEMx174 cells, in rhesus monkey peripheral blood mononuclear cells (PBMCs), or in rhesus monkey alveolar macrophages. Deletion of the vpx gene resulted in a greatly reduced rate of replication of the virus in the primary PBMC and macrophage cultures, but no significant reduction in replication of the virus in CEMx174 cells. Deletion of the vpx gene appeared to have a greater effect on virus replication in macrophages than in PBMCs. Deletion of the vif gene caused a dramatic reduction in replication in all cell types tested. However, even delta 5, which contains deletions in all five targeted regions (vif, vpx, vpr, nef, and U3), can still replicate in CEMx174 cells albeit with greatly delayed kinetics. Deletion of nef, alone or in combination with deletions in U3 and vpr, had no observable effect on replication of the virus in any of the cells tested. Because the disease induced by the parental SIVmac239 clone in rhesus monkeys has been well characterized and is remarkably similar to AIDS in humans, this collection of mutants will be useful for relating in vitro properties and gene function with in vivo pathogenic potential.
Deuterium‐reinforced polyunsaturated fatty acids improve cognition in a mouse model of sporadic Alzheimer's disease (2017)

Oxidative damage resulting from increased lipid peroxidation (LPO) is considered an important factor in the development of late onset/age-related Alzheimer's disease (AD). Deuterium-reinforced polyunsaturated fatty acids (D-PUFAs) are more resistant to the reactive oxygen species-initiated chain reaction of LPO than regular hydrogenated (H-) PUFAs. We investigated the effect of D-PUFA treatment on LPO and cognitive performance in aldehyde dehydrogenase 2 (Aldh2) null mice, an established model of oxidative stress-related cognitive impairment that exhibits AD-like pathologies. Mice were fed a Western-type diet containing either D- or H-PUFAs for 18 weeks. D-PUFA treatment markedly decreased cortex and hippocampus F<sub>2</sub> -isoprostanes by approximately 55% and prostaglandin F<sub>2α</sub> by 20-25% as compared to H-PUFA treatment. D-PUFAs consistently improved performance in cognitive/memory tests, essentially resetting performance of the D-PUFA-fed Aldh2<sup>-/-</sup> mice to that of wild-type mice fed a typical laboratory diet. D-PUFAs therefore represent a promising new strategy to broadly reduce rates of LPO, and combat cognitive decline in AD.
Cloning and Characterization of OSF-3, a New Member of the MER5 Family, Expressed in Mouse Osteoblastic Cells (1994)

A cDNA library prepared from the mouse osteoblastic cell line, MC3T3-E1, was screened for the presence of specifically expressed genes by employing subtraction hybridization/differential screening methods. A cDNA clone was identified and sequenced, encoding a protein designated as osteoblast specific factor 3 (OSF-3) comprising 199 amino acids. RNA dot blot analysis indicated weak OSF-3 expression in thymus, spleen, brain, lung, testis, and heart, and high expression in kidney and liver. A homology search of an amino acid sequence database revealed a strong relationship of OSF-3 to the MER5 (gene preferentially expression in murine erythroleukemia cells) protein and human pag (proliferation associated gene) product. This indicates that OSF-3 plays an intrinsic role in the proliferation and/or differentiation of bone cells.
Combining Experimental Information from Crystal and Solution Studies: Joint X-Ray and NMR Refinement (1992)

Joint refinement of macromolecules against crystallographic and nuclear magnetic resonance (NMR) observations is presented as a way of combining experimental information from the two methods. The model of interleukin-1 beta derived by the joint x-ray and NMR refinement is shown to be consistent with the experimental observations of both methods and to have crystallographic R value and geometrical parameters that are of the same quality as or better than those of models obtained by conventional crystallographic studies. The few NMR observations that are violated by the model serve as an indicator for genuine differences between the crystal and solution structures. The joint x-ray-NMR refinement can resolve structural ambiguities encountered in studies of multidomain proteins, in which low- to medium-resolution diffraction data can be complemented by higher resolution NMR data obtained for the individual domains.
Study of localization of response to fibroblast growth factor-2 in murine calvaria using Raman spectroscopic imaging (2004)

Raman spectral imaging provides the means to study spatially localized response to controlled external perturbations to tissue specimens with light microscopy resolution. We discuss use of heparin-acrylic microbeads soaked with the protein fibroblast growth factor-2 (FGF2). Microbeads containing FGF2 are placed in murine calvarial tissue and stimulate abnormally rapid mineralization. The tissue response simulated the effects of craniosynostosis, a birth defect occurring in 1 in 2400 live births. We describe Raman imaging measurements of the spatial distribution of apatitic mineral and matrix (predominantly type I collagen) from normal murine calvarial tissue and murine calvarial tissue modeling craniosynostosis. We also discuss spectroscopic evaluation of the state of the mineral induced by the FGF2 beads.
Pyrimidine Ribonucleotides with Enhanced Selectivity as P2Y6 Receptor Agonists: Novel 4-Alkyloxyimino, (S)-Methanocarba, and 5′-Triphosphate γ-Ester Modifications (2010)

The P2Y(6) receptor is a cytoprotective G-protein-coupled receptor (GPCR) activated by UDP (EC(50) = 0.30 microM). We compared and combined modifications to enhance P2Y(6) receptor agonist selectivity, including ribose ring constraint, 5-iodo and 4-alkyloxyimino modifications, and phosphate modifications such as alpha,beta-methylene and extension of the terminal phosphate group into gamma-esters of UTP analogues. The conformationally constrained (S)-methanocarba-UDP is a full agonist (EC(50) = 0.042 microM). 4-Methoxyimino modification of pyrimidine enhanced P2Y(6), preserved P2Y(2) and P2Y(4), and abolished P2Y(14) receptor potency, in the appropriate nucleotide. N(4)-Benzyloxy-CDP (15, MRS2964) and N(4)-methoxy-Cp(3)U (23, MRS2957) were potent, selective P2Y(6) receptor agonists (EC(50) of 0.026 and 0.012 microM, respectively). A hydrophobic binding region near the nucleobase was explored with receptor modeling and docking. UTP-gamma-aryl and cycloalkyl phosphoesters displayed only intermediate P2Y(6) receptor potency but had enhanced stability in acid and cell membranes. UTP-glucose was inactive, but its (S)-methanocarba analogue and N(4)-methoxycytidine 5'-triphospho-gamma-[1]glucose were active (EC(50) of 2.47 and 0.18 microM, respectively). Thus, the potency, selectivity, and stability of pyrimidine nucleotides as P2Y(6) receptor agonists may be enhanced by modest structural changes.
Hepatitis C virus core protein interacts with the cytoplasmic tail of lymphotoxin-beta receptor (1997)

Hepatitis C virus (HCV) core protein is a multifunctional protein. We examined whether it can interact with cellular proteins, thus contributing to viral pathogenesis. Using the HCV core protein as a bait to screen a human liver cDNA library in a yeast two-hybrid screening system, we have isolated several positive clones encoding cellular proteins that interact with the HCV core protein. Interestingly, more than half of these clones encode the cytoplasmic domain of lymphotoxin-beta receptor (LT betaR), which is a member of the tumor necrosis factor receptor family. Their binding was confirmed by in vitro glutathione S-transferase fusion protein binding assay and protein-protein blotting assay to be direct and specific. The binding sites were mapped within a 58-amino-acid region of the cytoplasmic tail of LT betaR. The binding site in the HCV core protein was localized within amino acid residues 36 to 91 from the N terminus, corresponding to the hydrophilic region of the protein. In mammalian cells, the core protein was found to be associated with the membrane-bound LT betaR. Since the LT betaR is involved in germinal center formation and developmental regulation of peripheral lymphoid organs, lymph node development, and apoptotic signaling, the binding of HCV core protein to LT betaR suggests the possibility that this viral protein has an immunomodulating function and may explain the mechanism of viral persistence and pathogenesis of HCV.
Effects of beta-hydroxy-beta-methylbutyrate (HMB) on exercise performance and body composition across varying levels of age, sex, and training experience: A review (2008)

The leucine metabolite beta-hydroxy-beta-methylbutyrate (HMB) has been extensively used as an ergogenic aid; particularly among bodybuilders and strength/power athletes, who use it to promote exercise performance and skeletal muscle hypertrophy. While numerous studies have supported the efficacy of HMB in exercise and clinical conditions, there have been a number of conflicting results. Therefore, the first purpose of this paper will be to provide an in depth and objective analysis of HMB research. Special care is taken to present critical details of each study in an attempt to both examine the effectiveness of HMB as well as explain possible reasons for conflicting results seen in the literature. Within this analysis, moderator variables such as age, training experience, various states of muscle catabolism, and optimal dosages of HMB are discussed. The validity of dependent measurements, clustering of data, and a conflict of interest bias will also be analyzed. A second purpose of this paper is to provide a comprehensive discussion on possible mechanisms, which HMB may operate through. Currently, the most readily discussed mechanism has been attributed to HMB as a precursor to the rate limiting enzyme to cholesterol synthesis HMG-coenzyme A reductase. However, an increase in research has been directed towards possible proteolytic pathways HMB may operate through. Evidence from cachectic cancer studies suggests that HMB may inhibit the ubiquitin-proteasome proteolytic pathway responsible for the specific degradation of intracellular proteins. HMB may also directly stimulate protein synthesis, through an mTOR dependent mechanism. Finally, special care has been taken to provide future research implications.
End-Adsorbed Polymer Brushes in High- and Low-Molecular-Weight Matrices (1996)

Numerical self-consistent-field theory (Scheutjens−Fleer theory) is used to describe the crossover from “dry” brush behavior, where the matrix from which the polymers adsorb is itself a high-molecular-weight polymer, to “wet” brush behavior, where the matrix is a small-molecule solvent. The free energy, f*, required to add an additional chain to an existing brush is calculated for different values of Na, Nb, χ, and z*, where Nb and Na are the respective degrees of polymerization of the adsorbing and nonadsorbing molecules, χ is the Flory interaction parameter between different segment types, and z* is the integrated volume fraction of adsorbing chains. In situations where the adsorbing and nonadsorbing molecules have the same statistical segment length, f* is completely specified by Nb/Na, χNa, and z*/Rg, where Rg is the unperturbed radius of gyration of the adsorbing molecules. For a large range of these parameters, results for f*, and the closely related adsorption isotherms, are in good agreement with analytic predictions from a simple scaling argument.
The Framingham Eye Study monograph: An ophthalmological and epidemiological study of cataract, glaucoma, diabetic retinopathy, macular degeneration, and visual acuity in a general population of 2631 adults, 1973-1975. (1981)

Ophthalmologic examinations for cataract, glaucoma, diabetic retinopathy, macular degeneration and visual acuity were performed on 2631 of the 3977 members of the Framingham (Massachusetts) Heart Study population still living in 1973-1975. The subjects ranged in age from 52 to 85 years. This monograph presents the detailed protocols and record forms for screening and diagnostic examinations, definitions of the specific abnormalities and characteristics used to screen for each disease, criteria for suspicion and diagnosis of diseases, detailed tables of the basic data from the study, evaluation of quality of the data, and discussion of selected findings. The tables provide data on the number and proportion of persons and of eyes with each type of abnormality and each disease, by age and sex. Where appropriate, the data are further classified by location of abnormality, severity, bilaterality and associated visual acuity limitation. The study was sponsored by the National Eye Institute.
Pd/P(t-Bu)3:  A Mild and General Catalyst for Stille Reactions of Aryl Chlorides and Aryl Bromides (2002)

Pd/P(t-Bu)(3) serves as an unusually reactive catalyst for Stille reactions of aryl chlorides and bromides, providing solutions to a number of long-standing challenges. An unprecedented array of aryl chlorides can be cross-coupled with a range of organotin reagents, including SnBu(4). Very hindered biaryls (e.g., tetra-ortho-substituted) can be synthesized, and aryl chlorides can be coupled in the presence of aryl triflates. The method is user-friendly, since a commercially available complex, Pd(P(t-Bu)(3))(2), is effective. Pd/P(t-Bu)(3) also functions as an active catalyst for Stille reactions of aryl bromides, furnishing the first general method for room-temperature cross-couplings.
Rationalization of the entrapping of bioactive molecules into a series of functionalized porous zirconium terephthalate MOFs (2013)

The encapsulation of two different bioactive molecules, the cosmetic caffeine and the analgesic and anti-inflammatory ibuprofen, has been evaluated by combining impregnation and advanced characterization experimental tools in a series of microporous rigid zirconium(iv) terephthalates UiO-66 bearing different polar or apolar functional groups (-H, -Br, -NH<sub>2</sub>, -2OH, -NO<sub>2</sub>, -Cl, -2CF<sub>3</sub>, -CH<sub>3</sub>, -2CH<sub>3</sub>). It has been first evidenced that these hybrid solids exhibit drug payloads that significantly outperform those obtained using current drug formulations or other conventional porous solids. A quantitative structure-activity relationship strategy has been further conducted with the aim of rationalizing the experimental drug uptakes and further emphasizing the most relevant chemical and structural features that significantly impact their encapsulation performances. Indeed, it appears that the caffeine loading is optimized when the functionalized organic linker both shows a large octanol-water partition coefficient and contains grafted functions with low hydrogen bond acceptor abilities, whereas the ibuprofen entrapping is enhanced when the organic linker contains functional groups with a large solvent surface area and free volume, and to a lesser extent low hydrogen bond acceptor abilities. Moreover, it has been shown that the solvent used as media for the biomolecule impregnation plays a crucial role in the encapsulation performance due to the formation of a competitive adsorption process between the solvent and the active molecule.
Aspirin and Dipyridamole in the Prevention of Re-Stenosis after Percutaneous Transluminal Coronary Angioplasty (1988)

To examine the role of antiplatelet therapy in the prevention of arterial restenosis after percutaneous transluminal coronary angioplasty (PTCA), we conducted a randomized, double-blind, placebo-controlled study in 376 patients. The active treatment consisted of an oral aspirin-dipyridamole combination (330 mg-75 mg) given three times daily, beginning 24 hours before PTCA. Eight hours before PTCA, the oral dipyridamole was replaced with intravenous dipyridamole at a dosage of 10 mg per hour for 24 hours, and oral aspirin was continued. Sixteen hours after PTCA, the initial combination was reinstituted. Treatment was continued in patients with a successfully dilated vessel until follow-up angiography four to seven months after PTCA--or earlier, if symptoms dictated. Of 249 patients who underwent follow-up angiography, 37.7 percent of patients receiving the active drug had restenosis in at least one segment, as compared with 38.6 percent of patients taking placebo (P not significant). The number of stenotic segments was virtually the same in the two groups. Among the 376 randomized patients, there were 16 periprocedural Q-wave myocardial infarctions--13 in the placebo group and 3 in the active-drug group (6.9 percent vs. 1.6 percent, P = 0.0113). Although the use of this antiplatelet regimen before and after PTCA did not reduce the six-month rate of restenosis after successful coronary angioplasty, it markedly reduced the incidence of transmural myocardial infarction during or soon after PTCA. Thus, the short-term use of antiplatelet agents in relation to PTCA can be recommended.
The wheat transcriptional activator SPA: a seed-specific bZIP protein that recognizes the GCN4-like motif in the bifactorial endosperm box of prolamin genes. (1997)

The conserved bifactorial endosperm box found in the promoter of wheat storage protein genes comprises two different cis elements that are thought to be involved in regulating endosperm-specific gene expression. Endosperm nuclear extracts contain binding activities. One is called ESBF-I, which binds to the endosperm motif (EM), and the other is called ESBF-II, which binds to the GCN4-like motif(GLM). Here, we present a functional analysis of the endosperm box of a low-molecular-weight glutenin gene found on the 1D1 chromosome of hexaploid wheat (LMWG-1D1) in transgenic tobacco plants. Our analysis demonstrates the necessity of the EM and GLM for endosperm-specific gene expression and suggests the presence in tobacco of functional counterparts of wheat ESBF-I and ESBF-II. Furthermore, we describe the isolation and characterization of cDNA clones encoding SPA, a seed-specific basic leucine zipper protein from wheat that can activate transcription from the GLMs of the -326-bp LMWG-1D1 promoter in both maize and tobacco leaf protoplasts. This activation is also partially dependent on the presence of functional EMs, suggesting interactions between SPA with ESBF-I-like activities.
Enhancement of DNA vaccine potency by linkage of antigen gene to an HSP70 gene. (2000)

Nucleic acid vaccines represent an attractive approach to generating antigen-specific immunity because of their stability and simplicity of delivery. However, there is still a need to increase the potency of DNA vaccines. Using human papillomavirus type 16 E7 as a model antigen, we evaluated the effect of linkage to Mycobacterium tuberculosis heat shock protein 70 (HSP70) on the potency of antigen-specific immunity generated by naked DNA vaccines. We found that vaccines containing E7-HSP70 fusion genes increased the frequency of E7-specific CD8+ T cells by at least 30-fold relative to vaccines containing the wild-type E7 gene. More importantly, this fusion converted a less effective vaccine into one with significant potency against established E7-expressing tumors. Surprisingly, E7-HSP70 fusion vaccines exclusively targeted CD8+ T cells; immunological and antitumor effects were completely CD4-independent. These results indicate that fusion of HSP70 to an antigen gene may greatly enhance the potency of DNA vaccines via CD8-dependent pathways.
Assessment of donor limb hemodynamics in femorofemoral bypass for claudication. (1981)

During a 5-year period (1975 to 1980), 44 patients underwent femorofemoral bypass for unilateral disabling claudication caused by iliac atheroocclusive disease. All patients had complete Doppler arterial examination performed pre- and postoperatively, including segmental thigh and ankle pressure and calculation of an ankle/brachial (A/B) index for each limb. In 37 patients, standard treadmill exercise testing was performed before and after femorofemoral grafting. Hemodynamic improvement in the symptomatic limb was evidenced by an increase in resting A/B index from a mean of 0.54 +/- 0.14 before to 0.76 +/- 0.22 after operation (P less than 0.001). Exercise tests which were abnormal in all 37 recipient limbs preoperatively were improved. Six of the seven unimproved recipient limbs had associated femoropopliteal occlusion. Donor limb mean resting ankle/brachial index fell from 0.93 +/- 0.22 before to 0.83 +/- 0.22 after surgery (P less than 0.05). However, in 13 of 23 donor limbs, exercise response which had been normal before surgery became abnormal. Additionally, in 14 patients with abnormal donor limb exercise response before grafting, seven limbs had a significantly worsening of the exercise response postoperatively. These findings were not related to the patency of the superficial femoral artery in the donor limb. Deterioration in donor limb hemodynamics noted in 20 (45%) of the 44 patients in this series suggests that strict patient selection criteria should be maintained. Unlike in healthy subjects, an arteriographically patent atherosclerosis iliac artery may not support flow requirements of bilateral lower limb exercise.