gebhart/patrepeval huggingface dataset:
Cryopreservation of human embryos and oocytes (1995)

Human embryo cryopreservation is now a fully established adjunct to assisted reproduction, with thawed embryos implanting at a rate approaching that of fresh embryos. As with fresh embryos, the quality of frozen-thawed embryos is affected by patient age at the time of oocyte retrieval, and by culture conditions. Ovarian stimulation incorporating gonadotropin-releasing hormone analogs does not appear to be detrimental to cryopreservation success, and natural or artificial thaw cycles seem equally effective. Successful cryopreservation seems feasible for one- to eight-cell embryos and blastocysts using a variety of protocols. Selection criteria for embryos to be frozen can vary, and embryo quality has the most significant impact on post-cryopreservation viability. Unfertilized oocyte cryopreservation is coming closer to routine clinical application.
Biosynthesis and identification of enzymes of the cellulase system of Trichoderma reesei (1977)

The biosynthesis of cellulolytic enzymes by resting cells of T. reesei QM 9414 incubated in 17 mM potassium phosphate buffer, pH 6.0, and Q-β-D-glucopyranosy1-(172)α-D-glucopyranose was investigated. A maximum of 200 mi1liunits aryl-β-D-g1ucosidase, 9000 mi1liunits endo-l,4-β-D-glucanaseand 200 milliunits Avicelase per milliliter of culture supernate was produced after 24 hours of incubation; at that time, extracellular protein production reached a maximum of 0.5 mg/ml. Optimum enzyme yields were obtained with 3-4 mg dry weight cells/ml, and 1 nIDi 0-β-D-glucopyranosyl-(1->2)α-D-glucopyranose. Inclusion of metals, e.g., zinc, cobalt, manganous and ferrous ions enhanced enzyme production when glutamic acid was present, in which case aryl-β-D-glucosidase, endoglucanase and Avicelase activity were enhanced by 20, 100 and 40 percent, respectively. Under the same conditions asparagine enhanced only ary1-β-D-glucosidase activity. Some of the enzymic components of the cellulase system produced by T. reesei under these conditions were purified by ion exchange chromatography on DEAE-Sephadex A-50. Two cellobiohydrolases were isolated in pure form. One of these was identical to the previously isolated ce1lobiohydrolase D on the basis of amino acid composition carbohydrate content, electrophoretic mobility and ultraviolet spectrum. Similar data for the other cellobiohydrolase suggest that it represents an enzyme not previously identified. An endoglucanase was also isolated which, on the basis of its amino acid composition and electrophoretic mobility, appears similar to the previously identified Endoglucanase IV. More precise characterization of these enzymes is currently under investigation.
Site specific protein labeling by enzymatic posttranslational modification (2009)

Site specific protein labeling plays a key role in elucidating the function of the proteins at the molecular level by revealing their locations in the cell, their interaction networks with other cellular components and the dynamic mechanisms of their bio-generation, trafficking and degradation in response to regulatory signals in a biological system. Site specific protein labeling is, in essence, artificial modification of proteins with new chemical entities at the posttranslational stage. Based on the analogy between protein labeling and protein posttranslational modification, enzymatic tools have been developed for site specific and efficient labeling of target proteins with chemical probes of diverse structures and functionalities. This perspective surveys a number of protein labeling methods based on the application of protein posttranslational modification enzymes.
CXXXVI.—The chlorodibromo- and dichlorobromobenzenes (1901)

ACCORDINU t o theory, there should be twelve trisubstituted benzenes containing either one atom of chlorine and two atoms of bromine, or two of chlorine and one of bromine. Six of these are unsymmetrical in structure, two symmetrical, and four vicinal. Of these twelve, the two symmetrical compounds have been obtained by Hantzsch, Schleissing, and Jager (Bey., 1897, 30, 2334) ; the s-chlorodibromobenzene by the transformation of the acid s-tribromobenzenediazonium chloride ; and the s-dichlorobromobenzene by the transformation of the same compound on standing and warming. The s-chlorodibromovor,. LXXIX.
Mechanisms responsible for the failure of protamine  to inactivate low‐molecular‐weight heparin (2002)

Protamine is unable to completely reverse the anticoagulant effect of the low-molecular-weight heparins (LMWH), a fact of clinical importance given the rapid increase in use of LMWH in clinical practice. This investigation sought to determine the mechanism by which LMWH were able to resist protamine-mediated inactivation. Affinity fractionation of LMWH by passage through a protamine column, with subsequent determination of molecular mass and sulphate charge density, demonstrated that the protamine-resistant fraction in LMWH is an ultra-low-molecular-weight fraction with low sulphate charge density. This group of molecules was not found in unfractionated heparin, even when species of similar molecular mass were compared. We then determined that different commercially available LMWH varied in their ability to be neutralized by protamine, and that this variability correlated with the total sulphate content of the LMWH. We conclude that reduced sulphate charge, not molecular mass, is the principle reason that protamine is unable to fully inactivate LMWH. Furthermore, different LMWH vary in their ability to be neutralized by protamine, suggesting that product-specific recommendations for neutralization might be developed.
Effect of Low Power Gallium Arsenide Laser on Healing of Venous Ulcers (1991)

The healing of venous ulcers of the leg with and without gallium arsenide laser treatment was studied in 42 patients randomly divided into two groups. One group received standard conservative treatment and gallium arsenide laser, and the other received the same standard treatment and placebo laser treatment. There were no differences in results between the two groups.
The Relationship of Dietary Lipid Intake and Age-Related Macular Degeneration in a Case-Control Study (2007)

Higher intake of omega-3 LCPUFAs and fish was associated with decreased likelihood of having NV AMD.
Chemistry of dicumyl peroxide‐induced crosslinking of linear polyethylene (1981)

Abstract The course of intermolecular reactions induced by peroxide decomposition in linear polyethylene has been determined and compared with similar reaction systems in which the substrate is a lowmolecular‐weight alkane. Efficiency of intermolecular coupling is 40% for an alkane and 25–30% for the polymer system. Competing reactions, which reduce coupling efficiency, are mainly disproportionation of the initially formed radicals and to a minor extent further reactions involving the products from the peroxide decomposition. The low efficiencies found are similar to those well studied when initial radicals are produced by radiolysis in polymer and alkane systems.
PHOTOBLEACHING OF MONO‐l‐ASPARTYL CHLORIN e6 (NPe6): A CANDIDATE SENSITIZER FOR THE PHOTODYNAMIC THERAPY OF TUMORS (1993)

Most sensitizers used for the photodynamic therapy (PDT) of tumors photobleach on illumination. Thus, it is of interest to examine the photobleaching behavior of new sensitizers proposed for use in PDT. This report surveys the quantum yields and kinetics of the photobleaching of mono-L-aspartyl chlorin e6(NPe6), a hydrophilic chlorin that has many of the photoproperties desirable in a sensitizer for clinical PDT. It is a very effective sensitizer for the PDT of several types of model tumors in animals and is now in Phase I clinical trials. The quantum yield of NPe6 photobleaching in pH 7.4 phosphate buffer in air was 8.2 x 10(-4); this is greater than the yields for typical porphyrin photosensitizers. For example, the yields for hematoporphyrin and uroporphyrin are 4.7 x 10(-5) and 2.8 x 10(-5), respectively. The yield decreased significantly in organic solvents of low dielectric constant. The Sn derivative of NPe6 was more light stable than NPe6 (yield = 5.7 x 10(-6), while the Zn derivative was more sensitive (yield = 1.9 x 10(-2). Oxygen appeared to be necessary for the photobleaching of NPe6; however, bleaching was not inhibited by 100 mM azide, an efficient quencher of singlet oxygen. The photooxidizable substrates cysteine, dithiothreitol and furfuryl alcohol increased the quantum yield of photobleaching two- to four-fold, while the electron acceptor, metronidazole, increased it almost six-fold. Photobleaching yields for several other chlorins were also measured.
Sensitization of human renal cell carcinoma cells to cis-diamminedichloroplatinum(II) by anti-interleukin 6 monoclonal antibody or anti-interleukin 6 receptor monoclonal antibody. (1995)

Cytotoxic chemotherapy has shown little antitumor activity against renal cell carcinoma (RCC). It has been demonstrated that RCC cells secrete interleukin 6 (IL-6) and express IL-6 receptors (IL-6Rs). IL-6 inhibits apoptosis and enhances manganese superoxide dismutase expression. Several anticancer chemotherapeutic agents exert their cytotoxic activity in part through the induction of apoptosis and the production of free radicals. Thus, the resistance of RCC cells to the anticancer agents might correlate with IL-6 expression. The present study tested this hypothesis by examining the effect of anti-IL-6 mAb and anti-IL-6R mAb on the sensitivity of human RCC cells to anticancer chemotherapeutic agents. Treatment of Caki-1 cells with anti-IL-6 mAb or anti-IL-6R mAb in combination with cis-diamminedichloroplatinum(II) (CDDP) or mitomycin C overcame their resistance to CDDP or mitomycin C. However, treatment of Caki-1 cells with anti-IL-6 mAb or anti-IL-6R mAb in combination with Adriamycin, vinblastine or 5-fluorouracil did not overcome their resistance to these anticancer agents. Treatment of CDDP-resistant Caki-1 cells (Caki-1/DDP), two other RCC cell lines (ACHN and A704), and three freshly derived RCC cells with CDDP in combination with anti-IL-6 mAb or anti-IL-6R mAb reversed the resistance to CDDP in all these tumors. We then studied the effectiveness of other platinum derivatives. Treatment of Caki-1 cells with anti-IL-6 mAb or anti-IL-6R mAb enhanced their sensitivity to carboplatin, but not to trans-diamminedichloroplatinum(II). Several experiments investigated the mechanism of the antibody-mediated sensitization of RCC cells to CDDP. Incubation of Caki-1 cells with anti-IL-6 mAb or anti-IL-6R mAb did not change the intracellular accumulation of CDDP. The expressions of the multidrug resistant phenotype (gp170) and c-myc oncogene were not affected by the antibody-mediated sensitization. Treatment of Caki-1 cells with the anti-IL-6 mAb or anti-IL-6R mAb down-regulated the expression of glutathione S-transferase pi mRNA. This study demonstrates that treatment of RCC cells with CDDP in combination with anti-IL-6 mAb or anti-IL-6R mAb can overcome their CDDP-resistance and that the down-regulation of glutathione S-transferase pi expression by anti-IL-6 mAb or anti-IL-6R mAb might play a role in the enhanced cytotoxicity obtained.(ABSTRACT TRUNCATED AT 400 WORDS)
Pulmonary involvement in systemic sclerosis (scleroderma) (1985)

One hundred sixty-five nonsmoking systemic sclerosis patients were evaluated by pulmonary function testing. Restrictive lung disease and an isolated reduction of the diffusing capacity of carbon monoxide were the most frequent abnormalities. Patients with the CREST syndrome (calcinosis, Raynaud's phenomenon, esophageal dysmotility, sclerodactyly, and telangiectasias) had a similar frequency and severity of pulmonary involvement compared with the patients who had diffuse scleroderma. CREST syndrome patients with restrictive lung disease rarely had the anticentromere antibody and had more skin and joint involvement of their hands, compared with other CREST syndrome patients. Dyspnea and rales were most commonly found in patients with restrictive lung disease. Fibrosis, shown on chest radiograph, and pulmonary function abnormalities correlated poorly with each other. Dyspnea was associated with restrictive disease, and rales were more commonly found in patients with fibrosis. Patients with a restrictive abnormality had the worst prognosis, with a 5-year survival rate of 58%, although death from pulmonary causes was uncommon. Comparison of these nonsmoking patients with 137 scleroderma patients who smoked, seen during the same time period, revealed more frequent and severe obstructive changes in smokers. Smoking patients with restrictive lung disease had more severe disease than nonsmoking patients. The single breath diffusing capacity for carbon monoxide was significantly decreased in the patients who smoked compared with the nonsmokers. These data confirm that pulmonary function abnormalities are common in patients with systemic sclerosis including CREST syndrome. Smoking appears to have an additive deleterious effect on pulmonary function and should be strongly discouraged.
Combining target enrichment with barcode multiplexing for high throughput SNP discovery (2010)

Our work describes the successful combination of a targeted enrichment method and index barcode multiplexing to reduce costs, time and labour associated with processing large sample sets. Furthermore, we have shown that the sequencing depth obtained is adequate for credible SNP genotyping analysis at uniplex, duplex and pentaplex levels.
Paper-supported 3D cell culture for tissue-based bioassays (2009)

Fundamental investigations of human biology, and the development of therapeutics, commonly rely on 2D cell-culture systems that do not accurately recapitulate the structure, function, or physiology of living tissues. Systems for 3D cultures exist but do not replicate the spatial distributions of oxygen, metabolites, and signaling molecules found in tissues. Microfabrication can create architecturally complex scaffolds for 3D cell cultures that circumvent some of these limitations; unfortunately, these approaches require instrumentation not commonly available in biology laboratories. Here we report that stacking and destacking layers of paper impregnated with suspensions of cells in extracellular matrix hydrogel makes it possible to control oxygen and nutrient gradients in 3D and to analyze molecular and genetic responses. Stacking assembles the "tissue", whereas destacking disassembles it, and allows its analysis. Breast cancer cells cultured within stacks of layered paper recapitulate behaviors observed both in 3D tumor spheroids in vitro and in tumors in vivo: Proliferating cells in the stacks localize in an outer layer a few hundreds of microns thick, and growth-arrested, apoptotic, and necrotic cells concentrate in the hypoxic core where hypoxia-sensitive genes are overexpressed. Altering gas permeability at the ends of stacks controlled the gradient in the concentration of the O(2) and was sufficient by itself to determine the distribution of viable cells in 3D. Cell cultures in stacked, paper-supported gels offer a uniquely flexible approach to study cell responses to 3D molecular gradients and to mimic tissue- and organ-level functions.
Biosynthesis of Abnormally Glycosylated α-Antitrypsin by a Human Hepatoma Cell Line† (1984)

The human hepatoma cell line PLC/PRF/5 synthesized and secreted a functional alpha 1-antitrypsin (alpha 1-AT) glycoprotein with normal molecular size but retarded electrophoretic mobility. The total process of translation, glycosylation and export required about 40 min and followed the same synthetic pattern as seen in rat hepatocytes, i.e., a signal peptide is cleaved cotranslationally; a core-glycosylated protein in the high-mannose form is formed in the rough endoplasmic reticulum, trimmed, and a stable complex-glycosylated alpha 1-AT is found intracellularly prior to export. alpha 1-AT export to medium was delayed by tunicamycin, inhibited by cycloheximide but unaffected by colchicine. After addition of exogenous alpha 1-AT to culture medium, neither negative nor positive feedback induction of synthesis could be demonstrated. Electrophoretic techniques indicated the presence of atypical, highly branched but incompletely sialylated carbohydrate chains in the hepatoma cell-derived alpha 1-AT. The accumulation of intracellular alpha 1-AT inclusions seen in the endoplasmic reticulum may reflect an imbalance between a high rate of polypeptide synthesis and terminal glycosylation.
Decreased macrophage release of TGF-β and TIMP-1 in chronic obstructive pulmonary disease (2005)

The present study tested the hypothesis that alveolar macrophages (AM) from patients with chronic obstructive pulmonary disease (COPD) release more pro-inflammatory and/or less anti-inflammatory mediators than those from smokers with normal lung function and never-smokers. AM were sorted by flow cytometry from bronchoalveolar lavage fluid in 13 patients with COPD (mean+/-SEM 67+/-2 yrs, forced expiratory volume in one second (FEV1) 61+/-4% reference), 16 smokers with normal lung function (55+/-2 yrs, FEV1 97+/-4% reference) and seven never-smokers (67+/-7 yrs, FEV1 94+/-4% reference). After sorting, AM were cultured (with and without lipopolysaccharide stimulation) after 4 h and 24 h, and the concentrations of leukotriene B4 (LTB4), transforming growth factor (TGF)-beta1 and tissue inhibitor of metalloproteinase (TIMP)-1 were quantified in the supernatant by ELISA. The production of reactive oxygen intermediates (ROI) in freshly isolated AM was determined by flow cytometry. LTB4 secretion and ROI production were not different between groups. In contrast, AM from COPD patients released significantly less TGF-beta1 and TIMP-1 than those from smokers with normal lung function and nonsmokers. In conclusion, these observations are compatible with reduced anti-inflammatory and anti-elastolytic capacity in chronic obstructive pulmonary disease, which is likely to contribute to the pathogenesis of the disease.
A Novel Muconic Acid Biosynthesis Approach by Shunting Tryptophan Biosynthesis via Anthranilate (2013)

Muconic acid is the synthetic precursor of adipic acid, and the latter is an important platform chemical that can be used for the production of nylon-6,6 and polyurethane. Currently, the production of adipic acid relies mainly on chemical processes utilizing petrochemicals, such as benzene, which are generally considered environmentally unfriendly and nonrenewable, as starting materials. Microbial synthesis from renewable carbon sources provides a promising alternative under the circumstance of petroleum depletion and environment deterioration. Here we devised a novel artificial pathway in Escherichia coli for the biosynthesis of muconic acid, in which anthranilate, the first intermediate in the tryptophan biosynthetic branch, was converted to catechol and muconic acid by anthranilate 1,2-dioxygenase (ADO) and catechol 1,2-dioxygenase (CDO), sequentially and respectively. First, screening for efficient ADO and CDO from different microbial species enabled the production of gram-per-liter level muconic acid from supplemented anthranilate in 5 h. To further achieve the biosynthesis of muconic acid from simple carbon sources, anthranilate overproducers were constructed by overexpressing the key enzymes in the shikimate pathway and blocking tryptophan biosynthesis. In addition, we found that introduction of a strengthened glutamine regeneration system by overexpressing glutamine synthase significantly improved anthranilate production. Finally, the engineered E. coli strain carrying the full pathway produced 389.96 ± 12.46 mg/liter muconic acid from simple carbon sources in shake flask experiments, a result which demonstrates scale-up potential for microbial production of muconic acid.
A Conformationally Preorganized Universal Solid Support for Efficient Oligonucleotide Synthesis (2003)

A novel, conformationally preorganized nonnucleosidic universal solid support for oligonucleotide synthesis was developed. The solid support featured two chemically equivalent hydroxy groups locked in syn-periplanar orientation and orthogonally protected with 4,4'-dimethoxytrityl and acetyl groups. The solid support was extensively tested in the preparation of oligonucleotides and their phosphorothioate analogues containing 2'-deoxy, 2'-O-methyl, and 2'-O-methoxyethylnucleoside residues at the 3'-terminus. Upon completion of oligonucleotide chain assembly, the support-bound oligonucleotide material was treated with concentrated ammonium hydroxide, which removed the O-acetyl protection. The deprotected hydroxy group then effected the transesterification of a phosphate linkage between the solid support and the 3'-terminal nucleoside residue to result in a facile release of the oligonucleotide to solution. The kinetics of the release process was studied in a continuous flow of concentrated aqueous ammonium hydroxide at a temperature of 300.15 K. Optimal conditions for the release of oligonucleotides depending on the chemistry of the backbone and 3'-terminal nucleoside residue were formulated.
Subsurface parameter estimation in full wavefield inversion and reverse time migration (2010)

We develop a method for directly estimating subsurface medium parameter updates from the gradient equations in full wavefield inversion. This is achieved by accounting for the effects of source and receiver illuminations, background medium properties, and seismic resolution volume in the gradient equations. Using this method, we directly compute the subsurface seismic parameters needed to minimize the difference between the measured and modeled seismic field. It is shown that this method, when used to precondition the gradients in iterative inversion processes, yields faster convergence than when gradients are used without preconditioning. It is also shown that this method can be used for inversion of amplitudes in reverse time migration into the difference bulk modulus of subsurface.
Dose finding with retroviral vectors: correlation of retroviral vector copy numbers in single cells with gene transfer efficiency in a cell population (2003)

Retroviral vectors are commonly used in clinical gene therapy, but recent observations of insertional oncogene activation in preclinical and clinical settings have forced a discussion of their safety. Here we investigated the relationship between retroviral transduction efficiency in mass cultures and the actual number of integrated vector copies in single cells using K562 leukemia and primary CD34+ cells. We found an exponential increase of integration numbers correlated to gene transfer rates and a linear increase of expression levels with insertion frequency. On average we detected one vector insertion per transduced cell for a gene transfer of less than 30%, 3 for 60%, and approximately 9 for 90% (in K562). Clonal analysis revealed strikingly increased variations of both transgene copy numbers (more than 20-fold in primary cells) and expression levels associated with higher transduction. Therefore, limiting retroviral gene transfer to approximately 30% may be suggested to avoid generating clones containing multiple insertions.
Hydrogels in Regenerative Medicine (2009)

Hydrogels, due to their unique biocompatibility, flexible methods of synthesis, range of constituents, and desirable physical characteristics, have been the material of choice for many applications in regenerative medicine. They can serve as scaffolds that provide structural integrity to tissue constructs, control drug and protein delivery to tissues and cultures, and serve as adhesives or barriers between tissue and material surfaces. In this work, the properties of hydrogels that are important for tissue engineering applications and the inherent material design constraints and challenges are discussed. Recent research involving several different hydrogels polymerized from a variety of synthetic and natural monomers using typical and novel synthetic methods are highlighted. Finally, special attention is given to the microfabrication techniques that are currently resulting in important advances in the field.