gebhart/patrepeval huggingface dataset:
Elucidation of N‐linked oligosaccharide structures of recombinant human factor VIII using fluorophore‐assisted carbohydrate electrophoresis (1996)

Characterization of the carbohydrate moiety is a critical measure of manufacturing process consistency of recombinant human Factor VIII (rFVIII) in Chinese-hamster ovary (CHO) cells. FVIII, a large (300 kDa) glycoprotein, is employed therapeutically for the correction of haemophilia A. While N-linked and O-linked oligosaccharides are found in this protein, the current study focuses on the N-linked oligosaccharides. The N-linked oligosaccharides from rFVIII were released using either peptide N-glycosidase F or endoglycosidase H, derivatized with the fluorophore 8-aminonaphthalene-1,3,6-trisulphonate, and analysed by fluorophore-assisted carbohydrate electrophoresis (FACE). The electrophoretically resolved oligosaccharide bands were isolated and individual bands subjected to digestion with defined pools of exoglycosidases and re-electrophoresed on FACE sequencing gels. The resulting gel patterns were interpreted, based on band mobility shifts, to obtain the sequence structure of the oligosaccharides. A total of eight acidic and 12 neutral structures were identified, and the majority of the oligosaccharides (approximately 92%) were found to be sialylated. All of the major oligosaccharide structures found in CHO-cell-derived rFVIII have also been reported to be present in plasma-derived FVIII. Among the most abundant are disialylated, biantennary, core-fucosylated (approximately 40%), followed by trisialylated, triantennary, core-fucosylated and monosialo, biantennary, core-fucosylated structures (each approximately 18%). The Gal alpha 1-3Gal structures reported to be present in baby-hamster-kidney-cell-derived rFVIII were not found in the CHO-cell-derived protein. The glycosylation patterns were consistent in six random lots of rFVIII [coefficient of variation (%) 3-14] based on percentage lane luminance data of bands that represent approximately 98% of all asparagine-linked oligosaccharides.
ZrO 2 gate dielectrics produced by ultraviolet ozone oxidation for GaN and AlGaN∕GaN transistors (2006)

We investigated the suitability of ZrO2 as a high-k dielectric for GaN material systems. Thin Zr films (4nm) were deposited by electron-beam evaporation at room temperature on n-type GaN and Al0.22Ga0.78N(29nm)∕GaN high electron mobility transistor (HEMT) structures. The Zr-coated samples were subsequently oxidized at temperatures in the range of 200–400 °C in an ozone environment. Atomic force microscopy studies after oxidation show that the ZrO2 forms a conformal layer on the underlying GaN template. Cross-section transmission electron microscopy studies showed little intermixing of the ZrO2 with the AlGaN∕GaN. The relative dielectric constant of the ZrO2 was determined to be 23. In comparison with HEMTs with bare gates (no dielectric between the gate metal and AlGaN), the HEMTs with ZrO2 showed two to three order of magnitude reduction in gate leakage current. Optimization of the HEMT process on sapphire substrates with ZrO2 under the gates yielded devices with powers of 3.8W∕mm and 58% power-added efficiency at 4GHz.
Distinguishing Single DNA Nucleotides Based on Their Times of Flight Through Nanoslits: A Molecular Dynamics Simulation Study (2013)

Transport of single molecules in nanochannels or nanoslits might be used to identify them via their transit (flight) times. In this paper, we present molecular dynamics simulations of transport of single deoxynucleotide 5'-monophoshates (dNMP) in aqueous solution under pressure-driven flow, to average velocities between 0.4 and 1.0 m/s, in 3 nm wide slits with hydrophobic walls. The simulation results show that, while moving along the slit, the mononucleotides are adsorbed and desorbed from the walls multiple times. For the simulations, the estimated minimum slit length required for separation of the dNMP flight time distributions is about 5.9 μm, and the minimum analysis time per dNMP is about 10 μs. These are determined by the nature of the nucleotide-wall interactions, channel width, and by the flow characteristics. A simple analysis using realistic dNMP velocities shows that, in order to reduce the effects of diffusional broadening and keep the analysis time per dNMP reasonably small, the nucleotide velocity should be relatively high. Tailored surface chemistry could lead to further reduction of the analysis time toward its minimum value for a given driving force.
The best thermoelectric. (1996)

What electronic structure provides the largest figure of merit for thermoelectric materials? To answer that question, we write the electrical conductivity, thermopower, and thermal conductivity as integrals of a single function, the transport distribution. Then we derive the mathematical function for the transport distribution, which gives the largest figure of merit. A delta-shaped transport distribution is found to maximize the thermoelectric properties. This result indicates that a narrow distribution of the energy of the electrons participating in the transport process is needed for maximum thermoelectric efficiency. Some possible realizations of this idea are discussed.
Interactions of phosphatidylinositol kinase, GTPase-activating protein (GAP), and GAP-associated proteins with the colony-stimulating factor 1 receptor. (1990)

The interactions of the macrophage colony-stimulating factor 1 (CSF-1) receptor with potential targets were investigated after ligand stimulation either of mouse macrophages or of fibroblasts that ectopically express mouse CSF-1 receptors. In Rat-2 cells expressing the mouse CSF-1 receptor, full activation of the receptor and cellular transformation require exogenous CSF-1, whereas NIH 3T3 cells expressing mouse c-fms are transformed by autocrine stimulation. Activated CSF-1 receptors physically associate with a phosphatidylinositol (PI) 3'-kinase. A mutant CSF-1 receptor with a deletion of the kinase insert region was deficient in its ability to bind functional PI 3'-kinase and to induce PI 3'-kinase activity precipitable with antiphosphotyrosine antibodies. In fibroblasts, CSF-1 stimulation also induced the phosphorylation of the GTPase-activating protein (GAP)-associated protein p62 on tyrosine, although GAP itself was a relatively poor substrate. In contrast to PI 3'-kinase association, phosphorylation of p62 and GAP was not markedly affected by deletion of the kinase insert region. These results indicate that the kinase insert region selectively enhances the CSF-1-dependent association of the CSF-1 receptor with active PI 3'-kinase. The insert deletion mutant retains considerable transforming activity in NIH 3T3 cells (G. Taylor, M. Reedijk, V. Rothwell, L. Rohrschneider, and T. Pawson, EMBO J. 8:2029-2037, 1989). This mutant was more seriously impaired in Rat-2 cell transformation, although mutant-expressing Rat-2 cells still formed small colonies in soft agar in the presence of CSF-1. Therefore, phosphorylation of GAP and p62 through activation of the CSF-1 receptor does not result in full fibroblast transformation. The interaction between the CSF-1 receptor and PI 3'-kinase may contribute to c-fms fibroblast transformation and play a role in CSF-1-stimulated macrophages.
Industrial-scale spray layer-by-layer assembly for production of biomimetic photonic systems (2013)

Layer-by-layer assembly is a powerful and flexible thin film process that has successfully reproduced biomimetic photonic systems such as structural colour. While most of the seminal work has been carried out using slow and ultimately unscalable immersion assembly, recent developments using spray layer-by-layer assembly provide a platform for addressing challenges to scale-up and manufacturability. A series of manufacturing systems has been developed to increase production throughput by orders of magnitude, making commercialized structural colour possible. Inspired by biomimetic photonic structures we developed and demonstrated a heat management system that relies on constructive reflection of near infrared radiation to bring about dramatic reductions in heat content.
Multiple myeloma–reactive T cells recognize an activation-induced minor histocompatibility antigen encoded by the ATP-dependent interferon-responsive (ADIR) gene (2007)

Minor histocompatibility antigens (mHags) play an important role in both graft-versus-tumor effects and graft-versus-host disease (GVHD) after allogeneic stem cell transplantation. We applied biochemical techniques and mass spectrometry to identify the peptide recognized by a dominant tumor-reactive donor T-cell reactivity isolated from a patient with relapsed multiple myeloma who underwent transplantation and entered complete remission after donor lymphocyte infusion. A frequently occurring single nucleotide polymorphism in the human ATP-dependent interferon-responsive (ADIR) gene was found to encode the epitope we designated LB-ADIR-1F. Although gene expression could be found in cells from hematopoietic as well as nonhematopoietic tissues, the patient suffered from only mild acute GVHD despite high percentages of circulating LB-ADIR-1F-specific T cells. Differential recognition of nonhematopoietic cell types and resting hematopoietic cells as compared with activated B cells, T cells, and tumor cells was demonstrated, illustrating variable LB-ADIR-1F expression depending on the cellular activation state. In conclusion, the novel mHag LB-ADIR-1F may be a suitable target for cellular immunotherapy when applied under controlled circumstances.
The preparation of unsymmetrical diglycerides (1967)

Racemic 1,2-di-O-acylglycerols containing stearic and palmitic acids were prepared from 1,2-di-O-acyl-3-O-2′-tetrahydropyranylglycerols by hydrolysis of the tetrahydropyranyl group with boric acid. The 1,2-di-O-acyl-3-O-2′-tetrahydropyranylglycerols were obtained by acylation of 3-O-2′-tetrahydropyranylglycerol which was prepared from glycerol 1,2-carbonate. Enzymic hydrolysis of the 1,2-di-O-acyl-3-O-2′-tetrahydropyranyl-glycerols with pancreatic lipase gave 2-O-acyl-3-O-2′-tetrahydropyranylglycerols which were reacylated with a different fatty acid and hydrolysed to give “mixed acid” diglycerides. The method should be general for the preparation of 1,2-di-O-acyl-L-glycerols containing any mixture of long-chain acyl groups (saturated or unsaturated) using L-glycerol 1,2-carbonate as a starting material. The latter compound was synthesised from 3-O-benzyl-L-glycerol. The hydrolysis of racemic 1-O-hept-1′-enyl-2,3-di-O-palmitoylglycerol with pancreatic lipase gave 1-O-hept-1′-enyl-2-O-palmitoylglycerol, a “plasmaloge nicdiglyceride” suitable as an intermediate for the synthesis of plasmalogens.
Tumor-Cell-Targeted Methionine-enkephalin Analogues Containing Unnatural Amino Acids:  Design, Synthesis, and in Vitro Antitumor Activity (2006)

A series of new peptides (8-25) containing different unnatural amino acids of the adamantane type (1-6), was synthesized. Possible cytotoxic activity on human cervical adenocarcinoma (HeLa), larynx carcinoma (HEp-2), colon carcinomas (HT-29, Caco-2), poorly differentiated cells from lymph node metastasis of colon carcinoma (SW-620), mammary gland adenocarcinoma (MCF-7), and melanoma (HBL) cells were tested by the MTT assay. The results were compared with the effect of methionine-enkephalin (Tyr-Gly-Gly-Phe-Met, or opioid growth factor, OGF), and its shorter N-terminal fragments. Peptide analogues containing C(alpha alpha)-dialkylated glycine (Aaa1, 1) or C(alpha)-alkylated glycine (Aaa2, 2) amino acid residues showed antitumor activity against melanoma, larynx carcinoma, colon carcinomas, and colon metastasis cell lines in vitro. The pentapeptide Tyr-(R,S)-Aaa2-Gly-Phe-Met (18) was the most effective analogue especially against the most antitumor drug-resistant cell lines HEp-2 and SW-620. Apoptosis as a mode of cell death was confirmed in these tumor cells after exposure to pentapeptide 18.
Functional analysis of the Arabidopsis centromere by T-DNA insertion-induced centromere breakage (2008)

Two minichromosomes (alpha and delta) in addition to two other aberrant chromosomes (beta and gamma) were found in a transgenic Arabidopsis plant produced by an in planta vacuum infiltration technique. The minichromosomes were successfully separated by successive crossing and selfing and added to wild-type Columbia (Col-0) as a supernumerary chromosome. FISH indicated that both of the two minichromosomes originated from the short arm of chromosome 2. The mini alpha chromosome contained the whole short-arm 2S and a truncated centromere (180-bp repeat cluster), whereas mini delta lacked the terminal region including telomere repeats. Pachytene FISH clearly revealed that mini delta comprised a ring chromosome carrying two copies of the region from the 180-bp repeat cluster to BAC-F3C11. Both of the 180-bp clusters (each approximately 500 kb in length) were thought to possess normal centromere functions because the centromere-specific histone H3 variant (HTR12) was detected on both clusters. Notwithstanding this dicentric and ring form, mini delta was stably transmitted to the next generations, perhaps because of its compact size (<4 Mb). Chromosome beta also comprised a dicentric-like structure, with one of the two 180-bp repeat sites derived from chromosome 1 and the other from chromosome 2. However, the latter was quite small and failed to bind HTR12. The data obtained in this study indicated that 500 kb of the 180-bp array of the chromosome 2 centromere, from the edge of the 180-bp array on the short-arm side, is sufficient to form a functional domain.
Specificity analysis of sera from breast cancer patients vaccinated with MUC1-KLH plus QS-21 (1999)

The mucin MUC1 is expressed on breast cancers in an underglycosylated form compared to normal tissues and is therefore a potential target for cancer immunotherapy. MUC1 contains multiple tandem repeats of the 20 amino acid (aa) peptide (VTSAPDTRPAPGSTAPPAHG). The APDTRPA epitope is particularly immunogenic since it is recognized by a variety of murine monoclonal antibodies and by some sera and cytotoxic T-cells from unimmunized patients with epithelial cancers. We have prepared a 30 aa peptide (C)VTSAPDTRPAPGSTAPPAHGVTSAPDTRPA with cysteine at the N-terminal end, and used the cysteine for chemical conjugation to keyhole limpet haemocyanin (KLH). Six breast cancer patients immunized with this conjugate plus the immunological adjuvant QS-21 have all produced high titre (by ELISA) IgG and IgM antibodies against the 30 aa MUC1 peptide, but these sera reacted moderately, or not at all, with MUC1-positive tumour cells. To understand this specificity better, we prepared a series of smaller peptides to determine the epitopes recognized by these immune sera in inhibition assays. Only peptides containing APDTRPA at the C-terminal end were able to completely inhibit ELISA reactivity for the full 30 aa peptide. No sera were completely inhibited by APDTR, APDTRP, PDTRPA or any other peptides that did not contain the full APDTRPA epitope. Remarkably, sera from all six patients recognized this same epitope and were completely inhibited by only this epitope. The specificity of these sera (1) primarily for C-terminal APDTRPA, and the absence of this epitope at the C-terminal end of any tumour mucins, and (2) the N-terminal APDTRPA alanine, which is normally buried in the beta turn MUC1 assumes in its secondary structure may explain the moderate to weak reactivity of these high titer sera against MUC1-positive tumour cells.
Data Structures and Network Algorithms (1983)

Foundations Disjoint Sets Heaps Search Trees Linking and Cutting Trees Minimum Spanning Trees Shortest Paths Network Flows Matchings.
Phase 2 study of the JAK kinase inhibitor ruxolitinib in patients with refractory leukemias, including postmyeloproliferative neoplasm acute myeloid leukemia (2012)

We conducted a phase 2 study of ruxolitinib in patients with relapsed/refractory leukemias. Patients with acceptable performance status (0-2), adequate organ function, and no active infection, received ruxolitinib 25 mg orally twice a day for 4 weeks (1 cycle). Response was assessed after every 2 cycles of treatment, and patients who completed 2 cycles were allowed to continue treatment until disease progression. Dose escalation to 50 mg twice daily was permitted in patients demonstrating a benefit. Thirty-eight patients, with a median age of 69 years (range, 45-88), were treated. The median number of prior therapies was 2 (range, 1-6). Twelve patients had JAK2V617F mutation. Patients received a median of 2 cycles of therapy (range, 1-22). Three of 18 patients with postmyeloproliferative neoplasm (MPN) acute myeloid leukemia (AML) showed a significant response; 2 achieved complete remission (CR) and one achieved a CR with insufficient recovery of blood counts (CRi). The responding patients with palpable spleens also had significant reductions in spleen size. Overall, ruxolitinib was very well tolerated with only 4 patients having grade 3 or higher toxicity. Ruxolitinib has modest antileukemic activity as a single agent, particularly in patients with post-MPN AML. The study was registered at www.clinicaltrials.gov as NCT00674479.
Exciplex formation at the organic solid-state interface: Yellow emission in organic light-emitting diodes using green-fluorescent tris(8-quinolinolato)aluminum and hole-transporting molecular materials with low ionization potentials (1998)

The bilayer organic light-emitting diodes using green-fluorescent tris(8-quinolinolato)aluminum (Alq3) as an emitting material and hole-transport materials with low ionization potentials, 1,3,5-tris(3-methylphenylphenylamino)triphenylamine and 4,4′,4″-tris[bis(4-tert-buthylbiphenyl4-yl)amino]triphenylamine, emitted bright yellow light instead of green light. The yellow emission is attributed to exciplex formation at the solid interface between Alq3 and the hole-transport material. The exciplex formation was evidenced by the measurement of the photoluminescence spectra and lifetimes of the mixture of an equimolar amount of Alq3 and each of the hole-transport materials. The emission color can be tuned by varying the applied voltage.
Fully-Digital Time-To-Digital Converter for ATE with Autonomous Calibration (2006)

Precise and fast time measurements have many applications in tests. An ATE that integrates a general purpose time-to-digital converter (TDC) into each pin benefits from a fully digital implementation and autonomous calibration. This paper presents two novel calibration methods and supporting HW for a vernier delay line (VDL) based TDC. A novel linearity calibration uses the deviation from a uniform code density, when measuring a large number of uncorrelated events from a local ring oscillator. A novel coarse/fine calibration corrects for supply voltage induced delay fluctuations by injecting a known time interval into the VDL after each measured event. Design parameters for 90 nm CMOS are described. SPICE and MATLAB simulations and a detailed statistical analysis indicate post calibration errors of 2 ps RMS with unlimited dynamic range, at sample rates of 100 Msa/s
Epstein–Barr virus and Burkitt lymphoma (2007)

Burkitt lymphoma (BL) is an aggressive B-cell malignancy with endemic, sporadic and immunodeficiency-associated variants. It has been known for many years that the fundamental transforming event in BL is the translocation of the MYC gene, and the events that bring about this translocation and those that allow cells to survive with the constitutive expression of MYC have been the subject of intense investigation. Epstein-Barr virus (EBV) infection, malaria, immunodeficiency and spontaneous, somatic mutation can all contribute to the origin and maintenance of this cancer and their mechanisms are the subject of this review.
N2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops (1998)

Modified nucleotides are resource-intensive alternatives to the four nucleotides that constitute the bulk of natural RNAs. Yet, even in cases where modifications are highly conserved, their functions are difficult to identify. One possible function might be to modulate the stability of RNA structures. To investigate this possibility for N 2-methylguanosine (m2G), which is present in a wide variety of RNAs, we have determined the thermodynamic consequences of substituting m2G for G in G-C Watson-Crick pairs and G@U wobble pairs within RNA duplexes. The m2G substitution is iso-energetic with G in all cases, except for aninternal m2G@U pair, where it has a modest (0.3 kcal/mol) stabilizing effect. We have also examined theconsequences of replacing G by m2G, and A by N 6, N 6-dimethyladenosine (m26A) in the helix 45 tetraloop of 16S rRNA, which would otherwise be a standard GNRA tetraloop. This loop is a conserved, hypermethylated region of the ribosome where methylation appears to modulate activity. m26A substitution destabilizes the tetraloop, presumably because it prevents the formation of the G@A sheared pair it would otherwise contain. m2G substitution has no effect on tetraloop stability. Together, these results suggest that m2G is equally stable as either the s-cis or s-trans rotamer. The lack of a significant effect on secondary structural stability in these systems suggests that m2G is introduced into naturally occurring RNAs for reasons other than modulation of duplex stability.
Glycosylation and stability of mature HIV envelope glycoprotein conformation under various conditions (1996)

The role of the glycans of the mature human immunodeficiency virus (HIV) envelope (gp160) in its stability in various conditions was studied. gp160 conformation was monitored through its subsequent ability to bind [125I]CD4. Treatment of glycosylated (CHO+) gp160 with (i) sodium dodecyl sulfate (SDS) concentrations above 0.01% impaired subsequent CD4 binding while 0.3% SDS abolished it; (ii) beta-mercaptoethanol (MSH) concentrations above 0.01% impaired CD4 binding while 0.03% MSH abolished it; (iii) 2 M guanidine-HCl had no effect; (iv) temperatures between 50 degrees C and 80 degrees C altered CD4 binding while, above 80 degrees C, the binding was abolished; (v) CD4 binding was decreased by 50% by 2 freeze-thaw cycles but was not further affected by subsequent (up to 15) cycles; (vi) gp160 incubation in serum or cell lysate had no effect on CD4 binding. Glycanase treated (CHO-) gp160 binding activity was only 3-fold lower than that of CHO+ gp160. Only 2 M guanidine-HCl and heating at 70 degrees C differentially affected the binding of CHO+ and CHO- gp160, the effects being larger for CHO- gp160. CHO- gp160 binding was impaired after incubation in either serum or cell lysate. Thus, glycans stabilize gp160 conformation in some environments. However, CHO- gp160 appears to be resistant to denaturation as compared to other glycoproteins reported in the literature.