gebhart/patrepeval huggingface dataset:
Emulsions: basic principles (1999)

Emulsions are metastable colloids made out of two immiscible fluids, one being dispersed in the other, in the presence of surface active agents. Emulsion droplets exhibit all the classical behaviours of metastable colloids: Brownian motion, reversible phase transitions as a result of droplet interactions that may be strongly modified, and irreversible transitions that generally involve their destruction. They are obtained by shearing two immiscible fluids leading to the fragmentation of one phase into the other. Because the lifetime of emulsions may become significant (more than a year), they become good candidates for various commercial applications. All these applications have already led to an important empirical control of these materials, from their formation to their destruction. Besides this empirical background, which is widespread among the various specific applications, the basics of emulsions are certainly progressing and we aim in this paper to give an overview of the most recent advances. We will particularly focus on interdroplet forces, reversible phase transitions and colloidal structures, monolayer adhesion and emulsion gels, coarsening and destruction and finally some stability criteria for double emulsions.
Microbial Transformation of Ibuprofen by a Nocardia Species (1994)

The carboxylic acid functional group of ibuprofen [alpha-methyl-4-(2-methylpropyl) benzene acetic acid] is reduced to the corresponding alcohol and subsequently esterified to the acetate derivative by cultures of Nocardia species strain NRRL 5646. The alcohol and ester microbial transformation products were isolated, and their structures were determined by H and C nuclear magnetic resonance spectroscopy and mass spectrometry. By derivatization of synthetic and microbiologically produced ibuprofen alcohols with S(+)-O-acetylmandelic acid, nuclear magnetic resonance analysis indicated that the carboxylic acid reductase of Nocardia sp. is R enantioselective, giving alcohol products with an enantiomeric excess of 61.2%. The R enantioselectivity of the carboxylic acid reductase enzyme system was confirmed by using cell extracts together with ATP and NADPH in the reduction of isomeric ibuprofens.
Primary Structures of Arabidopsis Calmodulin Isoforms Deduced from the Sequences of cDNA Clones (1991)

Complementary DNA (cDNA) clones encoding calmodulin isoforms were isolated from an Arabidopsis leaf lambdagt10 library by screening with cloned barley calmodulin cDNA probes. Two cDNAs, one a 626-base pair partial-length clone (ACaM-1) and one a 1400-base pair full-length clone (ACaM-2), encode calmodulin polypeptides that differ by four conservative amino acid substitutions. None of the amino acid sequence differences occur within the four Ca(2+)-binding domains of the proteins. Whereas the deduced amino acid sequences of the two Arabidopsis calmodulin isoforms share 97% identity, the nucleotide sequences encoding the two isoforms share 87% sequence identity. Most of these nucleotide sequence differences (80%) occur in codon wobble positions. ACaM-1 and ACaM-2 both hybridize with a distinct set of restriction fragments of Arabidopsis total DNA, indicating that they were derived from transcripts of separate genes; these genes are single- or very low-copy in the Arabidopsis genome. Both cDNAs hybridize to messenger RNA (mRNA) species of 0.8 kilobases that are expressed to a greater extent in developing siliques compared with leaves, flowers, and stems. Northern blot and polymerase chain reaction assays both indicate that ACaM-1 mRNA is more highly expressed than ACaM-2 mRNA in developing siliques. The steady-state levels of both isoform mRNAs increase as a result of touch stimulation; the kinetics and extent of increase are comparable for the two mRNAs.
Low-power low-phase-noise differentially tuned quadrature VCO design in standard CMOS (2001)

This paper describes the design and optimization of VCOs with quadrature outputs. Systematic design of fully integrated LC-VCOs with a high inductance tank leads to a cross-coupled double core LC-VCO as the optimal solution in terms of power consumption. Furthermore, a novel fully differential frequency tuning concept is introduced to ease high integration. The concepts are verified with a 0.25-/spl mu/m standard CMOS fully integrated quadrature VCO for zero- or low-IF DCS1800, DECT, or GSM receivers. At 2.5-V power supply voltage and a total power dissipation of 20 mW, the quadrature VCO features a worst-case phase noise of -143 dBc/Hz at 3-MHz frequency offset over the tuning range. The oscillator is tuned from 1.71 to 1.99 GHz through a differential nMOS/pMOS varactor input.
Lowering blood pressure: a systematic review of sustained effects of non-pharmacological interventions (1998)

These net changes are probably overestimates of the effects that might be achieved by non-pharmacological interventions. There is a need for large-scale, long duration trials of these non-pharmacological interventions in both hypertensive patients and normotensive people to determine effect sizes more accurately.
Fluorescein aldehyde with disulfide functionality as a fluorescence turn-on probe for cysteine and homocysteine in HEPES buffer (2013)

We developed a fluorescein aldehyde probe with disulfide functionality for the fluorescence detection of biologically important thiols. The probe displayed highly selective responses to cysteine (Cys) and homocysteine (Hcy) over glutathione (GSH) due to the rapid ring formation reaction of Cys and Hcy with the aldehyde group of the probe and the concomitant cleavage of the disulfide group followed by subsequent intramolecular cyclization. The fluorescent probe also exhibited a highly sensitive fluorescence turn-on response to Hcy with a detection limit of 2.4 μM Hcy in HEPES buffer.
Tailored HIV-1 Vectors for Genetic Modification of Primary Human Dendritic Cells and Monocytes (2012)

Monocyte-derived dendritic cells (MDDCs) play a key role in the regulation of the immune system and are the target of numerous gene therapy applications. The genetic modification of MDDCs is possible with human immunodeficiency virus type 1 (HIV-1)-derived lentiviral vectors (LVs) but requires high viral doses to bypass their natural resistance to viral infection, and this in turn affects their physiological properties. To date, a single viral protein is able to counter this restrictive phenotype, Vpx, a protein derived from members of the HIV-2/simian immunodeficiency virus SM lineage that counters at least two restriction factors present in myeloid cells. By tagging Vpx with a short heterologous membrane-targeting domain, we have obtained HIV-1 LVs incorporating high levels of this protein (HIV-1-Src-Vpx). These vectors efficiently transduce differentiated MDDCs and monocytes either as previously purified populations or as populations within unsorted peripheral blood mononuclear cells (PBMCs). In addition, these vectors can be efficiently pseudotyped with receptor-specific envelopes, further restricting their cellular tropism almost uniquely to MDDCs. Compared to conventional HIV-1 LVs, these novel vectors allow for an efficient genetic modification of MDDCs and, more importantly, do not cause their maturation or affect their survival, which are unwanted side effects of the transduction process. This study describes HIV-1-Src-Vpx LVs as a novel potent tool for the genetic modification of differentiated MDDCs and of circulating monocyte precursors with strong potential for a wide range of gene therapy applications.
The experimental use of antisense oligonucleotides: a guide for the perplexed (2001)

Antisense oligonucleotide biotechnology, at least in theory, provides a specific, rapid, and potentially high-throughput method for inhibiting gene expression and exploring gene function. Over the past decade, a plethora of experiments has been submitted, and a lesser number published, employing this approach to inhibiting gene expression at the mRNA level. The specificity of the antisense approach stems, of course, from the specificity (or, the “information content”) of the Watson-Crick base pair interaction.

The fact that antisense oligonucleotides carry significant information in addition to that denoted by their nucleotide sequences is frequently overlooked. This oversight has frequently led to the lack of rigorous controls for many antisense experiments, and, on all too many occasions, to the inappropriate interpretation of experimental data (1). Indeed, serious questions have arisen as to whether an observed biological effect in an antisense experiment has indeed been produced by an antisense mechanism, or whether it is due to a complex combination of non–sequence specific effects. Investigators must therefore understand how to employ antisense technology properly and should recognize its limitations.
Defocus transfer function for circularly symmetric pupils (1997)

We present a two-dimensional function that graphically illustrates the effects of defocus on the optical transfer function (OTF) associated with a circularly symmetric pupil function. We call it the defocus transfer function (DTF). The function is similar in application to the ambiguity function, which can be used to display the OTF associated with a defocused rectangularly separable pupil function. The properties of the DTF make it useful for analyzing optical systems with circularly symmetric pupils when one is interested in the OTF as a function of defocus. In addition to presenting these properties, we give examples of the DTF for systems with clear, bifocal, and annular pupil functions.
Artificial Niche Combining Elastomeric Substrate and Platelets Guides Vascular Differentiation of Bone Marrow Mononuclear Cells (2011)

Bone marrow-derived progenitor cells are promising cell sources for vascular tissue engineering. However, conventional bone marrow mesenchymal stem cell expansion and induction strategies require plating on tissue culture plastic, a stiff substrate that may itself influence cell differentiation. Direct scaffold seeding avoids plating on plastic; to the best of our knowledge, there is no report of any scaffold that induces the differentiation of bone marrow mononuclear cells (BMNCs) to vascular cells in vitro. In this study, we hypothesize that an elastomeric scaffold with adsorbed plasma proteins and platelets will induce differentiation of BMNCs to vascular cells and promote vascular tissue formation by combining soft tissue mechanical properties with platelet-mediated tissue repairing signals. To test our hypothesis, we directly seeded rat primary BMNCs in four types of scaffolds: poly(lactide-co-glycolide), elastomeric poly(glycerol sebacate) (PGS), platelet-poor plasma-coated PGS, and PGS coated by plasma supplemented with platelets. After 21 days of culture, osteochondral differentiation of cells in poly(lactide-co-glycolide) was detected, but most of the adhered cells on the surface of all PGS scaffolds expressed calponin-I and α-smooth muscle actin, suggesting smooth muscle differentiation. Cells in PGS scaffolds also produced significant amount of collagen and elastin. Further, plasma coating improves seeding efficiency, and platelet increases proliferation, the number of differentiated cells, and extracellular matrix content. Thus, the artificial niche composed of platelets, plasma, and PGS is promising for artery tissue engineering using BMNCs.
Towards a simple and accurate statistical approach to learning translation relationships among words (2001)

We report on a project to derive word translation relationships automatically from parallel corpora. Our effort is distinguished by the use of simpler, faster models than those used in previous high-accuracy approaches. Our methods achieve accuracy on single-word translations that seems comparable to any work previously reported, up to nearly 60% coverage of word types, and they perform particularly well on a class of multi-word compounds of special interest to our translation effort.
A peptide inhibitor of HIV‐1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120 (2008)

MAb 2G12 neutralizes HIV-1 by binding with high affinity to a cluster of high-mannose oligosaccharides on the envelope glycoprotein, gp120. Screening of phage-displayed peptide libraries with 2G12 identified peptides that bind specifically, with K(d)s ranging from 0.4 to 200 microM. The crystal structure of a 21-mer peptide ligand in complex with 2G12 Fab was determined at 2.8 A resolution. Comparison of this structure with previous structures of 2G12-carbohydrate complexes revealed striking differences in the mechanism of 2G12 binding to peptide vs. carbohydrate. The peptide occupies a site different from, but adjacent to, the primary carbohydrate-binding site on 2G12, and makes only slightly fewer contacts to the Fab than Man(9)GlcNAc(2) (51 vs. 56, respectively). However, only two antibody contacts with the peptide are hydrogen bonds in contrast to six with Man(9)GlcNAc(2), and only three of the antibody residues that interact with Man(9)GlcNAc(2) also contact the peptide. Thus, this mechanism of peptide binding to 2G12 does not support structural mimicry of the native carbohydrate epitope on gp120, since it neither replicates the oligosaccharide footprint on the antibody nor most of the contact residues. Moreover, 2G12.1 peptide is not an immunogenic mimic of the 2G12 epitope, since antisera produced against it did not bind gp120.
Molecular basis for some physical properties of alginates in the gel state (1974)

Alginate is a binary linear heteropolymer containing 1,4-linked β-D-mannuronic and α-L-guluronic acid residues in varying proportions. The monomers are arranged in a blockwise fashion along the chain; it contains the two homopolymeric blocks (MM and GG) together with blocks of the alternating sequence (MG) in the same molecule. Data from light scattering and viscometric experiments show that their relative unperturbed dimensions increase in the order: MG-blocks < MM-blocks < GG-blocks. Ion exchange data show that GG-blocks are characterized by a selective binding of calcium ions in solution, a strong autocooperative binding of calcium between the chains in the gel state, and hystrisis due to a slow dissociation of the cooperatively-formed functions between the chains. The two other blocks have much lower selectivity for calcium ions, no autocooperative binding mechanism and no detectable hysteresis. The mechanical strength of calcium alginate gels is mainly due to junctions formed by the GG-blocks. the modulus of rigidity of gels formed by different cations is directly dependent on their ability to bind to the polyuronides by a cooperative inter-chain binding mechanism.
Macrophage colony-stimulating factor mediates invasion of ovarian cancer cells through urokinase. (1995)

The macrophage colony-stimulating factor (CSF-1) is best known as a hematopoietic cytokine important to macrophage activation. Recently, the importance of CSF-1 and its receptor (encoded by the c-fms proto-oncogene) in epithelial ovarian cancer has also been recognized, with overexpression of CSF-1 denoting poor prognosis in ovarian cancer patients. During macrophage activation, CSF-1 promotes urokinase-type plasminogen activator (uPA) activity; in macrophages and in malignant cells of lung, breast, colon, and prostatic origin, uPA activity is strongly correlated with the ability to invade and, in the malignant cells, to metastasize. While there is clear evidence of CSF-1 and uPA expression in primary and metastatic ovarian cancer, the significance of their expression to invasion of these cells has not been explored. We find that all of our ovarian cancer cell lines which we have studied co-express CSF-1 and uPA transcripts and protein. Urokinase expression in these ovarian cancer cell lines correlates with the degree of tumorigenicity in nude mice, with the most virulent tumor resulting from Hey cells, a strong expressor of uPA. We studied the invasion of these primary and established ovarian cancer cells through a Matrigel (reconstituted basement membrane matrix) barrier. The ability of ovarian cancer cells to invade is strongly correlated with endogenous CSF-1 expression (Pearson's correlation, r = 0.91; P = 0.01). A total of 0.90 +/- 0.16% of Bix3 cells (very weak expressor of CSF-1) invaded through the barrier, in contrast to 6.95 +/- 0.75% of Hey cells (strong CSF-1 expressor) and 10.44 +/- 2.33% of Bixler cells (the strongest CSF-1 expressor). We studied the ability of two of the cell lines to invade human laminin and type IV collagen (Bix3, a weak invader of Matrigel, and Hey, a strong invader), to determine (a) whether our results on a Matrigel matrix may represent a relevant model for invasion in humans and (b) whether there is a potential confounding effect from the cytokines and proteases in Matrigel. On this human simple matrix, we confirm that Bix3 is a weakly invasive cell line (0.33 +/- 0.04% invasion) which contrasted to the strongly invasive Hey cell line (8.51 +/- 0.47%). Treatment of Bix3 cells with exogenous CSF-1 stimulates percentage of invasion by 2-fold and results in a similar increase in the level of uPA transcripts and cellular associated uPA antigen. Furthermore, cell surface-bound uPA increased from 74% in the absence of CSF-1 to 100% (fully saturated) in the presence of CSF-1.(ABSTRACT TRUNCATED AT 400 WORDS)
Centralized channel assignment and routing algorithms for multi-channel wireless mesh networks (2004)

The IEEE 802.11 Wireless LAN standards allow multiple non-overlapping frequency channels to be used simultaneously to increase the aggregate bandwidth available to end-users. Such bandwidth aggregation capability is routinely used in infrastructure mode operation, where the traffic to and from wireless nodes is distributed among multiple interfaces of an access point or among multiple access points to balance the traffic load. However, bandwidth aggregation is rarely used in the context of multi-hop 802.11-based LANs that operate in the ad hoc mode. Most past research efforts that attempt to exploit multiple radio channels require modifications to the MAC protocol and therefore do not work with commodity 802.11 interface hardware. In this paper, we propose and evaluate one of the first multi-channel multi-hop wireless ad-hoc network architectures that can be built using standard 802.11 hardware by equipping each node with multiple network interface cards (NICs) operating on different channels. We focus our attention on wireless mesh networks that serve as the backbone for relaying end-user traffic from wireless access points to the wired network. The idea of exploiting multiple channels is particularly appealing in wireless mesh networks because of their high capacity requirements to support backbone traffic. To reap the full performance potential of this architecture, we develop a set of centralized channel assignment, bandwidth allocation, and routing algorithms for multi-channel wireless mesh networks. A detailed performance evaluation shows that with intelligent channel and bandwidth assignment, equipping every wireless mesh network node with just 2 NICs operating on different channels can increase the total network goodput by a factor of up to 8 compared with the conventional single-channel ad hoc network architecture.
Amelioration of Sardinian 0 thalassemia by genetic modifiers (2009)

Sardinian beta-thalassemia patients all are homozygotes for the same null allele in the beta-globin gene, but the clinical manifestations are extremely variable in severity. Previous studies have shown that the coinheritance of alpha-thalassemia or the presence of genetic variants that sustain fetal hemoglobin production has a strong impact on ameliorating the clinical phenotype. Here we evaluate the contribution of variants in the BCL11A, and HBS1L-MYB genes, implicated in the regulation of fetal hemoglobin, and of alpha-thalassemia coinheritance in 50 thalassemia intermedia and 75 thalassemia major patients. We confirm that alpha-thalassemia and allele C of single nucleotide polymorphism rs-11886868 in BCL11A were selectively represented in thalassemia intermedia patients. Moreover, allele G at single nucleotide polymorphism rs9389268 in the HBS1L-MYB locus was significantly more frequent in the thalassemia intermedia patients. This trio of genetic factors can account for 75% of the variation differences in phenotype severity.
S100P-Derived RAGE Antagonistic Peptide Reduces Tumor Growth and Metastasis (2012)

RAP shows promise as a tool for the investigation of RAGE function and as an in vivo treatment for RAGE-related disorders.
An efficient architecture for adaptive deblocking filter of H.264/AVC video coding (2004)

This paper proposes an efficient hardware architecture to accelerate adaptive deblocking filter of H.264/A VC video coding. Compact data access unit, line-of-pixel (LOP) is defined in this paper. Line-of-pixel and build-in data buffer are employed to simplify data exchange between deblocking filter and outside data memory. Edge filter, which is designed to process each group of pixels on both sides of one edge, is kernel of deblocking filter. It is implemented in multiple parallel pipelines to increase efficiency. By carefully design, the proposed deblocking filter can be embedded in general-purpose processor or DSP to support special instructions for acceleration of software codec. This filter also can be used to full hardware H. 264/A VC codec.
A glioma-derived analog to platelet-derived growth factor: demonstration of receptor competing activity and immunological crossreactivity. (1984)

A human clonal glioma cell line, U-343 MGa Cl 2, cultured under serum-free conditions, was found to release a factor that competed with 125I-labeled platelet-derived growth factor (125I-PDGF) for binding to human foreskin fibroblasts. The concentration of competing activity in conditioned medium was equal to 20-30 ng of PDGF per ml. The PDGF receptor competing activity had an elution position on Sephadex G-200 close to that of tracer PDGF. The same fractions in the chromatogram also contained growth-promoting activity and material active in a PDGF radioimmunoassay. Incubation of partially purified, 125I-labeled glioma factor with fibroblasts, or rabbit anti-PDGF serum, led to the selective binding of a component with an estimated Mr of 31,000, as shown by NaDodSO4/gel electrophoresis under nonreducing conditions. After reduction this component migrated as a Mr 18,000 protein. Thus, the behavior in NaDodSO4/gel electrophoresis was similar to that of PDGF. Furthermore, incubation of partially purified glioma factor with immobilized PDGF antibodies markedly decreased the amount of PDGF receptor competing activity remaining in the supernatant. These results suggest that the factor produced by glioma cells has structural, immunological, and functional resemblance to PDGF. We previously reported that a human osteosarcoma cell line produces a PDGF-like molecule with growth-promoting activity. Taken together with the recent finding that PDGF is homologous to the transforming gene product of simian sarcoma virus, our present data give additional support for the idea that an autocrine activation of the PDGF receptor may be operational in the growth of human tumors of mesenchymal or glial origin.