gebhart/patrepeval huggingface dataset:
Acute lung injury and acute respiratory distress syndrome in malaria. (2008)

Malaria is an important treatable cause of acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) in the tropics and in the returning traveller in the non-endemic areas. ARDS is an important complication in severe, complicated falciparum malaria and has been described in P. vivax and P. ovale malaria also. Malarial ALI/ARDS is more common in adults than in children. Pregnant women and non-immune individuals are more prone to develop this condition. Increased alveolar capillary permeability resulting in intravascular fluid loss into the lungs appears to be the key pathophysiologic mechanism. In malaria, ARDS can develop either at initial presentation or after initiation of treatment when the parasitaemia is falling and the patient is improving. Patients present with acute onset dysnoea that can rapidly progress to respiratory failure. The diagnosis of malaria is confirmed by slide microscopy supported by the use of rapid antigen tests. Patients with malarial ARDS should be managed in an intensive care unit. Careful attention must be paid to haemodynamic stabilisation and optimising fluid balance. Currently, specific treatment choices for malaria include parenteral artemisinins or intravenous quinine along with doxycycline. Respiratory failure requires endotracheal intubation and assisted mechanical ventilation. Co-existent bacterial sepsis is frequently present in patients with malarial ARDS eventhough an obvious focus may not be evident. Appropriate broad spectrum antibiotic therapy must be started when there is a clinical suspicion after procuring the microbiological specimens. ARDS in malaria is a disease with a high mortality. Early diagnosis, institution of specific antimalarial treatment and assisted ventilation can be life-saving.
The Endoscopic Management of Pain in Chronic Pancreatitis (2012)

Pain resulting from chronic pancreatitis is often debilitating and difficult to manage. Many approaches have been used to treat these patients, including narcotic analgesia, antidepressants, pancreatic enzymes, octreotide, denervation procedures, such as celiac plexus block, and various palliative, decompression, or drainage procedures. Many of these procedures can be performed endoscopically, while others require a more invasive, surgical approach. The effectiveness of these therapies is not only highly variable but also often controversial. This review will discuss the endoscopic options for pain management in patients with chronic pancreatitis and their utility in treating this difficult disease.
Development of anti-MUC1 di-scFvs for molecular targeting of epithelial cancers, such as breast and prostate cancers. (2007)

Pretargeted radioimmunotherapy (RIT) is a promising approach to increase the therapeutic index of RIT for malignant solid tumors. For pretargeted RIT of epithelial cancers, such as breast and prostate, mucin 1 (MUC1), the epithelial mucin, was chosen as a target antigen (Ag). Overexpression, hypoglycosylation and loss of apical distribution on the cellular membrane distinguish the tumor associated MUC1 from normal MUC1. These characteristics of MUC1, best known in breast cancer, were validated in prostate cancer. The multivalent bispecific MUC1 pretargeting molecule under development consists of a tumor binding module and a radioactive hapten capturing module. The building blocks of each module were chosen as single chain antibody fragments (scFv) to be covalently attached to a multifunctional polyethylene glycol (PEG) scaffold. PEGylation studies with scFvs selected from anti-MUC1 libraries and engineered with a free thiol for site-specific conjugation showed that highest reaction yields were obtained with short monofunctional PEG molecules. To accommodate the use of a bifunctional PEG for covalent assembly of binding and capturing modules, the MUC1 binding module was developed into a di-scFv-SH format and optimized for linker length and location of the free thiol in respect to Ag binding and site-specific conjugation. Approaches under study to improve PEGylation yields with bifunctional PEG molecules include alkyne-azide cycloaddition. Assembly efficiencies, through PEGylation, of the binding and capturing modules and pharmacokinetics will influence the final valency of the MUC1 pretargeting molecule: anti-MUC1 di-scFv-PEG- anti-radioactive hapten scFv or di-scFv-PEG-anti-radioactive hapten di-scFv.
Laser-Machined Shape Memory Alloy Actuators for Active Catheters (2007)

Medicine is undergoing a transformation toward minimally invasive surgery, and with it comes an increasing need for more precise miniature instruments to accurately execute complex procedures. In catheter-based surgeries, the physician must control the tip of the catheter from a distal point outside the body, which makes it difficult to achieve precise manipulative control. Providing actuation local to the desired point of manipulation will greatly improve the physician's ability to intervene on diseases in a minimally invasive fashion. We present a new actuator made from laser machining shape memory alloy (SMA) tubes for use in an active steerable catheter. Using finite-element analysis and experimental verification, we have designed a 1.5-mm-long SMA actuator cut from 1.27-mm-diameter NiTi tubing that exhibits good fatigue properties, and can produce forces of 12 N at 20% elongation. We use an iterative rapid design process, so that many actuator geometries can be tested quickly to achieve the desired mechanical properties without complex material models. In this paper, we describe the design and testing of the actuator, and verify its force, elongation, and fatigue properties.
Encapsulation Through (Mini)Emulsion Polymerization (2006)

This chapter contains sections titled: Introduction The Miniemulsion Process Different Polymers for the Formation of Nanocapsules in Miniemulsions Radical Polymerization Polyaddition Polycondensation Anionic Polymerization Metal-Catalyzed Polymerization Reactions Enzymatic Polymerization Nanocapsule Particles by Miniemulsion Technologies Encapsulation of a Liquid: The Formation of Nanocapsules Nanocapsules with a Shell Obtained by Surface Coating of Miniemulsions with Inorganic Nanoparticles and Crystalline Building Blocks Encapsulation of Pigments by Direct Miniemulsification Encapsulation by Co-Miniemulsion Nanocapsules with Non-Radical Polymerizations in Miniemulsion Conclusions
Electro-optic polymer prism beam deflector (2009)

We report on an optical beam deflector capable of achieving a large beam deflection using a planar thermoplastic-based electro-optic (EO) polymer prism. By optimizing the prism's geometry, relative position, and incident angle of the input beam, the device shows that a large deflection angle can be achieved through a relatively small index change from a single EO polymer prism stage. In this paper, we present the design and fabrication of the deflector using a simple hot-embossing technique. Beam deflection experiments were conducted, and a maximum deflection angle of 5.6 deg was observed, in agreement with our predicted value.
Retinal VEGF mRNA measured by SYBR green I fluorescence: A versatile approach to quantitative PCR. (2000)

The sequence-independent detection of DNA with SYBR Green I means that it can be used to quantify the amplification of any cDNA using gene-specific primers. This rapid and flexible method is ideally suited for researchers in vision science wishing to quantify mRNAs from many different genes because it does not require investment in gene-specific hybridization probes.
Active segregation by the Bacillus subtilis partitioning system in Escherichia coli (2000)

Bacterial genes required for proper partitioning consist of two transacting genes that encode proteins and a cis-acting gene that functions like a centromere. Plasmids actively partitioning by means of these genes migrate from midcell to the cell quarters and are tethered to these sites until the cells divide. Previously the partitioning genes were mainly found on plasmids and phages in Escherichia coli. However, progress in genome sequencing reveals that partitioning genes are ubiquitous in many bacterial plasmids and chromosomes. Each homologue of the two transacting genes belongs to a family, ParA or ParB. Moreover, phylogenic analysis of members of the ParA and ParB families indicates that each member falls into a chromosomal group or an extrachromosomal group. It is known that the parAB genes in the chromosomal group are located on relatively conserved chromosomal regions in several bacterial species. This suggests that the parAB genes were transferred from a chromosome to plasmids and phages, so the genes have diverged among bacterial species. To support this possibility, we show that the Bacillus subtilis Soj and Spo0J members of the ParAB families are responsible for the specific localization of plasmids at cell quarters in E. coli and can function as partition proteins. Host factors to tether actively partitioning plasmids at subcellular sites may be conserved in Gram-negative and Gram-positive bacteria so that phages and plasmids with the ParAB partitioning system can be stably inherited in host cells across bacterial species.
Inhaled nonsteroidal anti-inflammatory medications in the treatment of asthma. (1999)

Asthma is characterized by airway inflammation even in the mildest cases. Multiple studies have confirmed evidence of significant elevations of inflammatory cells and mediators even at baseline in the airway of asthmatics. Cromolyn sodium (SCG) and nedocromil sodium (NS), the "nonsteroidal anti-inflammatory agents" are considered options for the management of mild persistent asthma in both adults and children as outlined by the Global Initiative for Asthma and the Expert Panel II, National Asthma Education and Prevention Program 1997 guidelines. These drugs may inhibit both the early and late asthmatic response, ostensibly by stabilizing mast cells and by reducing the total number of eosinophils and their recruitment. SCG and NS have extremely safe profiles, making them attractive for use even in young children. In addition to daily use for mild persistent asthma, SCG and NS are effective inhibitors of exercise-induced bronchospasm (EIB). Although these drugs are unlikely to eliminate the use of inhaled corticosteroids in patients with more significant obstructive airway disease, they have potentially beneficial steroid-sparing effects. Thus, the cromione, SCG and NS, are effective prophylactic drugs recommended for use in both adults and children in the management of mild persistent asthma, EIB, and potentially as modest steroid-sparing agents.
Triflavin, an Antiplatelet Arg-Gly-Asp-Containing Peptide, Is a Specific Antagonist of Platelet Membrane Glycoprotein IIb-IIIa Complex<xref ref-type="fn" rid="fn1"><sup>1</sup></xref> (1991)

Triflavin, an antiplatelet peptide containing Arg-Gly-Asp, purified from Trimeresurus flavoviridis venom, inhibits aggregation of human platelets stimulated by a variety of agonists. It blocks aggregation through interference with fibrinogen binding to its specific receptor on the platelet surface membrane in a competitive manner, but it has no apparent effect on intracellular events, such as thromboxane B2 formation, phosphoinositides breakdown and intracellular Ca2+ mobilization of thrombin-activated platelets. In this study, we determined the complete sequence of triflavin, which is composed of a single polypeptide chain of 70 amino acids. Its sequence is rich in cysteine and contains Arg-Gly-Asp at residues 49-51 in the carboxy-terminal domain. Triflavin shows about 68% identity of amino acid sequence with trigramin, which is a specific antagonist of the fibrinogen receptor associated with glycoprotein IIb/IIIa complex. [125I]Triflavin binds to unstimulated and ADP-stimulated platelets in a saturable manner and its Kd values are estimated to be 76 and 74 nM, respectively; the corresponding numbers of binding sites are 31,029 and 34,863 per platelet, respectively. [125I]Triflavin binding is blocked by Gly-Arg-Gly-Asp-Ser in a competitive manner. EDTA, the Arg-Gly-Asp-containing peptides (including naturally occurring polypeptides, trigramin and rhodostomin), and monoclonal antibody, 7E3, raised against GP IIb/IIIa complex, inhibit [125I]triflavin binding to unstimulated and ADP-stimulated human platelets. In conclusion, triflavin specifically binds to fibrinogen receptor associated with GP IIb/IIIa complex and its binding site is located at or near GP IIb/IIIa complex, overlapping with those of 7E3 and another Arg-Gly-Asp-containing polypeptide, rhodostomin.(ABSTRACT TRUNCATED AT 250 WORDS)
Automatically describing software faults (2013)

A developers ability to successfully debug a fault is directly related to their ability to comprehend the fault. Notwithstanding improvements in software-maintenance automation, this fault comprehension task remains largely manual and time consuming. I propose an automated approach to describe software faults, thus ameliorating comprehension and reducing manual effort. My approach leverages dynamic analysis, fault localization, and source-code mining to produce a succinct, natural-language fault summary.
Real-Time Quantification of Xeroderma pigmentosum mRNA From the Mammalian Cochlea (2010)

These data suggest that under normal conditions the cochlea is experiencing persistent genomic stress that helps to explain the hypersensitivity of the cochlea to exogenous stressors (ototoxic xenobiotics and/or acoustic-overexposure) as well as provide a basis to interpret hearing loss among patients with XP.
Validation of a general measure of treatment satisfaction, the Treatment Satisfaction Questionnaire for Medication (TSQM), using a national panel study of chronic disease. (2004)

The TSQM is a psychometrically sound and valid measure of the major dimensions of patients' satisfaction with medication. Preliminary evidence suggests that the TSQM may also be a good predictor of patients' medication adherence across different types of medication and patient populations.
A tale of two peptides, TyrTyrGluGlu and TyrGluTyrGlu, and their diverse immune behaviour. (1992)

Studies on a synthetic multichain polypeptide antigen, (T,G)-A--L, prepared by polymerization techniques, led to a better understanding of the molecular basis of antigenicity, and of many other immunological phenomena, as well as to the discovery of determinant-specific genetic control of immune response. In view of the intensity of studies with this polymer, we were interested in elucidating its major B and T cell epitopes. We investigated two tetrapeptides, TyrTyrGluGlu and TyrGluTyrGlu. Both were attached to multichain branched poly(DLalanine). Even though the two resulting synthetic immunogens are essentially identical in their molecular weight, size, shape and composition, and differ chemically only in the sequence of the tetrapeptide epitopes, the immunological differences observed were profound. Antibodies in the two systems do not cross-react. The major B cell epitope of (T,G)-A--L is TyrTyrGluGlu, whereas the major T cell epitope is TyrGluTyrGlu. The two antigens are under different genetic controls, and differ in their uptake by macrophages. The TyrTyrGluGlu polymer is thymus-dependent, whereas the TyrGluTyrGlu polymer is thymus-independent. Investigation of the two tetrapeptides in their polymeric form, by photochemically induced dynamic nuclear magnetic polarization techniques, shows that they differ strongly in their intra-epitope aromatic interactions. Phenolic groups in TyrGluTyrGlu interact with each other, whereas they are far apart in TyrTyrGluGlu, as seen also in computer-derived models.
Pseudo-Network Drivers and Virtual Networks (1990)

Many operating systems have long had pseudo-teletypes, inter-process communication channels that provide terminal semantics on one end, and a smart server program on the other. We describe an analogous concept, pseudo-network drivers. One end of the driver appears to be a real network device, with the appropriate interface and semantics; data written to it goes to a program, however, rather than to a physical medium. Using this and some auxiliary mechanisms, we present a variety of applications, including system test, network monitoring, dial-up TCP/IP, and ways to both improve and subvert network security. Most notably, we show how pseudo-network devices can be used to create virtual networks and to provide encrypted communications capability. We describe two implementations, one using a conventional driver for socket-based systems, and one using stream pipes for System V.
Acetylcholinesterase: electrostatic steering increases the rate of ligand binding (1993)

Brownian dynamics simulations have been used to calculate the diffusion-controlled rate constants for the binding of a positively charged ligand to several models of acetylcholinesterase (AChE). The crystal structure was used to define the detailed topography and the active sites of the dimeric enzyme. The electric field around AChE was then computed by solving the Poisson equation for different charge distributions in the enzyme at zero ionic strength. These fields were used in turn to calculate the forces on the diffusing ligand. Significant increases in the rate constant resulted in going from a model with no charges to one with the net charges concentrated at the centers of the monomers and then to a model with a realistic distribution of charges throughout the enzyme. The results show that electrostatic steering of ligands contributes to the high rate constants that are observed experimentally for AChE.
Predicting oligonucleotide-directed mutagenesis failures in protein engineering (2004)

Protein engineering uses oligonucleotide-directed mutagenesis to modify DNA sequences through a two-step process of hybridization and enzymatic synthesis. Inefficient reactions confound attempts to introduce mutations, especially for the construction of vast combinatorial protein libraries. This paper applied computational approaches to the problem of inefficient mutagenesis. Several results implicated oligonucleotide annealing to non-target sites, termed 'cross-hybridization', as a significant contributor to mutagenesis reaction failures. Test oligonucleotides demonstrated control over reaction outcomes. A novel cross-hybridization score, quickly computable for any plasmid and oligonucleotide mixture, directly correlated with yields of deleterious mutagenesis side products. Cross-hybridization was confirmed conclusively by partial incorporation of an oligonucleotide at a predicted cross-hybridization site, and by modification of putative template secondary structure to control cross-hybridization. Even in low concentrations, cross-hybridizing species in mixtures poisoned reactions. These results provide a basis for improved mutagenesis efficiencies and increased diversities of cognate protein libraries.
Optimizing creatively in multi-objective optimization (2015)

Designers will always face the challenge of designing well-performing buildings using what are often conflicting and competing objectives. Early stage design decisions influence significantly the final performance of a building and designers are often unable to explore large numbers of design alternatives with respect to the performative criteria set for the project. This research outlines a optimization workflow' using a Multi-Objective Optimization (MOO) engine called Octopus that runs within Grasshopper3D, a parametric modeling tool, and simulation software DIVA for daylight factor analysis. The workflow utilizes a optimization tool' which allows the designer to explore, sort and filter solutions, and analyze both quantitatively and qualitatively the trade-offs of the resultant design solution space. It enables the designer to visually compare alternative solutions in a gallery and subsequently analyze trade-offs through a radar-based chart, parallel coordinate plot graphs and conditional domain searches. This feedback tools allows the designer to quickly and efficiently identify potential solutions for either design development or to select preferred solutions for further optimization, i.e. optimizing creatively'. A retrospective design case study, the De Rotterdam' building, is used to demonstrate the application of the tools. The workflow demonstrates the ability to reduce design latency and to allow for better understanding of design solutions. Additional research is needed to better understand the application of MOO in the early stages of design; and the further improvement of the creative optimization tools to accommodate the designer's need for a more dynamic and synergistic process.
AUX/IAA Proteins Are Active Repressors, and Their Stability and Activity Are Modulated by Auxin (2001)

Aux/IAA genes are early auxin response genes that encode short-lived nuclear proteins with four conserved domains, referred to as I, II, III, and IV. Arabidopsis Aux/IAA proteins repressed transcription on auxin-responsive reporter genes in protoplast transfection assays. Mutations in domain II resulted in increased repression, whereas mutations in domains I and III partially relieved repression. Aux/IAA proteins fused to a heterologous DNA binding domain were targeted to promoters of constitutively expressed reporter genes and actively repressed transcription in an auxin-responsive and dose-dependent manner. In comparison with an unfused luciferase protein, luciferase fused to Aux/IAA proteins displayed less luciferase activity, which further decreased in the presence of auxin in transfected protoplasts. Domain II mutations increased and domain I mutations decreased luciferase activity with the fusion proteins. These results suggested that Aux/IAA proteins function as active repressors by dimerizing with auxin response factors bound to auxin response elements and that early auxin response genes are regulated by auxin-modulated stabilities of Aux/IAA proteins.
No Exception in the English Lexicon (2002)

This paper aims to review Hammond's (1999) analysis of English word stress and propose an alternative by exploring two questions: Why English words display flexible stress patterns and what are the conditions all English words have to obey. As answers to the questions I propose an invisible suffix after words with final stress, foot structures with two levels, and four constraints, two of them are attained by revision of Hammond's. As long as words satisfy the constraints, more than one foot structures are allowed. That is why the English lexicon displays flexibility.
Andrew as a multiparadigm environment for visual languages (2002)

Despite numerous innovations in visual languages, relatively little effort has been devoted to integrating visual languages with each other and with textual languages so each can be used for those purposes for which it is best suited. This paper advances a model for multiparadigm language environments which utilizes text in two roles, visual program organization and compiler input. The paper further shows that the Andrew User Interface System is a convenient framework for building language systems on this model. The approach is exemplified with a visual language for specification of string patterns.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>