gebhart/patrepeval huggingface dataset:
Oxidative cellulose degradation by cellobiose dehydrogenase from Phanerochaete chrysosporium: A model compound study (2005)

Abstract Cellobiose dehydrogenase (CDH) is an extracellular enzyme produced by various wood-degrading fungi. It oxidizes cellobiose to cellobionolactone under reduction of molecular oxygen to hydrogen peroxide, and Fe 3+ to Fe 2+ . These activated agents can thereafter form highly reactive hydroxyl radicals, which depolymerize wood polymers. In this work, cellulose depolymerization by CDH was studied using a model compound, methyl β-D-glucopyranoside. The formation of glucose, arabinose, gluconic acid, erythrulose and formaldehyde were detected and a mechanism for the reaction is proposed. The biological importance of this enzyme-initiated reaction is discussed.
ChemInform Abstract: Effective Ring‐Opening Reaction of Aziridines with Trimethylsilyl Compounds: A Facile Access to β‐Amino Acids and 1,2‐Diamine Derivatives. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
In vitro evaluation of combination therapies against hepatitis B virus replication (1996)

The HBV-producing human hepatoblastoma cell line, 2.2.15, has been shown to be an accurate model of chronic cellular viral infection and a predictive model of antiviral response for in vivo hepadnaviral infection. Our laboratory has utilized the 2.2.15 cell line in a standardized assay to examine treatment schemes which use combinations of clinically relevant nucleoside analogues, novel methods to deliver potentially useful nucleoside combinations, and treatments which simultaneously target different parts of the HBV replication pathway. For example, the combination of 3TC (lamivudine) with either alpha interferon or penciclovir significantly enhances the antiviral effectiveness of these agents against HBV replication in 2.2.15 cell culture.
Woodchuck hepatitis virus surface antigen produced in vitro fails to bind polymerized woodchuck serum albumin (1994)

Using a plasmid (pSWS) similar to one that has been successfully used for large-scale production of hepatitis B virus (HBV) envelope protein particles (pSVS) but containing the corresponding woodchuck hepatitis virus (WHV) envelope gene sequences, we have stably transformed the rodent dihydrofolate reductase-deficient cell line CHO dhfr-. Although production of WHV envelope particles in CHO/pSWS cell lines was low, it was sufficient to test whether these particles could bind to polymerized serum albumin. Whereas binding of HBV particles produced in CHO/pSVS cells to polymerized human serum albumin could readily be detected, we found no evidence that the WHV envelope protein particles produced in vitro bind to either human or woodchuck polymerized serum albumin.
Fast full-wavefield seismic inversion using encoded sources (2009)

Abstract Full-wavefield seismic inversion (FWI) estimates a subsurface elastic model by iteratively minimizing the difference between observed and simulated data. This process is extremely computationally intensive, with a cost comparable to at least hundreds of prestack reverse-time depth migrations. When FWI is applied using explicit time-domain or frequency-domain iterative-solver-based methods, the seismic simulations are performed for each seismic-source configuration individually. Therefore, the cost of FWI is proportional to the number of sources. We have found that the cost of FWI for fixed-spread data can be significantly reduced by applying it to data formed by encoding and summing data from individual sources. The encoding step forms a single gather from many input source gathers. This gather represents data that would have been acquired from a spatially distributed set of sources operating simultaneously with different source signatures. The computational cost of FWI using encoded simultaneous-source gathers is reduced by a factor roughly equal to the number of sources. Further, this efficiency is gained without significantly reducing the accuracy of the final inverted model. The efficiency gain depends on subsurface complexity and seismic-acquisition parameters. There is potential for even larger improvements of processing speed.
Bone Marrow Origin of Endothelial Progenitor Cells Responsible for Postnatal Vasculogenesis in Physiological and Pathological Neovascularization (1999)

Circulating endothelial progenitor cells (EPCs) have been isolated in peripheral blood of adult species. To determine the origin and role of EPCs contributing to postnatal vasculogenesis, transgenic mice constitutively expressing beta-galactosidase under the transcriptional regulation of an endothelial cell-specific promoter (Flk-1/LZ or Tie-2/LZ) were used as transplant donors. Localization of EPCs, indicated by flk-1 or tie-2/lacZ fusion transcripts, were identified in corpus luteal and endometrial neovasculature after inductive ovulation. Mouse syngeneic colon cancer cells (MCA38) were implanted subcutaneously into Flk-1/LZ/BMT (bone marrow transplantation) and Tie-2/LZ/BMT mice; tumor samples harvested at 1 week disclosed abundant flk-1/lacZ and tie-2/lacZ fusion transcripts, and sections stained with X-gal demonstrated that the neovasculature of the developing tumor frequently comprised Flk-1- or Tie-2-expressing EPCs. Cutaneous wounds examined at 4 days and 7 days after skin removal by punch biopsy disclosed EPCs incorporated into foci of neovascularization at high frequency. One week after the onset of hindlimb ischemia, lacZ-positive EPCs were identified incorporated into capillaries among skeletal myocytes. After permanent ligation of the left anterior descending coronary artery, histological samples from sites of myocardial infarction demonstrated incorporation of EPCs into foci of neovascularization at the border of the infarct. These findings indicate that postnatal neovascularization does not rely exclusively on sprouting from preexisting blood vessels (angiogenesis); instead, EPCs circulate from bone marrow to incorporate into and thus contribute to postnatal physiological and pathological neovascularization, which is consistent with postnatal vasculogenesis.
Enhanced Myocardial Angiogenesis by Gene Transfer With Transplanted Cells (2001)

Transplantation of heart cells transfected with VEGF induced greater angiogenesis than transplantation of unmodified cells. Combined gene transfer and cell transplantation strategies may improve postinfarction LV perfusion and function.
Demyelination reduces brain parenchymal stiffness quantified in vivo by magnetic resonance elastography (2012)

The detection of pathological tissue alterations by manual palpation is a simple but essential diagnostic tool, which has been applied by physicians since the beginnings of medicine. Recently, the virtual "palpation" of the brain has become feasible using magnetic resonance elastography, which quantifies biomechanical properties of the brain parenchyma by analyzing the propagation of externally elicited shear waves. However, the precise molecular and cellular patterns underlying changes of viscoelasticity measured by magnetic resonance elastography have not been investigated up to date. We assessed changes of viscoelasticity in a murine model of multiple sclerosis, inducing reversible demyelination by feeding the copper chelator cuprizone, and correlated our results with detailed histological analyses, comprising myelination, extracellular matrix alterations, immune cell infiltration and axonal damage. We show firstly that the magnitude of the complex shear modulus decreases with progressive demyelination and global extracellular matrix degradation, secondly that the loss modulus decreases faster than the dynamic modulus during the destruction of the corpus callosum, and finally that those processes are reversible after remyelination.
A Novel Suspension Formulation Enhances Intestinal Absorption of Macromolecules Via Transient and Reversible Transport Mechanisms (2014)

Oral octreotide/OS dosing was shown to be safe in monkeys. OS enhances intestinal absorption of active octreotide, likely by transient alteration of the tight junction protein complex.
The Jpred 3 secondary structure prediction server (2008)

Jpred (http://www.compbio.dundee.ac.uk/jpred) is a secondary structure prediction server powered by the Jnet algorithm. Jpred performs over 1000 predictions per week for users in more than 50 countries. The recently updated Jnet algorithm provides a three-state (alpha-helix, beta-strand and coil) prediction of secondary structure at an accuracy of 81.5%. Given either a single protein sequence or a multiple sequence alignment, Jpred derives alignment profiles from which predictions of secondary structure and solvent accessibility are made. The predictions are presented as coloured HTML, plain text, PostScript, PDF and via the Jalview alignment editor to allow flexibility in viewing and applying the data. The new Jpred 3 server includes significant usability improvements that include clearer feedback of the progress or failure of submitted requests. Functional improvements include batch submission of sequences, summary results via email and updates to the search databases. A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions.
PGAM5, a Bcl-XL-interacting Protein, Is a Novel Substrate for the Redox-regulated Keap1-dependent Ubiquitin Ligase Complex (2006)

Keap1 is a BTB-Kelch substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex that functions as a sensor for thiol-reactive chemopreventive compounds and oxidative stress. Inhibition of Keap1-dependent ubiquitination of the bZIP transcription factor Nrf2 enables Nrf2 to activate a cyto-protective transcriptional program that counters the damaging effects of oxidative stress. In this report we have identified a member of the phosphoglycerate mutase family, PGAM5, as a novel substrate for Keap1. The N terminus of the PGAM5 protein contains a conserved NXESGE motif that binds to the substrate binding pocket in the Kelch domain of Keap1, whereas the C-terminal PGAM domain binds Bcl-X(L). Keap1-dependent ubiquitination of PGAM5 results in proteasome-dependent degradation of PGAM5. Quinone-induced oxidative stress and the chemopreventive agent sulforaphane inhibit Keap1-dependent ubiquitination of PGAM5. The identification of PGAM5 as a novel substrate of Keap1 suggests that Keap1 regulates both transcriptional and post-transcriptional responses of mammalian cells to oxidative stress.
The Clinibook : Clinical gene transfer state of the art (2012)

This book provides a 2012 reference for state-of-the-art gene transfer technology and the different aspects of its clinical translation with a focus on European-based initiatives. As examples of successful outcomes, recent clinical trials are presented together with Ethical, Safety and Regulatory issues, which are discussed. The broad range of various technologies is covered whether addressing direct in vivo gene transfer like with AAV, Adeno or non-viral vectors or ex-vivo genetically engineered cells including induced pluripotent stem cells (iPS) with integrating vectors such as retrovirus, lentivirus or transposon-derived systems. The critical path to clinical implementation is covered in the second part describing currently available tools - such as molecular imaging, ex-vivo organ cultures and high-throughput technologies used for evaluation of criteria towards a go-or-no go decision to move to the clinic; in addition, utmost salient biosafety and immunotoxicology aspects are discussed. This book is ideal for postgraduates, undergraduates, scientists, clinicians, regulators and patients' advocacy groups looking for states-of-the-art information as well as emerging prospects - including gene targeting and homologous recombination - in gene transfer intended for clinical translation
Hypertension and Peripheral Insulin Resistance: Possible Mediating Role of Intracellular Free Magnesium (1990)

To investigate the association of hypertension and insulin resistance, we utilized 31P-NMR spectroscopy to noninvasively assess intracellular free magnesium levels (Mgif) in erythrocytes of normotensive (n = 20) and essential hypertensive (n = 20) subjects given an oral 100 g glucose load. In hypertensive compared with normotensive subjects, fasting glucose and insulin levels were similar, but the integrated insulinemic responses to glucose were 45% greater (312 +/- 13.4 v 215 +/- 7.5 microU/mL, P less than .001). In hypertension, Mgif levels were significantly reduced (183 +/- 9 v 251 +/- 9 mumol/L, P less than .001), and for all subjects were closely and inversely related to systolic (r = -0.77, P less than .001) and diastolic (r = -0.81, P less than .001) blood pressures, and to the integrated insulin response (r = -0.72, P less than .001). Furthermore, while insulin responses were also related to the underlying systolic (r = 0.69, P less than .001) and diastolic (r = .73, P less than .001) pressures, these relations were no longer significant when adjusted for Mgif levels. We hypothesize that hypertension and peripheral insulin resistance may be different clinical expressions of a common abnormal intracellular ionic environment, characterized at least in part by suppressed levels of intracellular free magnesium.
CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000 (2000)

CyanoBase provides an online resource for access to data on genomic information about the cyanobacterium Synechocystis sp. strain PCC6803. The database contains annotations for each protein-coding gene deduced from the entire nucleotide sequence of the genome, gene classification lists, and keyword and similarity search engines. Core portions of CyanoBase consist of annotations for each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. The contents of each gene were improved by updating with the results of similarity searches and by introducing references for analysis in bioinformatics. The database now contains repository facilities that store and provide experimental information, in addition to providing proposals for the function of each gene. This information should help to avoid unnecessary, overlapping experiments and should assist communication between scientists who wish to elucidate the function of putative genes on the cyanobacteria genome. The current URL of CyanoBase is http://www.kazusa.or.jp:8080/cyano/
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns (2010)

Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role in child health, most researchers have focused on specific bacterial taxa or on a single body habitat, the gut. Thus, the initiation stage of human microbiome development remains obscure. The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate's first microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers' skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates' skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother's vaginal microbiota, dominated by Lactobacillus, Prevotella, or Sneathia spp., and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. These findings establish an important baseline for studies tracking the human microbiome's successional development in different body habitats following different delivery modes, and their associated effects on infant health.
Prevention of Natural Colds by Contact Prophylaxis with Intranasal Alpha2-Interferon (1986)

We conducted a randomized, placebo-controlled, double-blind study to determine whether intranasal alpha 2-interferon could prevent respiratory illnesses in healthy contacts of ill family members. Beginning within 48 hours of the onset of illness in a family member, contacts self-administered interferon (5 X 10(6) IU) or placebo spray once daily for seven days. Respiratory illness developed during the eight-day period, starting with the second day of spraying, in 52 of 222 persons in the placebo group as compared with 32 of 226 in the interferon group (P = 0.02; efficacy, 39 percent). Among persons exposed to laboratory-documented rhinovirus colds, illness developed in 2 of 27 interferon recipients as compared with 12 of 34 placebo recipients (P = 0.02; efficacy, 79 percent). During the two-week period during and after spraying, rhinovirus colds developed in 1.3 percent of those spraying with interferon and in 15.1 percent of those spraying with placebo (P = 0.003; efficacy, 88 percent). Blood-tinged mucus or nasal mucosal bleeding or both were detected in 7.7 percent of placebo and 13.6 percent of interferon users (P = 0.04), but no evidence of cumulative nasal toxicity was found. We conclude that postexposure prophylaxis with intranasal interferon may in some cases provide an effective strategy for controlling the spread of natural colds, especially those caused by rhinoviruses.
Classical and Quantum Computation (2002)

Introduction Classical computation Quantum computation Solutions Elementary number theory Bibliography Index.
Synthese von 2‐Arylbenzofuranen (1974)

Abstract Benzylphenyläther, die in o ‐Stellung zum Äther‐Sauerstoffatom eine Formyl‐, Acetyl‐ oder Phenyliminomethylgruppe besitzen, lassen sich zu 2‐Arylbenzofuranen cyclisieren. Die intramolekularen Kondensationen verlaufen mit hohen Ausbeuten, wenn man als Kondensationsmittel stark basische Alkaliverbindungen (Natriumhydroxid, Kaliumhydroxid oder Kalium‐ tert.‐butanolat) und als Reaktionsmedium dipolare aprotische Lösungsmittel [Dimethylformamid, Phosphortris(dimethylamid) oder Acetonitril] verwendet.
Topographical Micropatterning of Poly(dimethylsiloxane) Using Laminar Flows of Liquids in Capillaries (2001)

“Micro-landscapes” suitable for investigating the behavior of living cells under different stimuli are cast from poly(dimethylsiloxane) by simultaneously etching a slab and a relief (see Figure) with a Bu4NF solution and flushing out dissolved material with N-methylpyrrolidone. It is crucial that all liquid streams during the etching process are laminar. Various accessible topographies for the relief and examples of applications are given.
Preferential interactions determine protein solubility in three-component solutions: the magnesium chloride system (1990)

The correlation between protein solubility and the preferential interactions of proteins with solvent components was critically examined with aqueous MgCl2 as the solvent system. Preferential interaction and solubility measurements with three proteins, beta-lactoglobulin, bovine serum albumin, and lysozyme, resulted in similar patterns of interaction. At acid pH (pH 2-3) and lower salt concentrations (less than 2 M), the proteins were preferentially hydrated, while at higher salt concentrations, the interaction was either that of preferential salt binding or low salt exclusion. At pH 4.5-5, all three proteins exhibited either very low preferential hydration or preferential binding of MgCl2. These results were analyzed in terms of the balance between salt binding and salt exclusion attributed to the increase in the surface tension of water by salts, which is invariant with conditions. It was shown that the increase in salt binding at high salt concentration is a reflection of mass action, while its decrease at acid pH is due to the electrostatic repulsion between Mg2+ ions and the high net positive charge on the protein. The preferential interaction pattern was paralleled by the variation of protein solubility with solvent conditions. Calculation of the transfer free energies from water to the salt solutions for proteins in solution and in the precipitate showed dependencies on salt concentration. This indicates that the nature of interactions between proteins and solvent components is the same in solution and in the solid state, which implies no change in protein structure during precipitation. Analysis of the transfer free energies and preferential interaction parameter in terms of the salting-in, salting-out, and weak ion binding contributions has led to the conclusions that, when the weak ion binding contribution is small, the predominant protein-salt interaction must be that of preferential salt exclusion most probably caused by the increase of the surface tension of water by addition of the salt. A necessary consequence of this is salting-out of the protein, if the protein structure is to remain unaltered.
A general weighted median filter structure admitting negative weights (1998)

Weighted median smoothers, which were introduced by Edgemore in the context of least absolute regression over 100 years ago, have received considerable attention in signal processing during the past two decades. Although weighted median smoothers offer advantages over traditional linear finite impulse response (FIR) filters, it is shown in this paper that they lack the flexibility to adequately address a number of signal processing problems. In fact, weighted median smoothers are analogous to normalized FIR linear filters constrained to have only positive weights. It is also shown that much like the mean is generalized to the rich class of linear FIR filters, the median can be generalized to a richer class of filters admitting positive and negative weights. The generalization follows naturally and is surprisingly simple. In order to analyze and design this class of filters, a new threshold decomposition theory admitting real-valued input signals is developed. The new threshold decomposition framework is then used to develop fast adaptive algorithms to optimally design the real-valued filter coefficients. The new weighted median filter formulation leads to significantly more powerful estimators capable of effectively addressing a number of fundamental problems in signal processing that could not adequately be addressed by prior weighted median smoother structures.