gebhart/patrepeval huggingface dataset:
Simulation of reactive ion etching pattern transfer (1989)

This paper describes a model that simulates etching profiles and process latitudes in glow-discharge bombardment-induced reactive-etching processes. Numerical results are presented for the pattern-transfer step in trilayer lithography, but this analysis is applicable to many other pattern-transfer processes. The inputs to the interface-evolution model described here are a kinetic model for the yield per incident energetic particle and a statistical mechanical model that relates the incident-yield-weighted angular distribution to the pressure, sheath thickness, and sheath voltage drop. The kinetic model is based on experimental evidence and assumes that the yield per bombarding particle is proportional to its energy. The resulting interface-evolution equation is mathematically analogous to a free-surface evolution equation in hydrodynamics. This convective partial differential equation is reduced to a coupled set of ordinary differential equations via the method of characteristics and solved numerically. More general energy-dependent yields are easily incorporated in the present formulation, but angle-dependent yields are more difficult and are not treated here. This model describes how shadowing of the surface being etched results in proximity effects in line etching and aspect-ratio-dependent etching rates in trench etching. Simulated profiles are compared to experimental trilayer etching profiles and qualitatively describe their shape and the trends that are observed as pressure or other processing parameters are varied. Simulations showing the effect of angular distributions, line proximity, and trench aspect ratio on process latitudes in trilayer lithography are presented and discussed.
Matrix‐assisted laser desorption/ionization mass spectrometry for the evaluation of the C‐terminal lysine distribution of a recombinant monoclonal antibody (2004)

Recombinant monoclonal antibodies produced using mammalian cell lines contain multiple chemical modifications. One specific modification resides on the C-terminus of the heavy chain. Enzymes inside the cell can cleave the C-terminal lysine from the heavy-chain molecules, and variants with and without C-terminal lysine can be produced. In order to fully characterize the protein, there is a need for analytical methods that are able to account for the different product variants. Conventional analytical methods used for the measurement of the distribution of the two different variants are based on chemical or enzymatic degradation of the protein followed by chromatographic separation of the degradation products. Chromatographic separations with gradient elution have long run times, and analyses of multiple samples are time-consuming. This paper reports development of a novel method for the determination of the relative amounts of the two C-terminal heavy-chain variants based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) measurements of the cyanogen bromide degraded recombinant monoclonal antibody products. The distribution of the variants is determined from the MALDI-TOF mass spectra by measuring the peak areas of the two C-terminal peptides. The assay was used for the assessment of the C-terminal lysine distribution in different development lots. The method was able to differentiate between the products obtained using the same cell line as well as between products obtained from different cell lines.
Weighted Random Sampling over Data Streams (2010)

In this work, we present a comprehensive treatment of weighted random sampling (WRS) over data streams. More precisely, we examine two natural interpretations of the item weights, describe an existing algorithm for each case ([2, 4]), discuss sampling with and without replacement and show adaptations of the algorithms for several WRS problems and evolving data streams.
Systemic inhibition of spontaneous calcification by the serum protein alpha 2-HS glycoprotein/fetuin. (2001)

The extracellular fluid is a metastable system with regard to calcium and phosphate ions. Active inhibitors of calcification must be present in serum to prevent the spontaneous formation of Ca2+.Pi solid phases which could otherwise precipitate to cause renal calcinosis and block small blood vessels. alpha 2-HS glycoproteins/fetuins, AHSGs, are ideal candidates for this function. AHSGs are ubiquitous and highly abundant in serum; they bind calcium and efficiently prevent de novo formation of apatitic mineral. Normocalcemic AHSG-deficient mice develop sporadic perivascular calcification. Hypercalcemia induced by dietary means or by hormone treatment results in lethal calcinosis in Ahsg-/-mice. A mineral binding structure is proposed for domain D1 of AHSG suggesting that the proposed EF-hand motif for calcium binding does not exist in AHSG. Unlike serum albumin, AHSG does not preferentially bind ionic Ca2+, but rather in the form of apatitic microcrystals.
HOTAIR: Flight of noncoding RNAs in cancer metastasis (2010)

The genetic makeup of most cells in the body is identical. Hence what makes one cell type different from another cell type in the body is largely determined by epigenetics, via differences in chromatin states. Changes in chromatin modifications can alter cell fate, causing cells to forget their cellular identity and take on different properties that may be detrimental to the overall organization of the body, including cancer. In metastasis, cancer cells proliferate, invade out of their tissue boundaries, enter the blood stream and colonize in a foreign tissue. The long intergenic noncoding RNA HOTAIR has been recently discovered to provide such a link between chromatin state, cell positional identity, and cancer metastasis1.
A commercial approach to successful persistent radar surveillance of sea, air and land along the northern border (2010)

The benefits of a commercial approach to the deployment of radar surveillance along the Great Lakes St. Lawrence Seaway System (GLSLSS) is discussed. Surveillance solutions must be multi-mission suitable, scalable, flexible, maintainable, upgradeable, interoperable, shareable, and affordable. This flexibility is fundamental to successfully leveraging tomorrow, investments made today in order to keep up with changing threats and technology. Not only can homeland security surveillance solutions benefit by leveraging commercial technologies, but non-sensitive target information, can drive significant human and commercial benefits. The paper presents a radar surveillance framework whose network architecture, COTS components, specially designed components and open interfaces are discussed. The modular nature of the framework includes software definable algorithms for acquisition of sea, air or land targets of interest, built-in integration of target information that fully scales in support of wide-area surveillance, and open interfaces in support of new, multi-mission situational awareness applications.
Toward Synthetic Transcription Activators:  Recruitment of Transcription Factors to DNA by a PNA-Peptide Chimera (2002)

A PNA-peptide chimera designed to mimic the biochemical function of transcription activators has been synthesized and characterized. The bis-PNA segment binds specifically to a DNA site while the 20-residue peptide is capable of binding to the transcription factors Gal11 and Gal80. The PNA-peptide chimera thus mimics one of the central functions of a native transcription activator, recruitment of transcription factors to a specific DNA site.
Suppression of survivin expression in glioblastoma cells by the Ras inhibitor farnesylthiosalicylic acid promotes caspase-dependent apoptosis (2006)

The Ras inhibitor farnesylthiosalicylic acid (FTS) has been shown to induce apoptosis in glioblastoma multiforme, but its mechanism of action was unknown. We show that FTS or dominant-negative Ras, by deregulating extracellular signal-regulated kinase and Akt signaling, decreases survivin gene transcripts in U87 glioblastoma multiforme, leading to disappearance of survivin protein and cell death. FTS affected both Ras-controlled regulators of survivin transcription and Ras-regulated survival signals. Thus, Ras inhibition by FTS resulted in release of the survivin "brake" on apoptosis and in activation of the mitochondrial apoptotic pathway: dephosphorylation of Bad, activation of Bax, release of cytochrome c, and caspase activation. FTS-induced apoptosis of U87 cells was strongly attenuated by forced expression of survivin or by caspase inhibitors. These results show that resistance to apoptosis in glioblastoma multiforme can be abolished by a single Ras inhibitor, which targets both survivin, a critical inhibitor of apoptosis, and the intrinsic mitochondrial apoptotic machinery.
DNAzyme-Functionalized Au Nanoparticles for the Amplified Detection of DNA or Telomerase Activity (2004)

DNAzyme-functionalized Au−NPs act as catalytic labels for the amplified detection of DNA and telomerase activity on nucleic acid-functionalized gold surface. The DNAzyme stimulates, in the presence of hemin, H2O2, and luminol, the generation of chemiluminescence. For DNA analysis, a nucleic acid unit complementary to the analyzed DNA is tethered to the DNAzyme structure associated with the Au−NPs. For telomerase activity, a nucleic acid complementary to the telomer repeat units generated on the surface is tethered to the DNAzyme structure associated with the Au−NPs. The detection limit for the detection of DNA is 1 × 10-10 M. The method enables the detection of telomerase activity originating from 1000 HeLa cells.
Poly(ADP-ribose) polymerase and XPF–ERCC1 participate in distinct pathways for the repair of topoisomerase I-induced DNA damage in mammalian cells (2011)

Poly(ADP-Ribose) (PAR) polymerase (PARP) inhibitors represent a promising class of novel anticancer agents. The present study explores the molecular rationale for combining veliparib (ABT-888) with camptothecin (CPT) and its clinical derivatives, topotecan and irinotecan. ABT-888 inhibited PAR induction by CPT and increased CPT-induced cell killing and histone γH2AX. Increased DNA breaks by ABT-888 were not associated with a corresponding increase of topoisomerase I cleavage complexes and were further increased by inactivation of tyrosyl-DNA phosphodiesterase 1. SiRNA knockdown for the endonuclease XPF-ERCC1 reduced the ABT-888-induced γH2AX response in non-replicating and replicating cells but enhanced the antiproliferative effect of ABT-888 in CPT-treated cells. Our findings indicate the involvement of XPF-ERCC1 in inducing γH2AX response and repairing topoisomerase I-induced DNA damage as an alternative pathway from PARP and tyrosyl-DNA phosphodiesterase 1.
Thiopurine S-methyltransferase pharmacogenetics: variant allele functional and comparative genomics (2005)

Thiopurine S-methyltransferase (TPMT) catalyses the S-methylation of thiopurine drugs. Genetic polymorphisms for TPMT are a major factor responsible for large individual variations in thiopurine toxicity and therapeutic effect. The present study investigated the functional effects of human TPMT variant alleles that alter the encoded amino acid sequence of the enzyme, TPMT*2, *3A, *3B, *3C and *5 to *13. After expression in COS-1 cells and correction for transfection efficiency, allozymes encoded by these alleles displayed levels of activity that varied from virtually undetectable (*3A,*3B and *5) to 98% (*7) of that observed for the wild-type allele. Although some allozymes had significant elevations in apparent Km values for 6-mercaptopurine and S-adenosyl-L-methionine (i.e. the two cosubstrates for the reaction), the level of enzyme protein was the major factor responsible for variation in activity. Quantitative Western blot analysis demonstrated that the level of enzyme protein correlated closely with level of activity for all allozymes except TPMT*5. Furthermore, protein levels correlated with rates of TPMT degradation. TPMT amino acid sequences were then determined for 16 non-human mammalian species and those sequences (plus seven reported previously, including two nonmammalian vertebrate species) were used to determine amino acid sequence conservation. Most human TPMT variant allozymes had alterations of residues that were highly conserved during vertebrate evolution. Finally, a human TPMT homology structural model was created on the basis of a Pseudomonas structure (the only TPMT structure solved to this time), and the model was used to infer the functional consequences of variant allozyme amino acid sequence alterations. These studies indicate that a common mechanism responsible for alterations in the activity of variant TPMT allozymes involves alteration in the level of enzyme protein due, at least in part, to accelerated degradation.
Alternative Excision Repair Pathways (2013)

Alternative excision repair (AER) is a category of excision repair initiated by a single nick, made by an endonuclease, near the site of DNA damage, and followed by excision of the damaged DNA, repair synthesis, and ligation. The ultraviolet (UV) damage endonuclease in fungi and bacteria introduces a nick immediately 5' to various types of UV damage and initiates its excision repair that is independent of nucleotide excision repair (NER). Endo IV-type apurinic/apyrimidinic (AP) endonucleases from Escherichia coli and yeast and human Exo III-type AP endonuclease APEX1 introduce a nick directly and immediately 5' to various types of oxidative base damage besides the AP site, initiating excision repair. Another endonuclease, endonuclease V from bacteria to humans, binds deaminated bases and cleaves the phosphodiester bond located 1 nucleotide 3' of the base, leading to excision repair. A single-strand break in DNA is one of the most frequent types of DNA damage within cells and is repaired efficiently. AER makes use of such repair capability of single-strand breaks, removes DNA damage, and has an important role in complementing BER and NER.
Simulation of resistance forces acting on surgical needles (1997)

High precision in the manual control of needles and biopsy probes in medical treatment requires high skill and dexterity levels. In anaesthesia, force sensation is an important feedback mechanism, and the practitioner needs to refresh or develop skills to improve on the interpretation of needle progress towards the target site. This paper describes an experimental tactile force simulator for uniaxial needle action for which the force resisting progress of the needle is derived from measured data. As an example, the approach taken to develop the simulation of the insertion of epidural needles is described. Adaptation to other procedures would be possible by adopting new reference models based on appropriate measured force data.
Computer-based fluorescence quantification: a novel approach to study nucleolar biology (2011)

Our protocols set the stage to analyze in a quantitative fashion the kinetics of shuttling nucleolar proteins, both at the single cell level as well as for a large number of cells. Moreover, the procedures described here are compatible with high throughput image acquisition and analysis using HTS automated platforms, thereby providing the basis to quantify nucleolar components and activities for numerous samples and experimental conditions. Together with the growing amount of information obtained for the nucleolar proteome, improvements in quantitative microscopy as they are described here can be expected to produce new insights into the complex biological functions that are orchestrated by the nucleolus.
Novel stage in the oligodendrocyte lineage defined by reactivity of progenitors with R‐mAb prior to O1 anti‐galactocerebroside (1992)

The developmentally regulated appearance of surface immuno-reactivity of proligodendroblasts [oligodendrocyte progenitors reacting with monoclonal antibodies A007 and O4, but not anti-galactocerebroside (GalC), i.e., A007/O4+GalC-] to monoclonal antibodies R-mAb and O1 was studied both in culture and in vivo. In both cases staining with R-mAb shortly preceded that with O1; that is, a transient population of R-mAb+O1- cells was observed. R-mAb-O1+ cells were not detected. Differential staining with R-mAb and O1 was also noted at the subcellular level. In younger cultures in which R-mAb+ cells were first acquiring O1 immunoreactivity, many of these cells were stained by O1 only on the cell bodies and proximal portions of the processes, whereas in contrast R-mAb stained the whole cell, including the distal portions of the processes. Only in older, more mature R-mAb+ cells did O1 also stain the distal portions of processes. The expression of reactivity to R-mAb and O1 was compared to the proliferative capacity of the cells. Proliferation [assessed by bromodeoxyuridine (BrdU) incorporation] of both R-mAb+ and O1+ cells was negligible both in culture and in vivo. However, treatment of cells in culture with 10 ng/ml basic fibroblast growth factor resulted in an enhancement of proliferation of the R-mAb+ cells. Within the proliferating R-mAb+BrdU+ population, 80% of the cells were O1- (i.e., anti-galactocerebroside negative). These events occur during a critical period of development when A007/O4+ proligodendroblasts begin to become post-mitotic and express surface galactocerebroside.(ABSTRACT TRUNCATED AT 250 WORDS)
Carrier detection in haemophilia B using two further intragenic restriction fragment length polymorphisms (1984)

A normal human population has been screened for the existence of further restriction fragment length polymorphisms (RFLPs) in the clotting factor IX gene in addition to the TaqI polymorphism already characterised (1,2). Two polymorphic loci were found, both within 6 Kb of the TaqI polymorphism within the body of the factor IX gene. One of the polymorphisms has been shown to be due to either the presence or absence of a particular recognition site for the restriction enzyme XmnI. The other, visualised as a difference in fragment pattern produced by digestion with either HinfI or DdeI, has two allelic forms differing by a 50 bp element of inserted DNA. Sequence analysis has shown the inserted element to be in a region of Z type DNA sequence, the insertion representing a duplication of flanking sequence on either side. The two polymorphisms are inherited in simple Mendelian fashion and have both been used to diagnose haemophilia B carrier status. It is estimated that the combined use of these polymorphisms in the factor IX gene, despite linkage disequilibrium between the 3 polymorphic loci, should enable carrier status to be determined in approximately 66% of all haemophilia B families.
Jejunal bacterial overgrowth and intestinal permeability in children with immunodeficiency syndromes. (1990)

Seventeen paediatric patients with immunodeficiency syndromes (10 with selective IgA deficiency, four with panhypogammaglobulinaemia, and three with selective T cell deficiency) were investigated for bacterial overgrowth of the small intestine and gut permeability to macromolecules. Five of 12 patients showed viable bacterial counts of more than 2 x 10(5)/ml in jejunal fluid. Bacterial overgrowth was also confirmed indirectly by breath hydrogen determination, which was higher than 10 ppm in four of the five patients with positive jejunal culture. Gut permeability to lactulose and L-rhamnose was abnormal in 16 of the 17 immunodeficient patients, who also had higher mean urinary excretion ratios than control subjects-mean (SD) values were 0.216 (0.160) and 0.029 (0.002), respectively. These studies indicate that bacterial overgrowth of the small intestine is a common feature in immunodeficient patients, regardless of the immunological abnormality. Moreover, these patients have an increased gut permeability to macromolecules.
A Potent and Selective Nonpeptide Antagonist of CXCR2 Inhibits Acute and Chronic Models of Arthritis in the Rabbit (2002)

Much evidence implicates IL-8 as a major mediator of inflammation and joint destruction in rheumatoid arthritis. The effects of IL-8 and its related ligands are mediated via two receptors, CXCR1 and CXCR2. In the present study, we demonstrate that a potent and selective nonpeptide antagonist of human CXCR2 potently inhibits (125)I-labeled human IL-8 binding to, and human IL-8-induced calcium mobilization mediated by, rabbit CXCR2 (IC(50) = 40.5 and 7.7 nM, respectively), but not rabbit CXCR1 (IC(50) = >1000 and 2200 nM, respectively). These data suggest that the rabbit is an appropriate species in which to examine the anti-inflammatory effects of a human CXCR2-selective antagonist. In two acute models of arthritis in the rabbit induced by knee joint injection of human IL-8 or LPS, and a chronic Ag (OVA)-induced arthritis model, administration of the antagonist at 25 mg/kg by mouth twice a day significantly reduced synovial fluid neutrophils, monocytes, and lymphocytes. In addition, in the more robust LPS- and OVA-induced arthritis models, which were characterized by increased levels of proinflammatory mediators in the synovial fluid, TNF-alpha, IL-8, PGE(2), leukotriene B(4), and leukotriene C(4) levels were significantly reduced, as was erythrocyte sedimentation rate, possibly as a result of the observed decreases in serum TNF-alpha and IL-8 levels. In vitro, the antagonist potently inhibited human IL-8-induced chemotaxis of rabbit neutrophils (IC(50) = 0.75 nM), suggesting that inhibition of leukocyte migration into the knee joint is a likely mechanism by which the CXCR2 antagonist modulates disease.
Targeting Mutated Plus Germline Epitopes Confers Pre-clinical Efficacy of an Instantly Formulated Cancer Nano-Vaccine (2019)

Personalized cancer vaccines hold promises for future cancer therapy. Targeting neoantigens is perceived as more beneficial compared to germline, non-mutated antigens. However, it is a practical challenge to identify and vaccinate patients with neoantigens. Here we asked whether two neoantigens are sufficient, and whether the addition of germline antigens would enhance the therapeutic efficacy. We developed and used a personalized cancer nano-vaccine platform based on virus-like particles loaded with toll-like receptor ligands. We generated three sets of multi-target vaccines (MTV) to immunize against the aggressive B16F10 murine melanoma: one set based on germline epitopes (GL-MTV) identified by immunopeptidomics, another set based on mutated epitopes (Mutated-MTV) predicted by whole exome sequencing and a last set combines both germline and mutated epitopes (Mix-MTV). Our results demonstrate that both germline and mutated epitopes induced protection but the best therapeutic effect was achieved with the combination of both. Our platform is based on Cu-free click chemistry used for peptide-VLP coupling, thus enabling bedside production of a personalized cancer vaccine, ready for clinical translation.