gebhart/patrepeval huggingface dataset:
EGF-induced activation of Akt results in mTOR-dependent p70S6 kinase phosphorylation and inhibition of HC11 cell lactogenic differentiation (2006)

PI-3-kinase signaling contributes to the EGF block of lactogenic differentiation via Akt and p70S6K. The EGF-induced activation of PI-3-kinase-Akt-mTOR regulates phosphorylation of molecules including ribosomal protein S6, eIF4E and 4E-BP1 that influence translational control in HC11 cells undergoing lactogenic differentiation.
Phylogeny of Sarocladium (Hypocreales) (2014)

The circumscription of the genus Acremonium (Hypocreales) was recently reviewed on the basis of a DNA phylogenetic study. Several species were subsequently transferred to Sarocladium, but the relationships between both genera remained unresolved. Based on multilocus phylogenetic inferences combined with phenotypic data, we have revised the species concepts within Sarocladium and some genetically related species of Acremonium. As a result of these studies, six species are described as new, viz. S. bifurcatum, S. gamsii, S. hominis, S. pseudostrictum, S. subulatum and S. summerbellii. In addition, the new combinations S. implicatum and S. terricola are proposed for A. implicatum and A. terricola, respectively. Sarocladium attenuatum is confirmed as synonym of the type species of the genus, S. oryzae. An epitype and neotype are also introduced for S. oryzae and S. implicatum, respectively. Although Sarocladium species have traditionally been considered as important phytopathogens, the genus also contains opportunistic human pathogens. This study extends the spectrum of clinical species that could be diagnosed as causal agents of human infections.
Cell surface heparan sulfate and its roles in assisting viral infections (2001)

Heparan sulfate, a highly sulfated polysaccharide, is present on the surface of mammalian cells and in the extracellular matrix in large quantities. The sulfated monosaccharide sequences within heparan sulfate determine the protein binding specificity and regulate biological functions. Numerous viruses and parasites utilize cell surface heparan sulfate as receptors to infect target cells. Due to the structural complexity of heparan sulfate, it was considered a nonspecific cell surface receptor by interacting with the positive motifs of viral proteins. However, recent studies reveal that heparan sulfate plays multiple roles in assisting viral infection, and the activities in promoting viral infections require unique monosaccharide sequences, suggesting that heparan sulfate could serve as a specific receptor for viral infection. The currently available techniques for the structural analysis of heparan sulfate provide essential information about the specific roles of heparan sulfate in assisting viral infections. The knowledge accumulated in this fast growing field will permit us to have a better understanding of the mechanism of viral infection and will lead to the development of new antiviral agents.
25th Anniversary Article: Galvanic Replacement: A Simple and Versatile Route to Hollow Nanostructures with Tunable and Well‐Controlled Properties (2013)

This article provides a progress report on the use of galvanic replacement for generating complex hollow nanostructures with tunable and well-controlled properties. We begin with a brief account of the mechanistic understanding of galvanic replacement, specifically focused on its ability to engineer the properties of metal nanostructures in terms of size, composition, structure, shape, and morphology. We then discuss a number of important concepts involved in galvanic replacement, including the facet selectivity involved in the dissolution and deposition of metals, the impacts of alloying and dealloying on the structure and morphology of the final products, and methods for promoting or preventing a galvanic replacement reaction. We also illustrate how the capability of galvanic replacement can be enhanced to fabricate nanomaterials with complex structures and/or compositions by coupling with other processes such as co-reduction and the Kirkendall effect. Finally, we highlight the use of such novel metal nanostructures fabricated via galvanic replacement for applications ranging from catalysis to plasmonics and biomedical research, and conclude with remarks on prospective future directions.
Zinc: biochemistry, physiology, toxicology and clinical pathology. (1988)

Among the transition and group II elements the abundance of zinc in biology is second only to that of iron. It is present in and indispensable to all forms of life. Knowledge regarding the biological occurrence and function of zinc, the development of methods that permit its detection and those aspects of biochemistry which have allowed an appreciation of the manner in which it participates in generating biological specificity have grown exponentially in the last two decades. The recognition that zinc is an essential, coenzyme-like component of many enzymes, indispensable to their function, is reminiscent of the role of some vitamins. Technical advances in the isolation and characterization of enzymes in general and metalloenzymes in particular were basic to the rapid growth of zinc metallobiochemistry during the last two decades. Zinc is now known to be an integral component of a large variety of proteins and enzymes and, hence, the total zinc content of tissues cannot serve as a guide to the multiple functions of the metal. Zinc participates in a wide variety of metabolic processes including carbohydrate, lipid, protein and nucleic acid synthesis or degradation. Most recently, zinc proteins have been shown to be involved in the transcription and translation of the genetic material, perhaps accounting for its essentiality to all forms of life. A number of zinc proteins have been described whose function is not known as yet. Among these, the metallothioneins are prominent. They are widely distributed, of low molecular weight (approximately 6700), and their content of cadmium and/or zinc as well as sulfur is exceptionally high.(ABSTRACT TRUNCATED AT 250 WORDS)
Effects of Clay on Fouling by Organic Substance in Ultrafiltration. (1994)

In the cross-flow ultrafiltration, effects of clay on the fouling due to organic substance were evaluated by fouling model materials and clay. Fouling model materials selected were BSA (Bovin serum albumin, MW68,000), Dextran (MW70,000), and humic acid (MW8,000-200,000) for larger size than molecular weight cut-off (MWCO50,000, polysulfone) and α-lactalbumin, Dextran (MW9,300) fulvic acid (MW8,000) for smaller size than that, and kaolin was selected as a clay material. The fluxes of BSA and Dextran (MW70,000) increased with an increase in the amount of kaolin, while the flux of α-lactalbumin, Dextran (MW9,300) did not increase with kaolin. The kaolin affected the flux decreased mainly more by adsorption and deposition (gel layer) on to the membrane surface than by the flux decline due to adsorption to the pore interior, but did not affect the flux decline that occurs by organic substance through the membrane pore. In contrast, the flux of humic substances decreased with an increase in the quantity of kaolin. The wasing recovery of flux with coexistence of kaolin was greater than that of fouling model material solution without kaolin.
Anti-microbial activities of mannose-binding lectin (2003)

Mannose-binding lectin (MBL; also known as mannan-binding lectin) is involved in first-line defence by binding to bacteria, viruses, protozoa and helminths through a pattern-recognition mode of detection and then initiating a range of host responses. Currently, we have been unable to extrapolate from what we know of the biochemistry of MBL binding to predict accurately the interaction of MBL with individual micro-organisms; even subtle surface alterations have been shown to have an extensive impact on MBL-mediated recognition of pathogens. MBL has a major protective effect through activation of the complement system via MBL-associated serine proteases (MASPs). This can cause the lysis of Gram-negative bacteria and also opsonize a wide spectrum of potential pathogens for phagocytosis. MBL may also influence phagocytosis in the absence of complement activation through an interaction with one or more collectin receptors. This may also be the basis for a direct effect of the protein on inflammatory responses. MBL can alter the function of microbial structures, such as gp120 of HIV, to prevent infection. The protein may also interact with the components of other cascade systems such as the clotting system, which will have a role in microbial pathogenesis. An understanding of these basic mechanisms will be vital if we are to use purified or recombinant MBL in therapeutic applications.
Filtering and selection of structural models: Combining docking and NMR (2003)

It is generally accepted that protein structures are more conserved than protein sequences, and 3D structure determination by computer simulations have become an important necessity in the postgenomic area. Despite major successes no robust, fast, and automated ab initio prediction algorithms for deriving accurate folds of single polypeptide chains or structures of intermolecular complexes exist at present. Here we present a methodology that uses selection and filtering of structural models generated by docking of known substructures such as individual proteins or domains through easily obtainable experimental NMR constraints. In particular, residual dipolar couplings and chemical shift mapping are used. Heuristic inclusion of chemical or biochemical knowledge about point-to-point interactions is combined in our selection strategy with the NMR data and commonly used contact potentials. We demonstrate the approach for the determination of protein-protein complexes using the EIN/HPr complex as an example and for establishing the domain-domain orientation in a chimeric protein, the recently determined hybrid human-Escherichia. coli thioredoxin.
Ultra-Sensitive Sequencing Reveals an Age-Related Increase in Somatic Mitochondrial Mutations That Are Inconsistent with Oxidative Damage (2013)

Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >10(7) wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ~5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G → T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G → A and T → C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA.
Generic approach for hierarchical modulation performance analysis: Application to DVB-SH (2011)

Broadcasting systems have to deal with channel diversity in order to offer the best rate to the users. Hierarchical modulation is a practical solution to provide several rates in function of the channel quality. Unfortunately the performance evaluation of such modulations requires time consuming simulations. We propose in this paper a novel approach based on the channel capacity to avoid these simulations. The method allows to study the performance in terms of spectrum efficiency of hierarchical and also classical modulations combined with error correcting codes. Our method will be applied to the DVB-SH standard which considers hierarchical modulation as an optional feature.
Rechargeable lithium-aluminum/iron sulfide batteries for high energy density (2003)

A rechargeable lithium aluminum/iron sulfide battery has been built and tested. Prismatic LiAl/FeS cells provide a delivered energy to 80% depth of discharge (DOD) of 217 Wh/1 and a peak power of 375 W/l. Cycle life of over 365 cycles was achieved at the C/3 rate. Pulse self-discharge and driving cycle tests were also performed for an electric vehicle application. The molten salt electrolyte requires an operational temperature of about 450 degrees C. A thermal control system composed of heating elements, thermal enclosure, and heat exchanger was engineered and tested. The components for a 8 kWh battery were developed and evaluated. This high temperature rechargeable battery is suitable for applications requiring high specific energy and minimal volume.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Proteomics applied to the clinical follow-up of patients after allogeneic hematopoietic stem cell transplantation (2004)

A phase 1 diagnostic study was performed to evaluate a novel technology for clinical proteomic research based on capillary electrophoresis and mass spectrometry. Urine from 40 patients after hematopoietic stem cell transplantation (HSCT; 35 allogeneic, 5 autologous) and 5 patients with sepsis was collected for a period of 100 days and analyzed. More than 1000 different polypeptides could be detected in individual samples. Polypeptide patterns excreted in the urine of patients were significantly different from those of healthy volunteers. No significant differences were detected comparing different conditioning regimens. The aim of this study was to identify polypeptide patterns functioning as early indicators of graft-versus-host disease (GVHD). Eighteen patients developed GVHD after allogeneic HSCT. Sixteen differentially excreted polypeptides formed a pattern of early GVHD markers, allowing discrimination of GVHD from patients without complications with 82% specificity and 100% sensitivity, cross-validated. Inclusion of 13 sepsis-specific polypeptides allowed us to distinguish sepsis from GVHD with a specificity of 97% and a sensitivity of 100%. Sequencing 2 prominent GVHD-indicative polypeptides led to the identification of a peptide from leukotriene A4 hydrolase and a peptide from serum albumin. The data reveal that capillary electrophoresis and mass spectrometry allow identification of biomarkers for a variety of diseases or related complications.
Evaluation of the role of the pneumococcal Forssman antigen (F-polysaccharide) in the cross-serotype protection induced by pneumococcal subcellular preparations (1981)

We tested the hypothesis that the capacity of subcellular preparations of rough pneumococci to give cross-serotype protection is due to the presence of the pneumococcal Forssman antigen (F-polysaccharide). We found by hemagglutination inhibition that the Forssman antigen is present in the subcellular extracts. However, we concluded that the Forssman antigen is not the protective immunogen in the pneumococcal subcellular preparation, since absorption with sheep erythrocytes failed to remove the protective capacity from antiserum raised against the vaccine. Other evidence mitigating against the pneumococcal Forssman antigen being the protective immunogen included the absence of a detectable hemolytic titer in protective antiserum raised against the subcellular preparation, the failure of high-titered sheep hemolysin to passively protect mice against pneumococcal infection, and the failure of purified F-polysaccharide to immunize mice against pneumococcal infection.
Linking the sounds of dolphins to their locations and behavior using video and multichannel acoustic recordings (2002)

It is difficult to attribute underwater animal sounds to the individuals producing them. This paper presents a system developed to solve this problem for dolphins by linking acoustic locations of the sounds of captive bottlenose dolphins with an overhead video image. A time-delay beamforming algorithm localized dolphin sounds obtained from an array of hydrophones dispersed around a lagoon. The localized positions of vocalizing dolphins were projected onto video images. The performance of the system was measured for artificial calibration signals as well as for dolphin sounds. The performance of the system for calibration signals was analyzed in terms of acoustic localization error, video projection error, and combined acoustic localization and video error. The 95% confidence bounds for these were 1.5, 2.1, and 2.1 m, respectively. Performance of the system was analyzed for three types of dolphin sounds: echolocation clicks, whistles, and burst-pulsed sounds. The mean errors for these were 0.8, 1.3, and 1.3 m, respectively. The 95% confidence bound for all vocalizations was 2.8 m, roughly the length of an adult bottlenose dolphin. This system represents a significant advance for studying the function of vocalizations of marine animals in relation to their context, as the sounds can be identified to the vocalizing dolphin and linked to its concurrent behavior.
<title>Laser repair of phase-shifting masks</title> (1994)

Results of a study to develop methods, based on UV laser ablation and chemical etching, for repairing defects in phase shifting masks will be discussed. The application of these techniques to a variety of candidate phase shifting mask types including attenuating Cr, embedded shifter Cr and SOG PSM will be discussed. The repair processes will be characterized in terms of process laser wavelength and energy flux, precursor gas type and material removal rate, transmission in the repaired area, and the phase shift, if any, introduced at the repair site. The effectiveness of various optical and gas delivery techniques will be compared with the types of defects likely to be encountered in the candidate masks. The results presented will include repair rate, etching uniformity and transmission data along with SEM and optical micrographs before and after repair events.
Molecular strategies for detection and quantitation of clonal cytotoxic T-cell responses in aplastic anemia and myelodysplastic syndrome (2006)

Immune mechanisms are involved in the pathophysiology of aplastic anemia (AA) and myelodysplastic syndrome (MDS). Immune inhibition can result from cytotoxic T cell (CTL) attack against normal hematopoiesis or reflect immune surveillance. We used clonally unique T-cell receptor (TCR) variable beta-chain (VB) CDR3 regions as markers of pathogenic CTL responses and show that while marrow failure syndromes are characterized by polyclonal expansions, overexpanded clones exist in these diseases and can serve as investigative tools. To test the applicability of clonotypic assays, we developed rational molecular methods for the detection of immunodominant clonotypes in blood and in historic marrow biopsies of 35 AA, 37 MDS, and 21 paroxysmal nocturnal hemoglobinuria (PNH) patients, in whom specific CDR3 sequences and clonal sizes were determined. CTL expansions were detected in 81% and 97% of AA and MDS patients, respectively. In total, 81 immunodominant signature clonotypes were identified. Based on the sequence of immunodominant CDR3 clonotypes, we designed quantitative assays for monitoring corresponding clones, including clonotypic Taqman polymerase chain reaction (PCR) and clonotype-specific sequencing. No correlation was found between clonality and disease severity but in patients treated with immunosuppression, truly pathogenic clones were identified based on the decline that paralleled hematologic response. We conclude that immunodominant clonotypes associated with marrow failure may be used to monitor immunosuppressive therapy.
Magnesium-free self-assembly of multi-layer DNA objects (2012)

Molecular self-assembly with DNA offers a route for building user-defined nanoscale objects, but an apparent requirement for magnesium in solution has limited the range of conditions for which practical utility of such objects may be achieved. Here we report conditions for assembling templated multi-layer DNA objects in the presence of monovalent ions, showing that neither divalent cations in general or magnesium in particular are essential ingredients for the successful assembly of such objects. The percentage of DNA strands in an object that do not form thermally stable double-helical DNA domains (T(m)>45 °C) with the template molecule correlated with the sodium requirements for obtaining folded objects. Minimizing the fraction of such weakly binding strands by rational design choices enhanced the yield of folding. The results support the view that DNA-based nanodevices may be designed and produced for a variety of target environments.
Structure-function relationship of Rous sarcoma virus leader RNA (1982)

Cells infected by RSV synthesize viral 35S RNA as well as subgenomic 28S and 22S RNAs coding for the Env and Src genes respectively. In addition, at least the 5' 101 nucleotides of the leader are also conserved and we have shown previously that this sequence contains a strong ribosome binding site (J.-L. Darlix et al., J. Virol. 29, 597). We now report the RNA sequence of Rous Sarcoma virus (RSV) leader RNA and propose a folding of this 5' untranslated region which brings the Cap, the initiation codon for Gag and the strong ribosome binding site close to each other. We also show that ribosomes protect a sequence just upstream from initiator Aug of Gag in vitro, and believed to interact with part of the strong ribosome binding site according to the folding proposed for the leader RNA.
A Tutorial on MM Algorithms (2004)

Most problems in frequentist statistics involve optimization of a function such as a likelihood or a sum of squares. EM algorithms are among the most effective algorithms for maximum likelihood estimation because they consistently drive the likelihood uphill by maximizing a simple surrogate function for the log-likelihood. Iterative optimization of a surrogate function as exemplified by an EM algorithm does not necessarily require missing data. Indeed, every EM algorithm is a special case of the more general class of MM optimization algorithms, which typically exploit convexity rather than missing data in majorizing or minorizing an objective function. In our opinion, MM algorithms deserve to be part of the standard toolkit of professional statisticians. This article explains the principle behind MM algorithms, suggests some methods for constructing them, and discusses some of their attractive features. We include numerous examples throughout the article to illustrate the concepts described. In addition to surveying previous work on MM algorithms, this article introduces some new material on constrained optimization and standard error estimation.