gebhart/patrepeval huggingface dataset:
Bis(2-methoxyethyl)aminosulfur Trifluoride:  A New Broad-Spectrum Deoxofluorinating Agent with Enhanced Thermal Stability (1999)

Bis(2-methoxyethyl)aminosulfur trifluoride, (CH3OCH2CH2)2NSF3 (Deoxo-Fluor reagent), is a new deoxofluorinating agent that is much more thermally stable than DAST (C2H5)2NSF3 and its congeners. It is effective for the conversion of alcohols to alkyl fluorides, aldehydes/ketones to the corresponding gem-difluorides, and carboxylic acids to the trifluoromethyl derivatives with, in some cases, superior performance compared to DAST. The enhanced stability is rationalized on the basis of conformational rigidity imposed by a coordination of the alkoxy groups with the electron-deficient sulfur atom of the trifluoride.
Analysis by Cell-Free Transcription of the Liver-Specific Pyruvate Kinase Gene Promoter (1989)

A DNA fragment spanning nucleotides -183 to -4 with respect to the cap site of the rat L-type pyruvate kinase (L-PK) gene contains at least four binding sites for putative transcriptional factors: hepatocyte nuclear factor 1 (HNF1), liver factor A1 (LF-A1), nuclear factor 1 (NF1), and major late transcription factor (MLTF). This fragment was used to direct transcription of a reporter sequence (a G-free cassette) in cell extracts. This L-PK promoter was active in liver nuclear extracts, but not in extracts from nonhepatic tissues. A reduction of 50% of the activity was obtained with a deleted L-PK promoter containing only the HNF1-binding site. In contrast, deletion of the HNF1-binding site inactivated the promoter by more than 90%. These results were confirmed by titration experiments with synthetic oligonucleotides. Titration of HNF1 resulted in an 85% decrease of transcriptional activity, while titration of LF-A1 resulted in only a 40% decrease. The influence of NF1 and MLTF seemed to be marginal in this system. The proximal 5'-flanking sequence of the L-PK gene therefore appears to function in vitro as an efficient liver-specific promoter which requires the binding of the liver factor HNF1 and which is also stimulated by the binding of another liver-specific factor, LF-A1.
Detection in Human Serum by Radioimmunoassay of Histidyl-Proline Diketopiperazine, a Metabolite of Thyrotropin-Releasing Hormone (1983)

Cyclo(His-Pro) is believed to be a metabolite of TRH. A specific antiserum directed against cyclo(His-Pro) was used to detect immunoreactive material in human serum. Gel filtration column chromatography was used to establish that cyclo(His-Pro)-like immunoreactivity was found not only in free form established to be identical to cyclo(His-Pro) by high pressure liquid chromatography analysis on reverse phase and cation exchange columns, but also in a fraction of about 100,000 mol wt. Free cyclo(His-Pro) was released by heating column fractions of 70,000 mol wt that were not immunoreactive before heating. A procedure for estimation of the content of free cyclo(His-Pro) in human serum was developed. Normal levels of cyclo(His-Pro) determined by this procedure were in the range of 11-33 pmol/ml. The level of cyclo(His-Pro) in sera of individuals with hypothyroidism, hyperthyroidism, or alcoholic cirrhosis was in the normal range, while patients with renal failure had approximately 3-fold elevated levels of the peptide. Analysis of human sera drawn at 3-h intervals over a 24-h period suggested a circadian rhythm of cyclo(His-Pro) levels.
Thioredoxin and Related Molecules–From Biology to Health and Disease (2006)

Thioredoxin and glutaredoxin systems in mammalian cells utilize thiol and selenol groups to maintain a reducing intracellular redox state acting as antioxidants and reducing agents in redox signaling with oxidizing reactive oxygen species. During the last decade, the functional roles of thioredoxin in particular have continued to expand, also including novel functions such as a secreted growth factor or a chemokine for immune cells. The role of thioredoxin and glutaredoxin in antioxidant defense and the role of thioredoxin in controlling recruitment of inflammatory cells offer potential use in clinical therapy. The fundamental differences between bacterial and mammalian thioredoxin reductases offer new principles for treatment of infections. Clinical drugs already in use target the active site selenol in thioredoxin reductases, inducing cell death in tumor cells. Thioredoxin and binding proteins (ASK1 and TBP2) appear to control apoptosis or metabolic states such as carbohydrate and lipid metabolism related to diseases such as diabetes and atherosclerosis.
Cellular characterization of blastocysts derived from rabbit 4-, 8- and 16-cell embryos and isolated blastomeres cultured in vitro (2000)

The purpose of this study was to investigate the developmental potential of isolated rabbit blastomeres under various culture conditions to gain insight into their ability to form the two cell lineages of a viable blastocyst. Intact embryos at the 4-cell, 8-cell, 16-cell stages and blastomeres isolated from 4-, 8- and 16-cell rabbit embryos (1/4, 1/8 or 1/16 blastomeres respectively) were cultured in drops of one of three different media, each supplemented with either fetal calf serum (FCS), bovine serum albumin (BSA) or polyvinyl alcohol (PVA). The effects of the extracellular matrix fibronectin (FN) on the development of isolated rabbit blastomeres were also investigated. Supplementation of the medium with FCS yielded a higher (P < 0.05) proportion of blastocysts than BSA or PVA, predominantly from 1/4 blastomeres. No major differences were found between the three basic culture media. In 1/4, 1/8 or 1/16 blastomeres, blastocyst formation rates were greater (P < 0.05) in groups cultured in matrix-free (54.5, 59.6 and 54.6% respectively) than in FN-coated groups (35.4, 46.0 and 26.1% respectively). Only in blastocysts derived from 1/4 blastomeres, were the numbers of inner cell mass (ICM) and total cells of blastocysts higher (P < 0.05) in FN-coated groups than in matrix-free groups (12.7 +/- 1.1 versus 8.5 +/- 0.7 ICM, 73.8 +/- 3. 7 versus 57.8 +/- 3.3 total cells). The percentage of blastocysts derived from single blastomeres with ICM cells decreased with increasing cell stage of the parent embryos in FN-coated (93.6, 78.3 and 44.0%, respectively) as well as matrix-free groups (96.2, 69.3 and 55.2%). In FN-coated groups, after 96 h (1/4) or 72 h (1/8 and 1/16) of culture, approximately 20-30% of blastomeres did not develop into normal blastocysts but formed sheets with 30-50 cells attached to the bottom of the dishes. These results indicate that the development of rabbit blastomeres shares important characteristics with those from mouse and domestic species and may thus aid in developing an efficient culture system for blastomeres, derived from human embryos.
The oligosaccharides of the glycoprotein pheromone of Volvox carteri f. nagariensis Iyengar (Chlorophyceae) (1990)

The sexuality-inducing glycoprotein of Volvox carteri f. nagariensis was purified from supernatants of disintegrated sperm packets of the male strain IPS-22 and separated by reverse-phase HPLC into several isoforms which differ in the degree of O-glycosylation. Total chemical deglycosylation with trifluoromethanesulphonic acid yields the biologically inactive core protein of 22.5 kDa. This core protein possesses three putative binding sites for N-glycans which are clustered in the middle of the polypeptide chain. The N-glycosidically bound oligosaccharides were obtained by glycopeptidase F digestion and were shown by a combination of exoglycosidase digestion, gaschromatographic sugar analysis and two-dimensional HPLC separation to possess the following definite structures: (A) Man beta 1-4GlcNAc beta 1-4GlcNAc; (B) (Man alpha)3 Man beta 1-4GlcNAc beta 1-4GlcNAc Xyl beta; (C) (Man alpha)2 Man beta 1-4GlcNAc beta 1-4GlcNAc; (D) (Man)2Xyl(GlcNAc)2. Xyl beta Two of the three N-glycosidic binding sites carry one B and one D glycan. The A and C glycans are shared by the third N-glycosylation site. The O-glycosidic sugars, which make up 50% of the total carbohydrate, are short (up to three sugar residues) chains composed of Ara, Gal and Xyl and are exclusively bound to Thr residues.
Orthopaedic knowledge update : Sports medicine 2 (1999)

This revised work offers the reader a selection of information designed to be of use to orthopaedic surgeons and physicians who treat sports medicine problems in patients ranging from infancy to old age. Topics covered include: outcomes research; training and conditioning; rehabilitation; exercise and health; sports nutrition guidelines; shoulder; elbow; hand and wrist; overuse injuries; injuries to the pelvis, hip, thigh, and abdomen; knee; foot and ankle; cervical spine; and lumbar spine.
meta-MEME: Motif-based hidden Markov models of protein families (1997)

This work attempts to solve that problem by generating smaller HMMs which precisely model only the conserved regions of the family. These HMMs are constructed from motif models generated by the EM algorithm using the MEME software. Because motif-based HMMs have relatively few parameters, they can be trained using smaller data sets. Studies of short chain alcohol dehydrogenases and 4Fe-4S ferredoxins support the claim that motif-based HMMs exhibit increased sensitivity and selectivity in database searches, especially when training sets contain few sequences.
Comparison of the effects of IL-3, granulocyte-macrophage colony-stimulating factor, and macrophage colony-stimulating factor in supporting monocyte differentiation in culture. Analysis of macrophage antibody-dependent cellular cytotoxicity. (1990)

Cultured human monocytes undergo a process of differentiation and maturation lasting 5 to 10 days that ultimately leads to the appearance of large macrophage-like cells. This differentiation is growth factor dependent: of all the cytokines tested, only macrophage colony-stimulating factor (M-CSF), granulocyte/macrophage-CSF (GM-CSF), and IL-3 proved capable of supporting the differentiation and the long term survival of the macrophage-like cells. Although all three cytokines yield cells with macrophage characteristics, cells developed in M-CSF have features distinct from those matured in either IL-3 or GM-CSF. At the morphologic level, the M-CSF-supported monocyte cultures yield elongated, spindle-shaped cells whereas those supported with IL-3 or GM-CSF yielded round cells with distinct nuclei. All three macrophage populations expressed similar levels of HLA-DR, CD11b, and CD11c, but the M-CSF-treated cultures yielded more CD14+ and CD16+ (Fc gamma RIII) cells. All three cell populations developed capacity for antibody-dependent cellular cytotoxicity (ADCC) as well as antibody-independent cytotoxicity with peak activity achieved after 8 to 12 days in culture. ADCC capacity developed earliest and the level of activity was usually greatest in the M-CSF-treated cultures, possibly correlating with the higher level of expression of CD16. Our findings indicate that any of these cytokines, but particularly M-CSF, may be useful clinically in enhancing the tumoricidal capacity of tumor-specific mAb through augmentation of macrophage capacity for ADCC.
Monoclonal antibody against human sperm acrosome inhibits sperm penetration of zona‐free hamster eggs (1987)

Human spermatozoa were exposed to a monoclonal antibody (C11H), which recognizes sperm acrosin. The antibody was presented to the sperm during capacitation and/or insemination, and its effect on penetration was tested using zona-free hamster eggs. An inhibitory effect on penetration was observed when the antibody was present during insemination but not when it was included only in the capacitation medium. As judged by immunofluorescence microscopy, most of the sperm bound to the egg surface were devoid of acrosomal staining. Some of the bound sperm were stained at their equatorial segments. Sperm that had penetrated the ooplasm did not exhibit immunofluorescence.
Molecular Cloning and Characterization of a Novel p38 Mitogen-activated Protein Kinase (1997)

The p38 mitogen-activated protein kinases (MAPK) are activated by cellular stresses and play an important role in regulating gene expression. We have isolated a cDNA encoding a novel protein kinase that has significant homology (57% amino acid identity) to human p38alpha/CSBP. The novel kinase, p38delta, has a nucleotide sequence encoding a protein of 365 amino acids with a putative TGY dual phosphorylation motif. Dot-blot analysis of p38delta mRNA in 50 human tissues revealed a distribution profile of p38delta that differs from p38alpha. p38delta is highly expressed in salivary gland, pituitary gland, and adrenal gland, whereas p38alpha is highly expressed in placenta, cerebellum, bone marrow, thyroid gland, peripheral leukocytes, liver, and spleen. Like p38alpha, p38delta is activated by cellular stress and proinflammatory cytokines. p38delta phosphorylates ATF-2 and PHAS-I, but not MAPK-activated protein kinase-2 and -3, known in vivo and in vitro substrates of p38alpha. We also observed that p38delta was strongly activated by MKK3 and MKK6, while p38alpha was preferentially activated by MKK6. Other experiments showed that a potent p38alpha kinase inhibitor AMG 2372 minimally inhibited the kinase activity of p38delta. Taken together, these data indicate that p38delta is a new member of the p38 MAPK family and that p38delta likely has functions distinct from that of p38alpha.
A weighting strategy for Active Shape Models (2017)

Active Shape Models (ASM) are an iterative segmentation technique to find a landmark-based contour of an object. In each iteration, a least-squares fit of a plausible shape to some detected target landmarks is determined. Finding these targets is a critical step: some landmarks are more reliably detected than others, and some landmarks may not be within the field of view of their detectors. To add robustness while preserving simplicity at the same time, a generalized least-squares approach can be used, where a weighting matrix incorporates reliability information about the landmarks. We propose a strategy to choose this matrix, based on the covariance of empirically determined residuals of the fit. We perform a further step to determine whether the target landmarks are within the range of their detectors. We evaluate our strategy on fluoroscopic X-ray images to segment the femur. We show that our technique outperforms the standard ASM as well as other more heuristic weighted least-squares strategies.
Hybrid Organic–Inorganic Inhibitors of a PDZ Interaction that Regulates the Endocytic Fate of CFTR (2012)

Together strong: Cooperative binding of organic (see picture, red) and inorganic fragments provides a strategy for the potent inhibition of protein-protein interactions. By targeting specific Lewis basic side chains in peripheral regions of the binding site for coordination to a rhodium(II) center, the affinity of otherwise weak ligands is improved.
A Phase 2 Controlled Study of SB206, a Topical Nitric Oxide-Releasing Drug for Extragenital Wart Treatment. (2018)

Berdazimer sodium (SB206) plus hydrogel was efficacious and well tolerated in the treatment of EGW/PAW. J Drugs Dermatol. 2018;17(10):1100-1105.
Expression of green fluorescent protein in insect larvae and its application for heterologous protein production (1997)

Many eukaryotic proteins have been successfully expressed in insect cells infected with a recombinant baculovirus derived from the Autographa californica nuclear polyhedrosis virus (AcNPV). There are, however, disadvantages with this cell-based system when carried out in suspension cultures at high bioreactor volume (e.g., limited oxygen transfer, susceptibility to contamination, high cost). These problems can be avoided by using whole larvae as the "reactors." There are, however, other problems encountered with larvae, one being their inaccessibility for product sampling. To combat this problem, we have investigated the expression of green fluorescent protein (GFP) as a reporter molecule in Trichoplusia ni insect larvae. A high production level of GFPuv (1.58 mg per larva, 26% of total protein) was obtained, enabling the rapid and non-invasive monitoring of GFP. Bright green light was emitted directly from the large opaque carcasses ( approximately 30mm) after illumination with UV light. Based on the green light intensity and a correlation between intensity and GFP mass, we determined the optimal harvest time (c.a. approximately 3 days post-infection). In parallel experiments, we expressed human interleukin-2 (IL-2) from another recombinant baculovirus with an almost identical expression profile. Since both GFP and IL-2 were rapidly degraded by protease activity during the fourth day post-infection (another disadvantage with larvae), we found an accurate determination of harvest time was critical. Correspondingly, our results demonstrated that GFP was an effective on-line marker for expression of heterologous protein in insect larvae.
Characterization of Casein Micelle Precipitation by Chitosans (2001)

We have found that the addition of chitosan, a cationic polymer, on whole or skim milk produces destabilization and coagulation of casein micelles that takes place without changes in the milk pH or the stability of most whey proteins. The amount of lipids recovered in the chitosan-casein aggregates was similar or higher than that obtained with rennet or acid precipitation. Approximately 70% of milk Ca2+ (approximately 750 mg/L) was found in the chitosan-induced aggregates, which is 10 and 50% higher than the amounts observed with acid or rennet coagulations, respectively. Purified alpha, beta-, and kappa-caseins were extensively precipitated by different molecular weight chitosans at pH 6.8. The phosphate groups of caseins seem not to be relevant in this interaction because dephosphorylated alpha- and beta-caseins were equally precipitated with chitosans. Analysis by optical microscopy of the chitosan-casein complex reveals that the size of the aggregates increase as the molecular weight of chitosans increase. Hydrophobic and electrostatic interactions particpate in the association and coagulation of casein micelles with chitosans of different molecular weights. The phenomenon is observed over a broad range of temperature (4 to 70 degrees C) with a reduction in the concentration of chitosan needed to precipitate the caseins that parallels a reduction in the viscosity of the chitosan solutions. Taken together, the results indicate that the electrostatic interactions may contribute energetically to the association between the two biopolymers, but the hydrophobicity of the complex would be the key determinant in the overall energetics of the reaction.
Carbon dioxide reduction by the Bosch process (1975)

Prototype units for carrying out the reduction of carbon dioxide to elementary carbon have been built and operated successfully. In some cases, however, startup difficulties have been reported. Moreover, the recycle reactor product has been reported to contain only small amounts of water and undesirably high yields of methane. This paper presents the results of the first phase of an experimental study that was carried out to define the mechanisms occurring in the reduction process. Conclusions are drawn and possible modifications to the present recycle process are suggested.
Evaluation and Rapid Scale-Up of the Synthesis of the Pyrrolopyrimidines U-101033E and U-104067F (1997)

Large quantities of pure bulk drug were required to initiate development for possible indications as antiasthma and neuroprotective agents. Safety concerns and reproducibility problems encountered with the laboratory procedures (Bundy, G. L.; et al. J. Med. Chem. 1995, 38, 4161) forced the development of a reliable large-scale process which within six months produced >100 kg of U-104067 free base in a single campaign. During the course of this work, procedures were also developed which allowed for the bulk preparation of analytically pure, pharmaceutically acceptable salt forms of both of the title compounds.
Hydrogen Lyman-alpha and Lyman-beta emissions from high-pressure microhollow cathode discharges in Ne-H2mixtures (1999)

We observed intense emission of the atomic hydrogen Lyman- (121.6 nm) and Lyman- (102.5 nm) lines from microhollow cathode discharges in high-pressure Ne (740 Torr) with a small admixture of H2 (up to 3 Torr). The atomic emission lines are spectrally clean with essentially no background of molecular emissions from the H2 Lyman and Werner bands. We attribute these atomic emissions to near-resonant energy transfer processes in the high-pressure discharge. In one case, near-resonant energy transfer between the Ne2* excimer and H2 leads to the formation of H(n = 2) atoms, a process similar to what was observed recently by Wieser et al (1998 J. Phys. B: At. Mol. Opt. Phys. 31 4589) in a high-pressure Ne/H2 mixture excited by energetic ion and electron impact. In the other case, near-resonant energy transfer between excited N* atoms (or vibrationally excited neon excimer molecules) and H2 leads to the formation of H(n = 3) atoms. The ratio of Lyman- to Lyman- emission intensity depends on the operating parameters of the discharge (gas pressure, gas mixture, discharge current) which supports the notion that different processes are involved in the formation of the H(n = 2) and H(n = 3) atoms, respectively.
Electro-Optic Characteristics of Single Gap Transflective Display Using In-Plane Switching Mode (2005)

ABSTRACT We have designed a single gap transflective liquid crystal display (LCD) using an in-plane switching mode, where the rotating angle of the LC director between electrodes, and above electrodes, is 45° and 22.5° in average, respectively. Optimization of the cell structures such as electrode structure, cell structure, physical properties of the LC and the LC cell retardation value have been perform to obtain a low-power transflective LCD with a single gap structure and a single driving circuit.
Treatment of Maternal Blood Samples with Formaldehyde Does Not Alter the Proportion of Circulatory Fetal Nucleic Acids (DNA and mRNA) in Maternal Plasma (2005)

Cell-free fetal DNA and fetal mRNA can be found in maternal plasma and used for noninvasive prenatal diagnosis and, potentially, for monitoring and prognosis of certain pregnancy-related clinical conditions (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). The excess of maternal DNA in these samples, however, complicates the detection of fetal genetic traits that are similar to those in the maternal genome (e.g., point mutations) (1)(13)(14). In normal pregnancies, fetal DNA represents only ∼3–6% of the total DNA in maternal plasma (15). Thus, technical challenges lie in either developing methods permitting the reliable differentiation of fetal genetic loci or in reducing the amount of circulatory maternal DNA.

Dhallan et al. (16) have recently reported that the addition of formaldehyde to maternal blood samples increases the proportion of cell-free fetal DNA in maternal plasma by decreasing the concentration of maternal DNA. This effect was proposed to reflect an ability of formaldehyde to stabilize the maternal blood cells, thereby preventing the release of DNA from these cells should they die during sample collection and processing.

We have sought to verify this report and have investigated whether the addition of formaldehyde to maternal blood samples does indeed significantly alter the proportion of fetal DNA in maternal plasma samples. We also examined whether such treatment would improve the yield of fetal RNA. The rationale for this additional analysis was provided by the recent observation that circulating fetal hematopoietic cells may contribute to the pool of mRNA molecules in plasma (17) and the view that formaldehyde treatment may inhibit the activity of any ribonucleases in the sample.

We also examined whether the effect mediated by formaldehyde described by Dhallan et al. (16) was specific for the …