gebhart/patrepeval huggingface dataset:
Sparse Phase Retrieval from Short-Time Fourier Measurements (2014)

We consider the classical 1D phase retrieval problem. In order to overcome the difficulties associated with phase retrieval from measurements of the Fourier magnitude, we treat recovery from the magnitude of the short-time Fourier transform (STFT). We first show that the redundancy offered by the STFT enables unique recovery for arbitrary nonvanishing inputs, under mild conditions. An efficient algorithm for recovery of a sparse input from the STFT magnitude is then suggested, based on an adaptation of the recently proposed GESPAR algorithm. We demonstrate through simulations that using the STFT leads to improved performance over recovery from the oversampled Fourier magnitude with the same number of measurements.
Net charge per residue modulates conformational ensembles of intrinsically disordered proteins (2010)

Intrinsically disordered proteins (IDPs) adopt heterogeneous ensembles of conformations under physiological conditions. Understanding the relationship between amino acid sequence and conformational ensembles of IDPs can help clarify the role of disorder in physiological function. Recent studies revealed that polar IDPs favor collapsed ensembles in water despite the absence of hydrophobic groups--a result that holds for polypeptide backbones as well. By studying highly charged polypeptides, a different archetype of IDPs, we assess how charge content modulates the intrinsic preference of polypeptide backbones for collapsed structures. We characterized conformational ensembles for a set of protamines in aqueous milieus using molecular simulations and fluorescence measurements. Protamines are arginine-rich IDPs involved in the condensation of chromatin during spermatogenesis. Simulations based on the ABSINTH implicit solvation model predict the existence of a globule-to-coil transition, with net charge per residue serving as the discriminating order parameter. The transition is supported by quantitative agreement between simulation and experiment. Local conformational preferences partially explain the observed trends of polymeric properties. Our results lead to the proposal of a schematic protein phase diagram that should enable prediction of polymeric attributes for IDP conformational ensembles using easily calculated physicochemical properties of amino acid sequences. Although sequence composition allows the prediction of polymeric properties, interresidue contact preferences of protamines with similar polymeric attributes suggest that certain details of conformational ensembles depend on the sequence. This provides a plausible mechanism for specificity in the functions of IDPs.
Comparison of principal modes and spatial eigenmodes in multimode optical fibre (2016)

Abstract Optical waveguide theory is an established part of optical physics. Yet only recently have fundamental phenomena such as spatial eigenmodes and principal modes been demonstrated experimentally. This work leverages recently developed techniques enabling detailed spatiotemporal characterisation of multimode fibre to provide new insights into the fundamentals of fibre propagation. This paper presents detailed analysis of all 420 of a fibre's principal modes and spatial eigenmodes and compares the similarity and differences between these two phenomena. It was found that even over very short lengths, the principal modes can not only significantly suppress modal dispersion but are also a more physically meaningful basis than spatial eigenmodes. image
Viral induction of the human beta interferon promoter: modulation of transcription by NF-kappa B/rel proteins and interferon regulatory factors (1994)

Multiple regulatory domains within the -100 region of the beta interferon (IFN-beta) promoter control the inducible response of the IFN gene to virus infection. In this study, we demonstrate that the formation of NF-kappa B-specific complexes on the positive regulatory domain II (PRDII) precedes the onset of detectable IFN-beta transcription in Sendai virus-infected cells. By using NF-kappa B subunit-specific antibodies, a temporal shift in the composition of NF-kappa B subunits in association with the PRDII domain is detected as a function of time after virus infection. Furthermore, a virus-induced degradation of I kappa B alpha (MAD3) protein is observed between 2 and 8 h after infection; at later times, de novo synthesis of I kappa B alpha restores I kappa B alpha to levels found in uninduced cells and correlates with the down regulation of IFN-beta transcription. In cotransfection experiments using various NF-kappa B subunit expression plasmids and two copies of PRDII/NF-kappa B linked to a chloramphenicol acetyltransferase reporter gene, we demonstrate that expression of p65, c-Rel, or p50 or combinations of p50-p65 and p65-c-Rel differentially stimulated PRDII-dependent transcription. Coexpression of I kappa B alpha completely abrogated p65-, c-Rel-, or p65-p50-induced gene activity. When the entire IFN-beta promoter (-281 to +19) was used in coexpression studies, synergistic stimulation of IFN-beta promoter activity was obtained when NF-kappa B subunits were coexpressed together with the IFN regulatory factor 1 (IRF-1) transcription factor. Overexpression of either I kappa B or the IRF-2 repressor was able to abrogate inducibility of the IFN-beta promoter. Thus, multiple regulatory events--including differential activation of DNA-binding NF-kappa B heterodimers, degradation of I kappa B alpha, synergistic interaction between IRF-1 and NF-kappa B, and decreased repression by I kappa B and IRF-2--are all required for the transcriptional activation of the IFN-beta promoter.
Digital television broadcasting with high spectral efficiency (modern design) (1992)

The use of digital modulation for the distribution of TV over the existing UHF/VHF terrestrial channels can become very attractive, providing one or several programmes in an 8 MHz band channel. The authors present a complete modulation-demodulation system based on a multicarrier approach and capable of conveying a 34 Mbit/s TV signal in an 8 MHz terrestrial channel. They first present the general principles of the system. Equalization and synchronization aspects and possible use of cross-polarizations to double the system capacity are considered. Finally the authors describe the hardware implementation of the system and present some experimental results.
Flux analysis and control of the central metabolic pathways in Escherichia coli (1996)

The growth of the bacterial cell involves the co-ordination of the fluxes of carbon into a considerable diversity of products that are the components of the cell. Fortunately the monomers from which the cell’s polymers are made are themselves synthesised from a relatively small group of precursors that are the products of the central metabolic pathways. This simplification renders cell metabolism accessible to flux analysis, a method for handling experimental data to derive metabolic fluxes. Through such analysis of the growth of Escherichia coli ML308 on 11 single carbon sources in batch, turbidostat or chemostat culture general patterns are discernible. Most significant among these are that growth on different carbon sources is achieved without any obvious enzyme acting as a regulator of metabolic flux, except when acetate is the sole source of carbon. In this case a junction is created at which isocitrate dehydrogenase (ICDH) and isocitrate lyase (ICL) compete for their common substrate and this competition is resolved by partial inactivation of ICDH to match flux through ICL and this balance limits growth rate. In this sense, flux through ICDH aand ICL is ‘rate-limiting’. Uptake of six of the remaining carbon inputs exceeds the capacity of the central metabolic pathways (CMPs) to sustain flux to the precursors required for growth and the CMPs are balanced by excretion of acetate. Restriction of carbon uptake by chemostat progressively diminishes growth rate and acetate excretion until acetate excretion is prevented. For the four remaining carbon sources, uptake is apparently restricted and the products are biomass, carbon dioxide and water. Carbon sources feeding the phosphorylated parts of the CMPs flux relatively more carbon to precursors (Pre-C) than CO2 when compared with carbon sources which feed into the non-phosphorylated pathways. Pre-C/CO2 ratios for the former are 1.73–3.91 and for the latter are 0.46–0.78. Flux analysis of all 11 carbon sources shows that there is an overabundant supply of ‘energy’ (ATP+[2H]), generated by the CMPs, in all phenotypes and conditions down to a glucose chemostat at μ of 0.72. This excess energy is a thermodynamic inefficiency which must be dissipated as heat. E. coli ML308 probably evolved in circumstances of ‘feast’ and ‘famine’. The two strategies selected (excretion of surplus carbon and restriction of μ) would appear to be defences against ‘feast’. Presumably there are defences against ‘famine’. These are not made obvious by flux analysis but allosteric control of irreversible enzymes would protect pools of essential nutrients from rapid depletion on the sudden onset of ‘famine’.
ADP ribosyl cyclase activity of a novel bone marrow stromal cell surface molecule, BST‐1 (1994)

Human BST-1, a bone marrow stromal cell surface molecule, is a GPI-anchored protein that facilitates the growth of pre-B cells. The deduced amino acid sequences of human and mouse BST-1 show around 30% homology with those of CD38 and Aplysia ADP ribosyl cyclase. Therefore, like CD38, BST-1 might possess ADP ribosyl cyclase activity. Here, we report the establishment of a stable transformant CHO cell line, which secretes truncated human soluble BST-1, and show that purified soluble BST-1 displays both ADP ribosyl cyclase and cADPR hydrolase activities.
Flavone acetic acid: a novel agent with preclinical antitumor activity against colon adenocarcinoma 38 in mice. (1986)

Flavone acetic acid, given on Days 2 and 9 at a dose of 267 mg/kg, inhibited tumor growth completely in 60%-80% of mice with early-stage Colon Adenocarcinoma 38. The therapeutic efficacy of the flavone against this tumor was retained when the sites of tumor implantation and drug administration were separated. Flavone acetic acid also caused regression of advanced (500-mg) Colon 38 tumors, with greatest efficacy observed following administration of high individual dose rather than high total dose. Unlike many previous potential anticancer agents, only modest activity was observed for this compound against either P388 or L1210 leukemia.
Familial defective apolipoprotein B-100: low density lipoproteins with abnormal receptor binding. (1987)

Previous in vivo turnover studies suggested that retarded clearance of low density lipoproteins (LDL) from the plasma of some hypercholesterolemic patients is due to LDL with defective receptor binding. The present study examined this postulate directly by receptor binding experiments. The LDL from a hypercholesterolemic patient (G.R.) displayed a reduced ability to bind to the LDL receptors on normal human fibroblasts. The G.R. LDL possessed 32% of normal receptor binding activity (approximately equal to 9.3 micrograms of G.R. LDL per ml were required to displace 50% of 125I-labeled normal LDL, vs. approximately equal to 3.0 micrograms of normal LDL per ml). Likewise, the G.R. LDL were much less effective than normal LDL in competing with 125I-labeled normal LDL for cellular uptake and degradation and in stimulating intracellular cholesteryl ester synthesis. The defect in LDL binding appears to be due to a genetic abnormality of apolipoprotein B-100: two brothers of the proband possess LDL defective in receptor binding, whereas a third brother and the proband's son have normally binding LDL. Further, the defect in receptor binding does not appear to be associated with an abnormal lipid composition or structure of the LDL: the chemical and physical properties of the particles were normal, and partial delipidation of the LDL did not alter receptor binding activity. Normal and abnormal LDL subpopulations were partially separated from plasma of two subjects by density-gradient ultracentrifugation, a finding consistent with the presence of a normal and a mutant allele. The affected family members appear to be heterozygous for this disorder, which has been designated familial defective apolipoprotein B-100. These studies indicate that the defective receptor binding results in inefficient clearance of LDL and the hypercholesterolemia observed in these patients.
Molecular cloning, sequencing, and expression of lytM, a unique autolytic gene of Staphylococcus aureus (1997)

A gene encoding an autolytic activity was identified in an autolysis-deficient mutant (Lyt-) of Staphylococcus aureus which produces only a single band in autolytic-activity gels (N. Mani, P. Tobin, and R. K. Jayaswal, J. Bacteriol. 175:1493-1499, 1993). An open reading frame, designated lytM, of 948 bp that could encode a polypeptide of 316 amino acid residues was identified. The calculated molecular mass of the lytM gene product (34.4 kDa) corresponded to that of the autolytic activity detected (approximately 36 kDa) in the Lyt- mutant. Results deduced from amino acid sequence analysis and N-terminal amino acid sequencing data suggest that LytM is a secreted protein. The C-terminal region of the putative protein encoded by lytM showed 51% identity with the N-terminal region of the mature lysostaphin from Staphylococcus simulans and 50% identity with the N-terminal region of ALE-1 from Staphylococcus capitis EPK1. Northern blot analysis showed that lytM expresses a transcript of approximately 955 bp, as predicted from the DNA sequence. Escherichia coli clones carrying the lytM gene exhibited autolytic-activity bands of approximately 36 kDa as well as of 19 and 22 kDa in activity gels. The lytM gene was mapped to the SmaI-D fragment on the S. aureus chromosome. Mapping data and results of hybridization experiments with primers generated from gene sequences of known autolytic genes of S. aureus clearly indicate that the lytM gene is distinct from other staphylococcal autolytic genes reported to date.
Update on viral hepatitis: 2005 (2006)

New insights into the management of viral hepatitis have been gained over the past year. The problem of antiviral resistance in chronic hepatitis B is real and treatment options need to keep evolving. Advances have been made in hepatitis C treatment including patients with genotypes 2 or 3 infection and decompensated cirrhosis.
Fractal elements in array antennas: investigating reduced mutual coupling and tighter packing (2002)

Effective array design should take into account mutual coupling. This becomes even more of a troublesome area as arrays are packed tighter to increase the scan angles in phased array systems. One attempt to control mutual coupling that is utilized here is to miniaturize the elements of the arrays. The smaller elements decrease the amount of coupling by increasing the spacing between the elements, thus enhancing the array performance. To miniaturize the elements, fractal geometries are used. Fractal geometries have also been used in arrays by defining the distribution of elements.
Modulation of crystal formation by bone phosphoproteins: role of glutamic acid-rich sequences in the nucleation of hydroxyapatite by bone sialoprotein (1994)

Bone sialoprotein (BSP) is a bone-specific glycoprotein containing phosphoserine and sulphotyrosine residues and regions of contiguous glutamic acid residues. Recent studies in this laboratory have shown that BSP is capable of nucleating the bone mineral hydroxyapatite in a steady-state agarose gel system. We show here that chemical modification of carboxylate groups abolishes the nucleation activity of BSP, but enzymic dephosphorylation has no effect. Formation of hydroxyapatite is also induced by poly(L-glutamic acid) and poly(D-glutamic acid), but not by poly(L-aspartic acid) or poly(L-lysine). Calreticulin, a muscle protein with short sequences of contiguous glutamic acid residues, also lacks nucleation activity. These findings suggest that the nucleation of hydroxyapatite by BSP involves one or both of the glutamic acid-rich sequences. Based on these findings and others, we propose that polycarboxylate sequences represent a general site for growth-modulating interactions between proteins and biological crystals.
Synthesis of xanthines by dehydrogenative cyclization of 6-amino-5-benzylideneaminouracils with diethyl azodicarboxylate. (1978)

The treatment of 6-amino-5-benzylideneaminouracil derivatives with diethyl azodicarboxylate gave the corresponding xanthines in high yields.
Cysteine proteases of positive strand RNA viruses and chymotrypsin‐like serine proteases (1989)

Evidence is presented, based on sequence comparison and secondary structure prediction, of structural and evolutionary relationship between chymotrypsin-like serine proteases, cysteine proteases of positive strand RNA viruses (3C proteases of picornaviruses and related enzymes of como-, nepo- and potyviruses) and putative serine protease of a sobemovirus. These observations lead to re-identification of principal catalytic residues of viral proteases. Instead of the pair of Cys and His, both located in the C-terminal part of 3C proteases, a triad of conserved His, Asp(Glu) and Cys(Ser) has been identified, the first two residues resident in the N-terminal, and Cys in the C-terminal beta-barrel domain. These residues are suggested to form a charge-transfer system similar to that formed by the catalytic triad of chymotrypsin-like proteases. Based on the structural analogy with chymotrypsin-like proteases, the His residue previously implicated in catalysis, together with two partially conserved Gly residues, is predicted to constitute part of the substrate-binding pocket of 3C proteases. A partially conserved ThrLys/Arg dipeptide located in the loop preceding the catalytic Cys is suggested to confer the primary cleavage specificity of 3C toward Glx/Gly(Ser) sites. These observations provide the first example of relatedness between proteases belonging, by definition, to different classes.
A critical cysteine is required for HMGB1 binding to Toll-like receptor 4 and activation of macrophage cytokine release (2010)

During infection, vertebrates develop "sickness syndrome," characterized by fever, anorexia, behavioral withdrawal, acute-phase protein responses, and inflammation. These pathophysiological responses are mediated by cytokines, including TNF and IL-1, released during the innate immune response to invasion. Even in the absence of infection, qualitatively similar physiological syndromes occur following sterile injury, ischemia reperfusion, crush injury, and autoimmune-mediated tissue damage. Recent advances implicate high-mobility group box 1 (HMGB1), a nuclear protein with inflammatory cytokine activities, in stimulating cytokine release. HMGB1 is passively released during cell injury and necrosis, or actively secreted during immune cell activation, positioning it at the intersection of sterile and infection-associated inflammation. To date, eight candidate receptors have been implicated in mediating the biological responses to HMGB1, but the mechanism of HMGB1-dependent cytokine release is unknown. Here we show that Toll-like receptor 4 (TLR4), a pivotal receptor for activation of innate immunity and cytokine release, is required for HMGB1-dependent activation of macrophage TNF release. Surface plasmon resonance studies indicate that HMGB1 binds specifically to TLR4, and that this binding requires a cysteine in position 106. A wholly synthetic 20-mer peptide containing cysteine 106 from within the cytokine-stimulating B box mediates TLR4-dependent activation of macrophage TNF release. Inhibition of TLR4 binding with neutralizing anti-HMGB1 mAb or by mutating cysteine 106 prevents HMGB1 activation of cytokine release. These results have implications for rationale, design, and development of experimental therapeutics for use in sterile and infectious inflammation.
The tobacco Cel7 gene promoter is auxin‐responsive and locally induced in nematode feeding sites of heterologous plants (2007)

Emerging evidence suggests that plant cell-wall-modifying enzymes induced by root-parasitic nematodes play important roles in feeding cell formation. We previously identified a tobacco endo-beta-1,4-glucanase (cellulase) gene, NtCel7, that was strongly induced in both root-knot and cyst nematode feeding cells. To characterize further the developmental and nematode-responsive regulation of NtCel7, we isolated the NtCel7 promoter and analysed its expression over a time course of nematode infection and in response to auxin, gibberellin, ethylene and sucrose in soybean and tomato hairy roots and in Arabidopsis containing the NtCel7 promoter fused to the beta-glucuronidase (GUS) reporter gene. Histochemical analyses of transgenic plant materials revealed that the NtCel7 promoter exhibited a unique organ-specific expression pattern during plant development suggestive of important roles for NtCel7 in both vegetative and reproductive growth. In all plant species tested, strong GUS expression was observed in root tips and lateral root primordia of uninfected roots with weaker expression in the root vasculature. Further analyses of transgenic Arabidopsis plants revealed expression in shoot and root meristems and the vasculature of most organs during plant development. We also determined that the NtCel7 promoter was induced by auxin, but not gibberellin, ethylene or sucrose. Moreover, strong GUS activity was observed in both cyst and root-knot nematode-induced feeding sites in transgenic roots of soybean, tomato and Arabidopsis. The conserved developmental and nematode-responsive expression of the NtCel7 promoter in heterologous plants indicates that motifs of this regulatory element play a fundamental role in regulating NtCel7 gene expression within nematode feeding sites and that this regulation may be mediated by auxin.
Molecular identification of a novel human rotavirus in relation to subgroup and electropherotype of genomic rna (1989)

A total of 41 stool rotavirus specimens collected from children with acute diarrhea at four different locations in Akita Prefecture, Japan, during the peak of the winter diarrhea epidemic in 1988 were analyzed by polyacrylamide gel electrophoresis of viral RNA in conjunction with subgrouping assay. We found that a single strain predominated, with cocirculating strains with less common electropherotypes at a given location, and that two different strains could predominate at geographically close but different locations even during a very limited time of the epidemic season. Furthermore, we isolated a human rotavirus strain (AU125) that was similar to the AU-1 strain in that it possessed a long RNA pattern yet belonged to subgroup I. Genetic analysis by RNA-RNA hybridization assay indicated that the AU125 strain was distinct from two previously identified human rotavirus gene groups (genogroups) represented by the Wa strain (subgroup II with long RNA electropherotype) and the DS-1 strain (subgroup I with short RNA electropherotype), but was very closely related to the AU-1 strain. These data suggest that the genetic diversity of human rotaviruses may be more extensive than was previously thought.