gebhart/patrepeval huggingface dataset:
Biomass Feedstock Pre-Processing – Part 2: Densification (2011)

Introduction 1.1 The need for densificationAgricultural biomass residues have the potential for the sustainable production of bio-fuels and to offset greenhouse gas emissions (Campbell et al., 2002;Sokhansanj et al., 2006).Straw from crop production and agricultural residues existing in the waste streams from commercial crop processing plants have little inherent value and have traditionally constituted a disposal problem.In fact, these residues represent an abundant, inexpensive and readily available source of renewable lignocellulosic biomass (Liu et al., 2005).New methodologies need to be developed to process the biomass making it suitable feedstock for bio-fuel production.In addition, some of the barriers in the economic use of agricultural crop residue are the variable quality of the residue, the cost of collection, and problems in transportation and storage (Bowyer and Stockmann, 2001;Sokhansanj et al., 2006).In order to reduce industry's operational cost as well as to meet the requirement of raw material for biofuel production, biomass must be processed and handled in an efficient manner.Due to its high moisture content, irregular shape and size, and low bulk density, biomass is very difficult to handle, transport, store, and utilize in its original form (Sokhansanj et al., 2005).Densification of biomass into durable compacts is an effective solution to these problems and it can reduce material waste.Densification can increase the bulk density of biomass from an initial bulk density of 40-200 kg/m 3 to a final compact density of 600-1200 kg/m 3 (Adapa et al., 2007;Holley, 1983;Mani et al., 2003;McMullen et al., 2005;Obernberger and Thek, 2004).Biomass can be compressed and stabilized to 7-10 times densities of the standard bales by the application of pressures between 400-800 MPa during the densification process (Demirbas and Sahin, 1998).Because of their uniform shape and size, densified products may be easily handled using standard handling and storage equipment, and they can be easily adopted in direct-combustion or co-firing with coal, gasification, pyrolysis, and utilized in other biomass-based conversions (Kaliyan and Morey, 2006a) such as biochemical processes.Upon densification, many agricultural biomass materials, especially those from straw and stover, result in a poorly formed pellets or compacts that are more often dusty, difficult to handle and costly to manufacture.This is caused by lack of complete understanding on the natural binding characteristics of the components that make up biomass (Sokhansanj et al., 2005).
Silsesquioxanes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSilsesquioxanesRonald H. Baney, Maki Itoh, Akihito Sakakibara, and Toshio SuzukiCite this: Chem. Rev. 1995, 95, 5, 1409–1430Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://doi.org/10.1021/cr00037a012Request reuse permissionsArticle Views8159Altmetric-Citations1396LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (5 MB) Get e-Alertsclose Get e-Alerts
Identification of a Glutamic Acid and an Aspartic Acid Residue Essential for Catalytic Activity of Aspergillopepsin II, a Non-pepsin Type Acid Proteinase (2000)

Aspergillopepsin II from Aspergillus niger var. macrosporus is a non-pepsin type or pepstatin-insensitive acid proteinase. To identify the catalytic residues of the enzyme, all acidic residues that are conserved in the homologous proteinases of family A4 were replaced with Asn, Gln, or Ala using site-directed mutagenesis. The wild-type and mutant pro-enzymes were heterologously expressed in Escherichia coli and refolded in vitro. The wild-type pro-enzyme was shown to be processed into a two-chain active enzyme under acidic conditions. Most of the recombinant mutant pro-enzymes showed significant activity under acidic conditions because of autocatalytic activation except for the D123N, D123A, E219Q, and E219A mutants. The D123A, E219Q, and E219A mutants showed neither enzymatic activity nor autoprocessing activity under acidic conditions. The circular dichroism spectra of the mutant pro- and mature enzymes were essentially the same as those of the wild-type pro- and mature enzyme, respectively, indicating that the mutant pro-enzymes were correctly folded. In addition, two single and one double mutant pro-enzyme, D123E, E219D, and D123E/E219D, did not show enzymatic activity under acidic conditions. Taken together, Glu-219 and Asp-123 are deduced to be the catalytic residues of aspergillopepsin II.
Localization of the Vpx packaging signal within the C terminus of the human immunodeficiency virus type 2 Gag precursor protein (1994)

Viral protein X (Vpx) is a human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency virus accessory protein that is packaged into virions in molar amounts equivalent to Gag proteins. To delineate the processes of virus assembly that mediate Vpx packaging, we used a recombinant vaccinia virus-T7 RNA polymerase system to facilitate Gag protein expression, particle assembly, and extracellular release. HIV genes were placed under control of the bacteriophage T7 promoter and transfected into HeLa cells expressing T7 RNA polymerase. Western immunoblot analysis detected p55gag and its cleavage products p39 and p27 in purified particles derived by expression of gag and gag-pol, respectively. In trans expression of vpx with either HIV-2 gag or gag-pol gave rise to virus-like particles that contained Vpx in amounts similar to that detected in HIV-2 virus produced from productively infected T cells. Using C-terminal deletion and truncation mutants of HIV-2 Gag, we mapped the p15 coding sequence for determinants of Vpx packaging. This analysis revealed a region (residues 439 to 497) downstream of the nucleocapsid protein (NC) required for incorporation of Vpx into virions. HIV-1/HIV-2 gag chimeras were constructed to further characterize the requirements for incorporation of Vpx into virions. Chimeric HIV-1/HIV-2 Gag particles consisting of HIV-1 p17 and p24 fused in frame at the C terminus with HIV-2 p15 effectively incorporate Vpx, while chimeric HIV-2/HIV-1 Gag particles consisting of HIV-2 p17 and p27 fused in frame at the C terminus with HIV-1 p15 do not. Expression of a 68-amino-acid sequence of HIV-2 containing residues 439 to 497 fused to the coding regions of HIV-1 p17 and p24 also produced virus-like particles capable of packaging Vpx in amounts similar to that of full-length HIV-2 Gag. Sucrose gradient analysis confirmed particle association of Vpx and Gag proteins. These results demonstrate that the HIV-2 Gag precursor (p55) regulates incorporation of Vpx into virions and indicates that the packaging signal is located within residues 439 to 497.
NMR Studies of Mass Transport in High-Acid-Content Fuel Cell Membranes Based on Phosphoric Acid and Polybenzimidazole (2007)

Mass-transport studies of phosphoric acid (PA)-doped meta-polybenzimidazole (PBI) fuel cell membranes are described. In this study, the fundamental differences in transport properties between -PBI/PA membranes prepared by conventional imbibing procedures and the polyphosphoric acid (PPA) process are explored. The membranes were characterized by proton conductivity and multinuclear ( and ) magnetic resonance measurements. Both short-range and long-range dynamical processes were investigated by spin–lattice and spin–spin relaxation time measurements and by pulsed field gradient diffusion, respectively. Comparative data for pure PA and PPA are included. The high proton conductivity ( at ) of the PPA-processed membranes is correlated with rapid proton self-diffusion ( at ). The results reveal the presence of both PA and the dimeric pyrophosphoric acid and indicate strong interaction between the phosphate groups and the -PBI matrix, with negligible anionic transport for both kinds of membranes. The higher concentration of PA in the PPA-processed membranes and differences in membrane morphology may provide an additional proton-transport mechanism involving rapid exchange between the PA and pyrophosphoric acid species.
Characterization of the substrate specificity of the major cysteine protease (cruzipain) from Trypanosoma cruzi using a portion-mixing combinatorial library and fluorogenic peptides (1997)

The substrate specificity of the major cysteinyl proteinase of the parasitic protozoan Trypanosoma cruzi (cruzipain) was investigated, by combinatorial replacement of amino acid residues at positions P5-P'5, using a fluorescent quenched solid-phase library assay. Positively charged residues appear to be a general preference in the P5-P3 and the P'5-P'3 positions, while a hydrophobic residue was always required at the P2 position. A broad range of amino acids could be accepted at the P'1 position. A clear difference in terms of specificity between cruzipain and human cathepsin L was observed for the accommodation of Pro at the P2 position. The P1 specificity was investigated by a more detailed enzyme kinetic analysis using peptidyl-MCA (where MCA is methylcoumarin amide) and Abz-peptidyl-EDDnp [where Abz is o-aminobenzoic acid and EDDnp is N-(2,4-dinitrophenyl)ethylenediamine] as substrates, and the results were compared with those obtained using human cathepsin L. Cruzipain showed a clear preference for benzyl-Cys or Arg at the P1 position. Human cathepsin L presented similar behaviour to that of cruzipain for the hydrolysis of the epsilon-NH2-Cap-Leu-Xaa-MCA (where Cap is epsilon-aminocaproyl) and Abz-Lys-Leu-Xaa-Phe-Ser-Lys-Gln-EDDnp series, whereas the mammalian enzyme was able to tolerate large P1 residues, such as phenylalanine, better than cruzipain in the latter series.
Monoclonal antibody covalently coupled to liposomes: Specific targeting to cells (1981)

We have evaluated optimal conditions for coupling monoclonal antibody to small unilamellar liposomes. Coupling of an IgG2 alpha monoclonal anti-beta 2-microglobulin antibody, which reacts with human cells, was examined in detail. Liposomes were composed of dipalmitoyl lecithin and cholesterol, and variable quantities of phosphatidylethanolamine substituted with the heterobifunctional cross-linking reagent N-hydroxysuccinimidyl 3-(2-pyridyldithio) propionate (SPDP). They were reacted with antibody derivatized with the same reagent at a 5- to 20-fold molar excess, and activated by mild reduction. This degree of SPDP modification had no effect on the capacity of the antibody to bind to its target antigen. More than 40% of antibody could be reproducibly bound to liposomes, resulting in the coupling of from 1 to 10 antibody molecules per liposome (mean diameter:580 A). The coupling reaction did not lead to loss of carboxyfluorescein encapsulated within liposomes. At least 80% of liposomes carried nondenatured antibody, as confirmed by precipitation of liposomes and encapsulated carboxyfluorescein by Staphylococcus aureus, strain Cowan I. The liposome-coupled antibody retained its immunological specificity: only cells expressing human beta 2-microglobulin bound liposomes in vitro, and the binding was inhibited by the free antibody in solution. Results with antibodies of different antigens specificity confirm that the technique can be generally applied.
Long-Term Expansion and Pluripotent Marker Array Analysis of Wharton’s Jelly-Derived Mesenchymal Stem Cells (2009)

Mesenchymal stem cells (MSCs) with their multilineage developmental plasticity comprise a promising tool for regenerative cell-based therapy. Despite important biological properties, which the MSCs from different sources share, the differences between them are poorly understood. Hence, it is required to assign a molecular signature to each of these MSC populations, based on stem cell related genes and early lineage or developmental markers. Understanding their propensity to differentiate to different lineages is fundamental for the development of successful cell-based therapies. Culture expansion of MSCs is a prerequisite, since high absolute numbers of stem cells are required to attain a clinical dose. Here, we compared the different culture conditions for long-term expansion of human MSCs isolated from the Wharton's jelly (WJ) of the umbilical cord while preserving their stem cell characteristics and differentiation potential. We find that DMEM-KO and DMEM-F12 are superior as compared to the other media tested in supporting the in vitro expansion of the WJ-MSCs. We studied the gene expression profile of WJ and bone marrow-derived MSCs (BM-MSCs) both at early and late passages using Human Stem Cell Pluripotency Array, and our data revealed differences at the transcriptional level between the two MSC types. Compared to BM-MSCs, WJ-MSCs had higher expression of undifferentiated human embryonic stem cell (hES) markers like NANOG, DNMT3B, and GABRB3, pluripotent/stem cell markers, as well as some early endodermal markers both at early and late passages. To conclude, WJ-MSCs possess properties of true stem cells, which they retain even after extended in vitro culturing.
Direct Quantification of Cell-Free, Circulating DNA from Unpurified Plasma (2014)

Cell-free DNA (cfDNA) in body tissues or fluids is extensively investigated in clinical medicine and other research fields. In this article we provide a direct quantitative real-time PCR (qPCR) as a sensitive tool for the measurement of cfDNA from plasma without previous DNA extraction, which is known to be accompanied by a reduction of DNA yield. The primer sets were designed to amplify a 90 and 222 bp multi-locus L1PA2 sequence. In the first module, cfDNA concentrations in unpurified plasma were compared to cfDNA concentrations in the eluate and the flow-through of the QIAamp DNA Blood Mini Kit and in the eluate of a phenol-chloroform isoamyl (PCI) based DNA extraction, to elucidate the DNA losses during extraction. The analyses revealed 2.79-fold higher cfDNA concentrations in unpurified plasma compared to the eluate of the QIAamp DNA Blood Mini Kit, while 36.7% of the total cfDNA were found in the flow-through. The PCI procedure only performed well on samples with high cfDNA concentrations, showing 87.4% of the concentrations measured in plasma. The DNA integrity strongly depended on the sample treatment. Further qualitative analyses indicated differing fractions of cfDNA fragment lengths in the eluate of both extraction methods. In the second module, cfDNA concentrations in the plasma of 74 coronary heart disease patients were compared to cfDNA concentrations of 74 healthy controls, using the direct L1PA2 qPCR for cfDNA quantification. The patient collective showed significantly higher cfDNA levels (mean (SD) 20.1 (23.8) ng/ml; range 5.1-183.0 ng/ml) compared to the healthy controls (9.7 (4.2) ng/ml; range 1.6-23.7 ng/ml). With our direct qPCR, we recommend a simple, economic and sensitive procedure for the quantification of cfDNA concentrations from plasma that might find broad applicability, if cfDNA became an established marker in the assessment of pathophysiological conditions.
Information Exchange in Wireless Networks with Network Coding and Physical-layer Broadcast (2004)

Abstract — The exchange of independent information between two nodes in a wireless network can be viewed as two unicast sessions, corresponding to information transfer along one direction and the opposite direction. In this paper we show such information exchange can be efficiently performed by exploiting network coding and the physical-layer broadcast property offered by the wireless medium, which improves upon conventional solutions that separate the processing of the two unicast sessions. We propose a distributed scheme that obviates the need for synchronization and is robust to random packet loss and delay, and so on. The scheme is simple and incurs minor overhead. I.
Forward masking as a function of frequency, masker level, and signal delay (1982)

The forward masking of a sinusoidal signal by a sinusoid of the same frequency was investigated for frequencies ranging from 125 to 4000 Hz. Forward masking in dB is proportional to both masker level and log signal delay at each frequency. More forward masking occurs at very low frequencies than at high frequencies, given equal-sensation-level maskers, and masked thresholds are greater at low frequencies than at high frequencies given equal-SPL maskers. The data can be described equally well by assuming that the difference in forward masking as a function of frequency is due to a change in the time course of recovery from masking or to a change in the growth of masking at each signal delay. The frequency effect is not large enough to change the interpretation of forward-masking data in studies of suppression or psychophysical tuning curves.
Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease (2004)

The term 'genomic disorder' refers to a disease that is caused by an alteration of the genome that results in complete loss, gain or disruption of the structural integrity of a dosage sensitive gene(s). In most of the common chromosome deletion/duplication syndromes, the rearranged genomic segments are flanked by large (usually >10 kb), highly homologous low copy repeat (LCR) structures that can act as recombination substrates. Recombination between non-allelic LCR copies, also known as non-allelic homologous recombination, can result in deletion or duplication of the intervening segment. Recent findings suggest that other chromosomal rearrangements, including reciprocal, Robertsonian and jumping translocations, inversions, isochromosomes and small marker chromosomes, may also involve susceptibility to rearrangement related to genome structure or architecture. In several cases, LCRs, AT-rich palindromes and pericentromeric repeats are located at such rearrangement breakpoints. Analysis of the products of recombination at the junctions of the rearrangements reveals both homologous recombination and non-homologous end joining as causative mechanisms. Thus, a more global concept of genomic disorders emerges in which susceptibility to rearrangements occurs due to underlying complex genomic architecture. Interestingly, this architecture plays a role not only in disease etiology, but also in primate genome evolution. In this review, we discuss recent advances regarding general mechanisms for the various rearrangements of our genome, and potential models for rearrangements with non-homologous breakpoint regions.
Antiviral Activity and Intracellular Metabolism of Bis(tButylSATE) Phosphotriester of β-L-2′,3'Dideoxyadenosine, a Potent Inhibitor of HIV and HBV Replication (2001)

The beta-L-nucleoside analogue beta-L-2',3'-dideoxy adenosine (beta-L-ddA) has been shown to exhibit limited antiviral activities. This was attributed to its rapid catabolism through cleavage of the glycosidic bond and poor phosphorylation to the nucleotide beta-L-2',3'-dideoxyadenosine-5'-mono phosphate (beta-L-ddAMP) (Placidi et al., 2000). However, the nucleotide beta-L-2',3'-dideoxyadenosine-5'-triphosphate (beta-L-ddATP) inhibited the activity of both HIV-1 reverse transcriptase (RT) and viral DNA polymerase isolated from woodchuck hepatitis virus-infected serum (a model of hepatitis B) with an inhibitory concentration (IC50) of 2.0 microM without inhibiting human DNA polymerases alpha, beta, or gamma up to a concentration of 100 microM. These results suggested that prodrugs of beta-L-ddAMP may bypass the poor metabolic activation of beta-L-ddA and lead to more potent and selective antiviral activity. Therefore, the mononucleoside phosphotriester derivative of beta-L-ddAMP incorporating the S-pivaloyl-2-thioethyl (tButylSATE) groups, beta-L-ddAMP-bis(tButylSATE) was synthesized. Beta-L-ddAMP-bis(tButylSATE) inhibited HIV replication in human peripheral blood mononuclear cells (PBMCs) and HBV replication in 2.2.15 cells with effective concentrations (EC50s) of 2 and 80 nM, respectively. Intracellular metabolism of beta-L-ddAMP-bis(tButylSATE) demonstrated that beta-L-ddATP was the predominant intracellular metabolite in PBMC and liver cells. The intracellular half-life of beta-L-ddATP was 5.4 and 9.2 h in HepG2 and PBMCs, respectively. The intracellular concentrations of beta-L-ddATP were maintained above the EC50 for the inhibition of HIV RT and hepatitis B virus (HBV) for as long as 24 h after removal of the drug.
The SARS Coronavirus S Glycoprotein Receptor Binding Domain: Fine Mapping and Functional Characterization (2005)

The entry of the SARS coronavirus (SCV) into cells is initiated by binding of its spike envelope glycoprotein (S) to a receptor, ACE2. We and others identified the receptor-binding domain (RBD) by using S fragments of various lengths but all including the amino acid residue 318 and two other potential glycosylation sites. To further characterize the role of glycosylation and identify residues important for its function as an interacting partner of ACE2, we have cloned, expressed and characterized various soluble fragments of S containing RBD, and mutated all potential glycosylation sites and 32 other residues. The shortest of these fragments still able to bind the receptor ACE2 did not include residue 318 (which is a potential glycosylation site), but started at residue 319, and has only two potential glycosylation sites (residues 330 and 357). Mutation of each of these sites to either alanine or glutamine, as well as mutation of residue 318 to alanine in longer fragments resulted in the same decrease of molecular weight (by approximately 3 kDa) suggesting that all glycosylation sites are functional. Simultaneous mutation of all glycosylation sites resulted in lack of expression suggesting that at least one glycosylation site (any of the three) is required for expression. Glycosylation did not affect binding to ACE2. Alanine scanning mutagenesis of the fragment S319-518 resulted in the identification of ten residues (K390, R426, D429, T431, I455, N473, F483, Q492, Y494, R495) that significantly reduced binding to ACE2, and one residue (D393) that appears to increase binding. Mutation of residue T431 reduced binding by about 2-fold, and mutation of the other eight residues--by more than 10-fold. Analysis of these data and the mapping of these mutations on the recently determined crystal structure of a fragment containing the RBD complexed to ACE2 (Li, F, Li, W, Farzan, M, and Harrison, S. C., submitted) suggested the existence of two hot spots on the S RBD surface, R426 and N473, which are likely to contribute significant portion of the binding energy. The finding that most of the mutations (23 out of 34 including glycosylation sites) do not affect the RBD binding function indicates possible mechanisms for evasion of immune responses.
Reaction between Lithium Anode and Polysulfide Ions in a Lithium–Sulfur Battery (2016)

The reaction between polysulfides and a lithium anode in a Li-S battery was examined using HPLC. The results demonstrated that the polysulfide species with six sulfur atoms or more were reactive with regard to lithium metal. Although the reaction can be greatly inhibited by the addition of LiNO3 in the electrolyte, LiNO3 cannot form a stable protection layer on the Li anode to prevent the reaction during storage.