gebhart/patrepeval huggingface dataset:
Functional significance of cumulus expansion in the mouse: Roles for the preovulatory synthesis of hyaluronic acid within the cumulus mass (1993)

Gonadotropin-stimulated expansion of the mouse cumulus oocyte complex (COC) in vitro, measured with a quantitative videographic method, is comparable to that observed to occur in vivo when medium is supplemented with porcine follicle stimulating hormone (pFSH), 10% fetal bovine serum (FBS), and 2.5 mM glucosamine or optimal concentrations of glutamine and glucose. In the absence of glucosamine, the volumetric expansion of COCs in vitro is never more than 25% of that occurring in its presence. The addition of 6-diazo-5-oxo-1-norleucine (DON), an inhibitor of glucosamine synthesis to medium supplemented with glutamine and glucose, completely inhibits cumulus expansion in vitro. This system was utilized to examine the relationship between cumulus expansion and fertilization rates, and the maintenance of fertilizability in culture. Successful fertilization (as determined by development to the 2-cell stage) was correlated with the quantity and quality of the expanded cumulus mass, and conversely, the spontaneous loss or mechanical removal of the cumulus was correlated with a loss of fertilizability following additional incubation in culture medium. In addition, the i.p. injection of DON inhibited cumulus expansion within the intact follicle and suppressed ovulation.
High Throughput Screening for Compounds That Alter Muscle Cell Glycosylation Identifies New Role for N-Glycans in Regulating Sarcolemmal Protein Abundance and Laminin Binding (2012)

Duchenne muscular dystrophy is an X-linked disorder characterized by loss of dystrophin, a cytoskeletal protein that connects the actin cytoskeleton in skeletal muscle cells to extracellular matrix. Dystrophin binds to the cytoplasmic domain of the transmembrane glycoprotein β-dystroglycan (β-DG), which associates with cell surface α-dystroglycan (α-DG) that binds laminin in the extracellular matrix. β-DG can also associate with utrophin, and this differential association correlates with specific glycosylation changes on α-DG. Genetic modification of α-DG glycosylation can promote utrophin binding and rescue dystrophic phenotypes in mouse dystrophy models. We used high throughput screening with the plant lectin Wisteria floribunda agglutinin (WFA) to identify compounds that altered muscle cell surface glycosylation, with the goal of finding compounds that increase abundance of α-DG and associated sarcolemmal glycoproteins, increase utrophin usage, and increase laminin binding. We identified one compound, lobeline, from the Prestwick library of Food and Drug Administration-approved compounds that fulfilled these criteria, increasing WFA binding to C2C12 cells and to primary muscle cells from wild type and mdx mice. WFA binding and enhancement by lobeline required complex N-glycans but not O-mannose glycans that bind laminin. However, inhibiting complex N-glycan processing reduced laminin binding to muscle cell glycoproteins, although O-mannosylation was intact. Glycan analysis demonstrated a general increase in N-glycans on lobeline-treated cells rather than specific alterations in cell surface glycosylation, consistent with increased abundance of multiple sarcolemmal glycoproteins. This demonstrates the feasibility of high throughput screening with plant lectins to identify compounds that alter muscle cell glycosylation and identifies a novel role for N-glycans in regulating muscle cell function.
Secure distributed genome analysis for GWAS and sequence comparison computation (2015)

This work describes our techniques, findings, and experimental results developed and obtained as part of iDASH 2015 research competition to secure real-life genomic computations and shows feasibility of securely computing with genomic data in practice.
Glycopeptides and related compounds : synthesis, analysis, and applications (1997)

Glycopeptides and glycoproteins - their past, present, and future recent advances in the synthesis of glycopeptides enzymatic synthesis of oligosaccharides and glycopeptides chemical synthesis of glycoprotein glycans synthesis of oligosaccharides and glycopeptides on insoluble and soluble supports chemical synthesis of the peptide moiety of glycopeptides synthesis of glycosylphosphatidylinositol anchors analysis of GPI protein anchors and related glycolipids synthesis of intermediates in the dolichol pathway of protein glycosylation synthesis of inhibitors of the glycosidases and glycosyltransferases involved in the biosynthesis and degradation of glycoproteins use of permethylation with GC-MS for linkage and sequence analysis of oligosaccharides historical perspectives and recent developments structural determination of protein-bound oligosaccharides by mass spectrometry approaches to the structural determination of oligosaccharides and glycopeptides by NMR conformational studies of glycoprotein glycans using NMR and molecule dynamics glycopeptides in the immunotherapy of cancer.
Association between ankyrin and the cytoplasmic domain of band 3 isolated from the human erythrocyte membrane. (1980)

A 43,000-dalton proteolytic fragment of the cytoplasmic domain of band 3 was purified, and monospecific antibodies against this fragment were prepared.1z61-Labeled 43,000-dalton fragment associated with pure ankyrin in solution, with a KO of 8 X lo"' M and with a stoichiometry of 0.85 mol of fragment/mol of ankyrin (with limiting concentrations of ankyrin).Anti-43,000dalton fragment IgG, which cross-reacted only with band 3, immunoprecipitated ankyrin, and band 4.2, as well as band 3 from detergent extracts of membranes, provided these were not denatured.1261-Labeled ankyrin associated selectively with the cytoplasmic surface of inside-out vesicles depleted of ankyrin as well as spectrin, actin, and bands 4.1,4.2,and 6.The binding of '2sI-labeled ankyrin was decreased over 90% by preincubating this protein above 54"C, or by preincubating the vesicles in 3 M guanidine.Scatchard plots of binding were biphasic, with high affinity (KO = 5 x M) and low affinity (KO = 1.4 X 10" M) components, and extrapolated to 65 to 75 p g of ankyrin/mg of ghost protein, or about 10' sites/erythrocyte.Selective proteolytic cleavage of vesicles and release of the cytoplasmic domain of band 3 abolished the high affinity binding of 12%labeled ankyrin, and decreased the number of low affinity sites by about 50%.Anti-43,OOO-dalton fragment IgG at 12 pg/ml inhibited over 90% of binding of low concentrations of '261-labeled ankyrin, and decreased binding by 60% at high concentrations of ankyri n.The 43,000-dalton fragment blocked binding of '2611-labeled ankyrin to vesicles by a competitive type of inhibition with a ki of 6.6 X 10" M.It is concluded that ankyrin and the cytoplasmic domain of band 3 associate directly without requirement for intermediary proteins, and that the cytoplasmic domain of band 3 participates, perhaps with other protein@), in attachment of ankyrin to the inner surface of the membrane.Human erythrocyte ankyrin (band 2.1') is a polypeptide of M, = 215,000 localized on the cytoplasmic surface of the membrane which has been identified as the high affinity membrane attachment site for spectrin (Bennett and Stenbuck, 1979a; Luna et al., 1979 Yu andGoodman, 1979).Association of spectrin with ankyrin has been demonstrated
Molecular Mechanisms of Holoprosencephaly (1999)

Holoprosencephaly (HPE) is the most common developmental defect of the forebrain in humans. Several distinct human genes for holoprosencephaly have now been identified. They include Sonic hedgehog (SHH), ZIC2, and SIX3. Many additional genes involved in forebrain development are rapidly being cloned and characterized in model vertebrate organisms. These include Patched (Ptc), Smoothened (Smo), cubitus interuptus (ci)/Gli, wingless (wg/Wnt, decapentaplegic (dpp)/BMP, Hedgehog interacting protein (Hip), nodal, Smads, One-eyed pinhead (Oep), and TG-Interacting Factor (TGIF). However, further analysis is needed before their roles in HPE can be established. Here we present an overview of the presently known genes causing human holoprosencephaly and describe candidate genes involved in forebrain development identified in other systems. A model is discussed for how these genes may interact within and between several different signaling pathways to direct the formation of the forebrain.
The use of Internet-based technologies-beyond e-mail and search engines (1998)

With the continuing explosive growth of the world wide web and the Internet, there are many opportunities to use these technologies to enhance our ability to function in an engineering and a management capacity. Most of the emphasis relates to the world wide web and developing websites based on the latest and greatest programming languages and tools. There is also a great interest in information processing, centered around using search engines and push technologies. Although e-mail has been part of the Internet experience since the very early days, it has evolved into an effective communications tool. However, there are still opportunities to use the Internet to become more effective in communication, project management, general management, and content-specific information exchange. There are companies that provide services to the on-line community that allow for the interaction of two or more people in real-time in a number of fashions. Some of the possible actions include: on-line and off-line messaging, multi-user chatting, real-time file and URL transfer, notification of other users currently on-line, Internet phone facilitation, and message history logging. Some of these services are free to the user, while others charge for the technology. The discussion of one program's capabilities generates ideas for how the technology can make engineers and managers more effective.
Timing-driven Steiner trees are (practically) free (2006)

Traditionally, rectilinear Steiner minimum trees (RSMT) are widely used for routing estimation in design optimizations like floorplanning and physical synthesis. Since it optimizes wirelength, an RSMT may take a "non-direct" route to a sink, which may give the designer an unnecessarily pessimistic view of the delay to the sink.Previous works have addressed this issue through performance-driven constructions, minimum Steiner arborescence, and critical sink based Steiner constructions. Physical synthesis and routing flows have been reticent to adapt universal timing-driven Steiner constructions out of fear that they are too expensive (in terms of routing resource and capacitance). This paper studies several different performance-driven Steiner tree constructions in order to show which ones have superior performance.A key result is that they add at most 2%-4% extra capacitance, and are thus a promising avenue for today's increasingly aggressive performance-driven P&R flows.We demonstrate using a production P&R flow that timing-driven Steiner topologies can be easily embedded into an incremental routing subflow to obtain significantly improved timing (3.6% and 5.1% improvements in cycle time for two industry testcases) at practically no cost of wirelength or routability.
Pituitary and gonadal function during the use of progesterone- or progesterone-estradiol-releasing vaginal rings. (1980)

Six women used polysiloxane vaginal rings impregnated with progesterone, or progesterone and estradiol. Nineteen 3-week treatment cycles were studied. Subjects kept records of bleeding. Plasma progesterone, estradiol, and gonadotropins were measured by radioimmunoassay. The patient acceptance was poor. None of the subjects experienced regular withdrawal bleedings during the treatment-free week. Fifty-three percent of the cycles were ovulatory as judged by plasma progesterone, but the plasma concentration of progesterone was low during the luteal phase. However, no pregnancies were discovered during the study period. Several high estradiol peaks were present during the treatment. Plasma LH fluctuated in the range of the normal menstrual cycle. Some suppression of plasma FSH was observed. The combination of estradiol and progesterone in the rings caused stronger suppression of FSH, but no diminution in the rate of ovulations or in disturbances of bleeding were observed in comparison to rings impregnated only with progesterone. Rings released the same amounts of progesterone in vitro and produced plasma concentrations which varied between 0.4 and 1.9 ng/ml.
High-Performance Stable Field Emission with Ultralow Turn on Voltage from rGO Conformal Coated TiO2 Nanotubes 3D Arrays (2015)

A facile method to produce conformal coated reduced graphene oxide (rGO) on vertically aligned titanium oxide (TiO2) nanotubes three dimensional (3D) arrays (NTAs) is demonstrated for enhanced field emission display applications. These engineered nano arrays exhibit efficient electron field emission properties such as high field emission current density (80 mA/cm(2)), low turn-on field (1.0 V/μm) and field enhancement factor (6000) with high emission current stability. Moreover, these enhancements observed in nano arrays attribute to the contribution of low work function with non-rectifying barriers, which allow an easy injection of electrons from the conduction band of TiO2 into the Fermi level of reduced graphene oxide under external electric field. The obtained results are extremely advantageous for its potential application in field emission devices.
The Erythroid Phenotype of EKLF-Null Mice: Defects in Hemoglobin Metabolism and Membrane Stability (2005)

Development of red blood cells requires the correct regulation of cellular processes including changes in cell morphology, globin expression and heme synthesis. Transcription factors such as erythroid Kruppel-like factor EKLF (Klf1) play a critical role in erythropoiesis. Mice lacking EKLF die around embryonic day 14 because of defective definitive erythropoiesis, partly caused by a deficit in beta-globin expression. To identify additional target genes, we analyzed the phenotype and gene expression profiles of wild-type and EKLF null primary erythroid progenitors that were differentiated synchronously in vitro. We show that EKLF is dispensable for expansion of erythroid progenitors, but required for the last steps of erythroid differentiation. We identify EKLF-dependent genes involved in hemoglobin metabolism and membrane stability. Strikingly, expression of these genes is also EKLF-dependent in primitive, yolk sac-derived, blood cells. Consistent with lack of upregulation of these genes we find previously undetected morphological abnormalities in EKLF-null primitive cells. Our data provide an explanation for the hitherto unexplained severity of the EKLF null phenotype in erythropoiesis.
Die Chemie der α‐Carbonyl‐Azoverbindungen (1966)

Abstract α‐Carbonyl‐Azoverbindungen wie Azodicarbonsäurediester, Diacyl‐Azoverbindungen und Aryl‐azo‐carbonsäureester sind recht reaktionsfreudige Verbindungen. Sie addieren sich z. B. an Amine, Aromaten, Olefine, CH‐acide Substanzen, Grignard‐ und Diazo‐Verbindungen, Aldehyde, Ketone und Ketene. Dabei sind u. a. Triazane, Hydrazone, Oxadiazolin‐, Azomethin‐imin‐ und Diazetidin‐Derivate zugänglich. α,α'‐Dicarbonyl‐Azoverbindungen gehören zu den besten Dienophilen.
Ionic Liquid Coatings for Titanium Surfaces: Effect of IL Structure on Coating Profile (2015)

Dicationic imidazolium-based ionic liquids (ILs) having bis(trifluoromethylsulfonyl)imide (NTf2) and amino acid-based (methionine and phenylalanine) anionic moieties were synthesized and used to coat titanium surfaces using a dip-coating technique. Dicationic moieties with varying alkyl chains (8 and 10 carbons) and anions with distinct characteristics were selected to understand the influence of IL structural features on deposition profile. X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used in this study to help elucidate intermolecular interactions within ILs as well as between ILs and TiO2 surfaces and to investigate IL coating morphology. Charge concentration on IL moieties, as well as the presence of functional groups that can interact via hydrogen bond, such as carboxylate and amino groups, were observed to influence the deposition profile. ILs containing amino acids as the anionic moiety were observed to interact strongly with TiO2, which resulted in more pronounced changes in Ti 2p binding energy. The higher hydrophobicity of the IL having NTf2 as the anionic moiety resulted in higher adhesion strength between the IL coating and TiO2.
Pharmacological targeting of the PDGF-CC signaling pathway for blood–brain barrier restoration in neurological disorders (2016)

Neurological disorders account for a majority of non-malignant disability in humans and are often associated with dysfunction of the blood-brain barrier (BBB). Recent evidence shows that despite apparent variation in the origin of neural damage, the central nervous system has a common injury response mechanism involving platelet-derived growth factor (PDGF)-CC activation in the neurovascular unit and subsequent dysfunction of BBB integrity. Inhibition of PDGF-CC signaling with imatinib in mice has been shown to prevent BBB dysfunction and have neuroprotective effects in acute damage conditions, including traumatic brain injury, seizures or stroke, as well as in neurodegenerative diseases that develop over time, including multiple sclerosis and amyotrophic lateral sclerosis. Stroke and traumatic injuries are major risk factors for age-associated neurodegenerative disorders and we speculate that restoring BBB properties through PDGF-CC inhibition might provide a common therapeutic opportunity for treatment of both acute and progressive neuropathology in humans. In this review we will summarize what is known about the role of PDGF-CC in neurovascular signaling events and the variety of seemingly different neuropathologies it is involved in. We will also discuss the pharmacological means of therapeutic interventions for anti-PDGF-CC therapy and ongoing clinical trials. In summary: inhibition of PDGF-CC signaling can be protective for immediate injury and decrease the long-term neurodegenerative consequences.
Sequence of human haptoglobin cDNA: evidence that the α and β subunits are coded by the same mRNA (1983)

We have isolated and sequenced a cDNA clone coding for human haptoglobin. Our sequence shows that haptoglobin is very likely synthesized as a single polypeptide chain which is then cleaved at an Arg residue to generate its two characteristic alpha and beta subunit. Southern blot analysis suggests that there are at least two copies of the haptoglobin gene per haploid genome.
Corrosion of mild steel underneath aerobic biofilms containing sulfate‐reducing bacteria part I: At low dissolved oxygen concentration (1993)

The sulfate‐reducing bacteria (SRB)‐enhanced corrosion of mild steel in the presence of 1.5 mg·l−1 dissolved oxygen (DO) in bulk liquid was investigated. The biofilm process analysis was combined with microelectrode measurements, electrochemical measurements, and surface analysis. In the early stages of biofilm accumulation, the cathodic polarization and the decreasing corrosion rate were attributed to DO consumption by aerobic bacteria. During that time, limited SRB activity was observed. The DO concentration near the steel surface was between 0.6 and 1 mg·l−1. After total depletion of dissolved oxygen near the steel surface, the cathodic depolarization and the increased corrosion rate were associated with the proliferation of SRB near the steel surface. Auger electron spectroscopy analysis indicated localized sulfide attack. High pit density appeared where the coincidence of oxygen and sulfur occurred. The bottom of the pit was enriched with sulfur.
[Chemical reactions in double-stranded nucleic acids. V. Directed introduction into the DNA sugar-phosphate backbone of aliphatic diamine or glycol residues]. (1988)

The chemical ligation method was used for directed introduction of aliphatic diamines or glycols into sugar-phosphate backbone of DNA. Via condensation of heptanucleotide derivatives at the terminal phosphate (aminoalkylamides or hydroxyalkyl esters) with the adjacent heptanucleotide on the corresponding template, 14 bp DNA duplexes containing residues of ethylene-, propylene- or hexamethylenediamine, as well as residues of ethylene- or propyleneglycol in one of its strands, were synthesised. In a similar way duplexes were obtained in which residues of the above diamines or glycols are substituted for a mononucleotide in one of the complementary strands. Examplified by synthesis of DNA duplexes containing ethylenediamine or ethyleneglycol residues, three methods of the phosphate group activation using carbodiimide, imidazolide and N-hydroxybenzotriazole ester were tested; the last method gave the highest yields and purity of the products. Yields of duplexes without nucleotide omissions were 50, 36 and 7% for aminoethyl, aminopropyl and aminohexylamides, and 20 and 17% for hydroxyethyl and hydroxypropyl esters, respectively, whereas duplexes with nucleotide omissions were synthesised with lower yields. Each of the modified DNA duplexes thus obtained contains a recognition site of EcoRII, SsoII or MvaI restriction nucleases, thus being a potential substrate of these enzymes.
Replacement of Dietary Saturated Fatty Acids by <i>Trans</i> Fatty Acids Lowers Serum HDL Cholesterol and Impairs Endothelial Function in Healthy Men and Women (2001)

We tested whether trans fatty acids and saturated fatty acids had different effects on flow-mediated vasodilation (FMD), a risk marker of coronary heart disease (CHD). Consumption of trans fatty acids is related to increased risk of CHD, probably through effects on lipoproteins. Trans fatty acids differ from most saturated fatty acids because they decrease serum high-density lipoprotein (HDL) cholesterol, and this may increase the risk of CHD. We fed 29 volunteers 2 controlled diets in a 2x4-week randomized crossover design. The "Trans-diet" contained 9.2 energy percent of trans fatty acids; these were replaced by saturated fatty acids in the "Sat-diet." Mean serum HDL cholesterol after the Trans-diet was 0.39 mmol/L (14.8 mg/dL), or 21% lower than after the Sat-diet (95% CI 0.28 to 0.50 mmol/L). Serum low density lipoprotein and triglyceride concentrations were stable. FMD+SD was 4.4+/-2.3% after the Trans-diet and 6.2+/-3.0% after the Sat-diet (difference -1.8%, 95% CI -3.2 to -0.4). Replacement of dietary saturated fatty acids by trans fatty acids impaired FMD of the brachial artery, which suggests increased risk of CHD. Further studies are needed to test whether the decrease in serum HDL cholesterol caused the impairment of FMD.