gebhart/patrepeval huggingface dataset:
Predicting sequence‐dependent melting stability of short duplex DNA oligomers (1997)

Many important applications of DNA sequence-dependent hybridization reactions have recently emerged. This has sparked a renewed interest in analytical calculations of sequence-dependent melting stability of duplex DNA. In particular, for many applications it is often desirable to accurately predict the transition temperature, or tm, of short duplex DNA oligomers (∼ 20 base pairs or less) from their sequence and concentration. The thermodynamic analytical method underlying these predictive calculations is based on the nearest-neighbor model. At least 11 sets of nearest-neighbor sequence-dependent thermodynamic parameters for DNA have been published. These sets are compared. Use of the nearest-neighbor sets in predicting tm from the DNA sequence is demonstrated, and the ability of the nearest-neighbor parameters to provide accurate predictions of experimental tm's of short duplex DNA oligomers is assessed. © 1998 John Wiley & Sons, Inc. Biopoly 44: 217–239, 1997
Clostridium difficile-associated diarrhea in a region of Quebec from 1991 to 2003: a changing pattern of disease severity (2004)

An epidemic of CDAD with an increased case-fatality rate has had important consequences on the elderly population of our region. Our observational data suggest that the equivalence of vancomycin and metronidazole in the treatment of CDAD needs to be questioned.
A Catalytic Antibody Produces Fluorescent Tracers of Gap Junction Communication in Living Cells (2001)

The antibody 38C2 efficiently catalyzed a retro-Michael reaction to convert a novel, cell-permeable fluorogenic substrate into fluorescein within living cells. In vitro, the antibody converted the substrate to fluorescein with a k(cat) of 1.7 x 10(-5) s(-1) and a catalytic proficiency (k(cat)/k(uncat)K(m)) of 1.4 x 10(10) m(-1) (K(m) = 7 microm). For hybridoma cells expressing antibody or Chinese Hamster Ovarian (CHO) cells injected with antibody, incubation of the substrate in the extracellular medium resulted in bright intracellular fluorescence distinguishable from autofluorescence or noncatalyzed conversion of substrate. CHO cells loaded with antibody were 12 times brighter than control cells, and more than 85% of injected cells became fluorescent. The fluorescein produced by the antibody traveled into neighboring cells through gap junctions, as demonstrated by blocking dye transfer using the gap junction inhibitor oleamide. The presence of functional gap junctions in CHO cells was confirmed through oleamide inhibition of lucifer yellow transfer. These studies demonstrate the utility of the intracellular antibody reaction, which could generate tracer dyes in specific cells within complex multicellular environments simply by bathing the system in substrate.
Short protocols in cell biology : a compendium of methods from Current protocols in cell biology (2004)

Chapter 1. Cell Culture. Chapter 2. Preparation and Isolation of Cells. Chapter 3. Subcellular Fractionation and Isolation of Organelles. Chapter 4. Antibodies as Cell Biological Tools. Chapter 5. Microscopy. Chapter 6. Characterization of Cellular Proteins. Chapter 7. Electrophoresis and Immunoblotting. Chapter 8. Protein Labeling and Immunoprecipitation. Chapter 9. Protein Phosphorylation. Chapter 10. Protein Trafficking. Chapter 11. Cell Proliferation, Cell Aging, and Cell Death. Chapter 12. In Vitro Reconstitution. Chapter 13. Cell Adhesion and Extracellular Matrix. Chapter 14. Cell Motility. Chapter 15. Organelle Motility. Appendix 1: Reagents and Solutions. Appendix 2: Useful Information and Data. Appendix 3: Commonly Used Techniques. Appendix 4: Suppliers. References.
Processing of iduronate 2-sulphatase in human fibroblasts (1995)

Iduronate 2-sulphatase (IDS) is a lysosomal enzyme involved in degradation of dermatan sulphate and heparan sulphate. Antigenic material was obtained either by purification of placental IDS (A and B forms) or by expression of three different fusion peptides in Escherichia coli allowing the production of five specific antibodies. Pulse-chase-labelling experiments in over-expressing fibroblasts showed poor IDS processing but large amounts of precursors were secreted into the medium. The endocytosis of the 35S- or 33P-labelled precursors by deleted fibroblasts together with glycosylation studies and proteolysis inhibition by leupeptin allowed better elucidation of IDS maturation. The initial 73-78 kDa form is converted into a phosphorylated 90 kDa precursor after modification of its oligosaccharide chains in the Golgi apparatus. This precursor is processed by proteolytic cleavage through various intermediates to a major 55 kDa intermediate, with the release of an 18 kDa polypeptide. Further proteolytic cleavage by a thiol protease gives the 45 kDa mature form containing hybrid and complex-type oligosaccharide chains.
Efficient Broadcasting Using Network Coding (2008)

We consider the problem of broadcasting in an ad hoc wireless network, where all nodes of the network are sources that want to transmit information to all other nodes. Our figure of merit is energy efficiency, a critical design parameter for wireless networks since it directly affects battery life and thus network lifetime. We prove that applying ideas from network coding allows to realize significant benefits in terms of energy efficiency for the problem of broadcasting, and propose very simple algorithms that allow to realize these benefits in practice. In particular, our theoretical analysis shows that network coding improves performance by a constant factor in fixed networks. We calculate this factor exactly for some canonical configurations. We then show that in networks where the topology dynamically changes, for example due to mobility, and where operations are restricted to simple distributed algorithms, network coding can offer improvements of a factor of , where is the number of nodes in the network. We use the insights gained from the theoretical analysis to propose low-complexity distributed algorithms for realistic wireless ad hoc scenarios, discuss a number of practical considerations, and evaluate our algorithms through packet level simulation.
AIRLIFT REACTORS: CHARACTERISTICS, APPLICATIONS AND DESIGN CONSIDERATIONS (1987)

Bioreactors of the airlift type are a promising design for aerobic fermentations. The basic knowledge required for understanding and predicting the performance of these reactors is only now beginning to emerge. In this review we present our observations and those of other investigators in an attempt to build up a coherent picture of airlift devices. All the major aspects—mixing and hydrodynamics, mass and heat transfer—in these reactors are considered. Comparisons between bubble columns and airlift systems are made where analogies, similarities and/or differences between them provide insight into airlift systems. Throughout, the areas of particular concern and those in need of further research in this field are mentioned. Extensive work on all forms of airlift reactors, particularly in non-Newtonian media—homogeneous and suspensions—remains to be done. Current knowledge does not permit airlift reactor design with a high degree of confidence. However, the technical feasibility of all types of fermentations—plant cell, tissue culture, bacterial, fungal, and those utilizing yeasts—in airlift vessels has been demonstrated.
Identification of Neutral and Charged NxOySurface Species by IR Spectroscopy (2000)

The infrared spectral performance of the N x O y species observed on oxide surfaces [N2O, NO−, NO, (NO)2, N2O3, NO+, NO2 − (different nitro and nitrito anions), NO2, N2O4, N2O5, NO2, and NO3 − (bridged, bidentate, and monodentate nitrates)] is considered. The spectra of related compounds (N2, H-, and C-containing nitrogen oxo species, C─N species, NH x species) are also briefly discussed. Some guidelines for spectral identification of N x O y adspecies are proposed and the transformation of the nitrogen oxo species on catalyst surfaces are regarded.
Lack of Long-Term Durability of Cultured Keratinocyte Burn-Wound Coverage (1991)

Cultured epithelial autografts have been advocated for permanent closure of skin surfaces after massive thermal injuries. A 10-year-old boy sustained a nearly 100% total body surface area burn (98% full-thickness) in an explosion accident. Cultured epithelial autograft was used to cover 70% of the total body surface area on postburn day 26. In spite of early success of coverage, 60% of cultured epithelial autograft areas blistered and sloughed over the ensuing weeks. Electron microscopic examination of a biopsy specimen of the healed cultured epithelial autograft (80 days after placement) revealed a lack of dermal attachments of the anchoring fibrils. Additionally, blister fluid that was taken from the bullae of the cultured epithelial autograft revealed levels of 18 ng/ml thromboxane and 24 ng/ml prostaglandin E2. These levels are significantly higher than those seen in acute burn blister fluid and indicate an ongoing inflammatory process. Cultured keratinocytes, although they provide early wound closure, may not provide adequate long-term coverage for patients with massive burns.
Gemcitabine-loaded liposomes: rationale, potentialities and future perspectives (2012)

This review describes the strategies used in recent years to improve the biopharmaceutical properties of gemcitabine, a nucleoside analog deoxycytidine antimetabolite characterized by activity against many kinds of tumors, by means of liposomal devices. The main limitation of using this active compound is the rapid inactivation of deoxycytidine deaminase following administration in vivo. Consequently, different strategies based on its encapsulation/complexation in innovative vesicular colloidal carriers have been investigated, with interesting results in terms of increased pharmacological activity, plasma half-life, and tumor localization, in addition to decreased side effects. This review focuses on the specific approaches used, based on the encapsulation of gemcitabine in liposomes, with particular attention to the results obtained during the last 5 years. These approaches represent a valid starting point in the attempt to obtain a novel, commercializable drug formulation as already achieved for liposomal doxorubicin (Doxil(®), Caelyx(®)).
No longer an untreatable disease: How targeted and immunotherapies have changed the management of melanoma patients (2014)

The discovery that BRAF is a driver oncogene in cancer, and complementary improvements in our understanding of the immune system have resulted in new targeted and immune-therapies for metastatic melanoma. Targeted therapies achieve impressive clinical results in carefully selected patients but the development of resistance seems inevitable in most cases. Conversely, immune-checkpoints inhibitors can achieve long-term remission and cures, but in a smaller proportion of patients, and biomarkers to predict which patients will respond are not available. Nevertheless, melanoma has led the evolution of cancer treatment from relatively nonspecific cytotoxic agents to highly selective therapies and here we review the lessons from this paradigm shift in treatment and the opportunities for further improvements in outcomes for melanoma patients.
Synthesis, Antimuscarinic Activity and Quantitative Structure-Activity Relationship (QSAR) of Tropinyl and Piperidinyl Esters. (1998)

A series of tropinyl and piperidinyl esters was synthesized and evaluated for inhibitory activities on the endothelial muscarinic receptors of rat (M3) and rabbit (M2) aorta. Some of the esters (cyclohexylphenylglycolates and cyclohexylphenylpropionates) were found to be better antimuscarinic compounds than standard M2 and M3 inhibitors such as AFDX116 and 4-diphenylacetoxy-N-methylpiperidine (DAMP), with pKEC50 values in the range of 8-9. A few esters were found to be more selective M3 than M2 inhibitors, but these tended to have low activities. The hydrophobic, electronic and steric characteristics of these esters were correlated with antimuscarinic activity by using appropriate parameters representing hydrophobicity (HPLC capacity factor, log kw), size (molecular volume) and electronic character (Taft's polar substituent constant sigma * and 13C chemical shift difference delta delta). Finally, 92% of the M2-inhibitory activities of the esters could be accounted for by the size and electronic character sigma * of the side chain. In contrast, the M3-inhibitory activities of these esters were mainly attributed to the electronic nature (sigma *, delta delta) of the side chain, with good activity being associated with electron-withdrawing groups. Visualization of the comparative molecular field analysis (CoMFA) steric and electrostatic fields provided further confirmation of the structure-activity relationship (SAR) derived from traditional quantitative structure activity relationship (QSAR) approaches.
Part-of-Speech Tagging Guidelines for the Penn Treebank Project (3rd Revision) (1990)

This manual addresses the linguistic issues that arise in connection with annotating texts by part of speech ("tagging"). Section 2 is an alphabetical list of the parts of speech encoded in the annotation systems of the Penn Treebank Project, along with their corresponding abbreviations ("tags") and some information concerning their definition. This section allows you to find an unfamiliar tag by looking up a familiar part of speech. Section 3 recapitulates the information in Section 2, but this time the information is alphabetically ordered by tags. This is the section to consult in order to find out what an unfamiliar tag means. Since the parts of speech are probably familiar to you from high school English, you should have little difficulty in assimilating the tags themselves. However, it is often quite difficult to decide which tag is appropriate in a particular context. The two sections 4 and 5 therefore include examples and guidelines on how to tag problematic cases. If you are uncertain about whether a given tag is correct or not, refer to these sections in order to ensure a consistently annotated text. Section 4 discusses parts of speech that are easily confused and gives guidelines on how to tag such cases, while Section 5 contains an alphabetical list of specific problematic words and collocations. Finally, Section 6 discusses some general tagging conventions. One general rule, however, is so important that we state it here. Many texts are not models of good prose, and some contain outright errors and slips of the pen. Do not be tempted to correct a tag to what it would be if the text were correct; rather, it is the incorrect word that should be tagged correctly.
Profiling a warehouse-scale computer (2015)

With the increasing prevalence of warehouse-scale (WSC) and cloud computing, understanding the interactions of server applications with the underlying microarchitecture becomes ever more important in order to extract maximum performance out of server hardware. To aid such understanding, this paper presents a detailed microarchitectural analysis of live datacenter jobs, measured on more than 20,000 Google machines over a three year period, and comprising thousands of different applications.
The role of voice processing in telecommunications (2002)

During the decade of the 1990s, the fields of communications, computing, and networking are coming together in the form of personal information/communication terminals, and in the associated services (so-called personal communications services, PCS). Several technologies will play major roles in this communications revolution, but one of the key ones will be voice processing. The authors review several voice processing technologies, discuss current capabilities and the associated applications, and try to forecast where they see progress being achieved in the next decade and what applications will become commonplace as a result of the increased capabilities. They show how progress in voice processing is accompanied and stimulated by progress in microelectronics (memory and processing power of single chip architectures), and how, by the 21st century, telecommunications will have made major advances as a result of the use of voice processing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Early Development of Cyclin Dependent Kinase Modulators (2001)

The protein kinase family presents remarkable opportunities for drug discovery and development targeting mainly to the ATP binding cleft. Cyclin-dependent kinases CDKs control the cell division in by controlling its sub phases. The regulation of CDKs is altered in a number of tumor types, and therefore CDKs are a particularly attractive target group of kinases with reference to proliferative disorders including cancer, but also extending to graft stenosis, and autoimmune disorders. Screening of chemical modulators of CDKs that modulate aberrant CDK activity might be beneficial for cancer therapy by directly inhibiting kinase activity, or influencing cell cycle "checkpoint" function, which is mediated through effects of exogenous cellular regulators of CDK activity. In this regard small molecule modulators such as flavopiridol and UCN-01 are in early clinical trials. Other more selective modulators of CDK function are being actively sought, and initial results with flavopiridol analogs, indirubins, paullones, and purine-based inhibitors will be considered.
Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications forin vivoapplications (2018)

Nanolipoprotein particles (NLPs) are reconstituted high-density lipoproteins, consisting of a phospholipid bilayer stabilized by an apolipoprotein scaffold protein. This class of nanoparticle has been a vital tool in the study of membrane proteins, and in recent years has been increasingly used for in vivo applications. Previous work demonstrated that the composition of the lipid bilayer component affects the stability of these particles in serum solutions. In the current study, NLPs assembled with phosphatidylcholine lipids featuring different acyl chain structures were systematically tested to understand the effect that lipid composition has on NLP stability in both neat serum and cell culture media supplemented with 10% serum by volume. The time at which 50% of the particles dissociate, as well as the fraction of the initial population that remains resistant to dissociation, were correlated to key parameters obtained from all-atom simulations of the corresponding lipid bilayers. A significant correlation was observed between the compressibility modulus of the lipid bilayer and particle stability in these complex biological milieu. These results can be used as a reference to tune the stability of these versatile biological nanoparticles for in vitro and in vivo applications.
Cortical Map Reorganization Enabled by Nucleus Basalis Activity (1998)

Little is known about the mechanisms that allow the cortex to selectively improve the neural representations of behaviorally important stimuli while ignoring irrelevant stimuli. Diffuse neuromodulatory systems may facilitate cortical plasticity by acting as teachers to mark important stimuli. This study demonstrates that episodic electrical stimulation of the nucleus basalis, paired with an auditory stimulus, results in a massive progressive reorganization of the primary auditory cortex in the adult rat. Receptive field sizes can be narrowed, broadened, or left unaltered depending on specific parameters of the acoustic stimulus paired with nucleus basalis activation. This differential plasticity parallels the receptive field remodeling that results from different types of behavioral training. This result suggests that input characteristics may be able to drive appropriate alterations of receptive fields independently of explicit knowledge of the task. These findings also suggest that the basal forebrain plays an active instructional role in representational plasticity.
Primary structure of human complement component C2 Homology to two unrelated protein families (1986)

The primary structure of the second component of human complement (C2) was determined by cDNA cloning and sequence analysis. C2 has 39% identity with the functionally analogous protein Factor B. The C-terminal half of C2a is homologous to the catalytic domains of other serine proteinases. C2b contains three direct repeats of approx. 60 amino acid residues. They are homologous to repeats in Factor B, C4b-binding protein and Factor H, suggesting a functional significance of the repeat in C4b and C3b binding. The repeats are also found in the non-complement proteins beta 2-glycoprotein I and interleukin-2 receptor, and this repeat family may be widespread.
Biochemical Conservation and Evolution of Germacrene A Oxidase in Asteraceae (2010)

Sesquiterpene lactones are characteristic natural products in Asteraceae, which constitutes approximately 8% of all plant species. Despite their physiological and pharmaceutical importance, the biochemistry and evolution of sesquiterpene lactones remain unexplored. Here we show that germacrene A oxidase (GAO), evolutionarily conserved in all major subfamilies of Asteraceae, catalyzes three consecutive oxidations of germacrene A to yield germacrene A acid. Furthermore, it is also capable of oxidizing non-natural substrate amorphadiene. Co-expression of lettuce GAO with germacrene synthase in engineered yeast synthesized aberrant products, costic acids and ilicic acid, in an acidic condition. However, cultivation in a neutral condition allowed the de novo synthesis of a single novel compound that was identified as germacrene A acid by gas and liquid chromatography and NMR analyses. To trace the evolutionary lineage of GAO in Asteraceae, homologous genes were further isolated from the representative species of three major subfamilies of Asteraceae (sunflower, chicory, and costus from Asteroideae, Cichorioideae, and Carduoideae, respectively) and also from the phylogenetically basal species, Barnadesia spinosa, from Barnadesioideae. The recombinant GAOs from these genes clearly showed germacrene A oxidase activities, suggesting that GAO activity is widely conserved in Asteraceae including the basal lineage. All GAOs could catalyze the three-step oxidation of non-natural substrate amorphadiene to artemisinic acid, whereas amorphadiene oxidase diverged from GAO displayed negligible activity for germacrene A oxidation. The observed amorphadiene oxidase activity in GAOs suggests that the catalytic plasticity is embedded in ancestral GAO enzymes that may contribute to the chemical and catalytic diversity in nature.